RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2618
(390 letters)
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 157 bits (400), Expect = 3e-48
Identities = 58/75 (77%), Positives = 67/75 (89%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
HIFVGDLSPEI+T+TL+ AFAPFGEIS+ R+V+D QT KSKGY FVSFVKK +AENAI +
Sbjct: 1 HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60
Query: 157 MNGQWLGSRSIRTNW 171
MNGQWLG R+IRTNW
Sbjct: 61 MNGQWLGGRAIRTNW 75
Score = 56.6 bits (137), Expect = 1e-10
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ G +++ E + F+PFG I D RV K+ KGY FV F KE A +AI+S+
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 263 HNTDINGHTVKCFW 276
+ + G ++ W
Sbjct: 62 NGQWLGGRAIRTNW 75
Score = 47.0 bits (112), Expect = 3e-07
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
++VG+L + E L A F+ G + +V+++ Y F+ FV A A+ +M
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 67 NKRVFLEKEMKVNW 80
N + + ++ NW
Sbjct: 62 NGQWLGGRAIRTNW 75
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated
apoptosis.TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 125 bits (315), Expect = 9e-36
Identities = 48/72 (66%), Positives = 57/72 (79%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
LYVGNLD +VTE+LL LFSQIGP+K CK+IRE GNDPYAF+E+ H AA AL MN R
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60
Query: 70 VFLEKEMKVNWA 81
+ L +E+KVNWA
Sbjct: 61 LILGQEIKVNWA 72
Score = 65.4 bits (160), Expect = 1e-13
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L + L E F+ G I +C+++R+ + YAFV + A A+ M
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQTM 57
Query: 158 NGQWLGSRSIRTNWS 172
NG+ + + I+ NW+
Sbjct: 58 NGRLILGQEIKVNWA 72
Score = 40.7 bits (96), Expect = 5e-05
Identities = 20/71 (28%), Positives = 40/71 (56%), Gaps = 3/71 (4%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG---YAFVKFTTKETATHAIESIHNT 265
+Y G + + E+L++++FS G I ++ +E G YAFV++ +A A+++++
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60
Query: 266 DINGHTVKCFW 276
I G +K W
Sbjct: 61 LILGQEIKVNW 71
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 121 bits (305), Expect = 3e-34
Identities = 41/73 (56%), Positives = 50/73 (68%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
TVY G L EE + + FSPFG I ++RVFK+KGYAFV+F T E A AI +++ T
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60
Query: 267 INGHTVKCFWGKE 279
ING TVKC WGKE
Sbjct: 61 INGQTVKCSWGKE 73
Score = 66.5 bits (163), Expect = 4e-14
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L + + L+ F+PFG I R+ +D KGYAFV F A AI A+
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56
Query: 158 NGQWLGSRSIRTNWS 172
NG + ++++ +W
Sbjct: 57 NGTSINGQTVKCSWG 71
Score = 63.4 bits (155), Expect = 4e-13
Identities = 29/73 (39%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TT+YVGNL +TEE L FS G ++ +V ++ G YAF+ F H AATA+ A+N
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKG---YAFVRFDTHEAAATAIVAVN 57
Query: 68 KRVFLEKEMKVNW 80
+ +K +W
Sbjct: 58 GTSINGQTVKCSW 70
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 120 bits (303), Expect = 4e-34
Identities = 54/80 (67%), Positives = 64/80 (80%)
Query: 95 HYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
H+H+FVGDLSPEI T+ +K AFAPFG+IS+ R+V+D T KSKGY FVSF K +AENAI
Sbjct: 1 HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 60
Query: 155 TAMNGQWLGSRSIRTNWSTR 174
M GQWLG R IRTNW+TR
Sbjct: 61 VHMGGQWLGGRQIRTNWATR 80
Score = 42.4 bits (99), Expect = 2e-05
Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
V+ G ++ E + F+PFG I D RV K+ KGY FV F K A +AI +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 263 HNTDINGHTVKCFWG 277
+ G ++ W
Sbjct: 64 GGQWLGGRQIRTNWA 78
Score = 33.1 bits (75), Expect = 0.034
Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE---PGNDPYAFLEFVHHTVAATALAAM 66
++VG+L +T E + + F+ G + +V+++ + Y F+ F + A A+ M
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 67 NKRVFLEKEMKVNWAS 82
+ ++++ NWA+
Sbjct: 64 GGQWLGGRQIRTNWAT 79
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 119 bits (300), Expect = 1e-33
Identities = 54/80 (67%), Positives = 62/80 (77%)
Query: 95 HYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
H+H+FVGDLSPEI T +K AFAPFG IS+ R+V+D T KSKGY FVSF K +AENAI
Sbjct: 1 HFHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60
Query: 155 TAMNGQWLGSRSIRTNWSTR 174
M GQWLG R IRTNW+TR
Sbjct: 61 QQMGGQWLGGRQIRTNWATR 80
Score = 43.1 bits (101), Expect = 9e-06
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
V+ G ++ + + F+PFG I D RV K+ KGY FV F K A +AI+ +
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 263 HNTDINGHTVKCFWG 277
+ G ++ W
Sbjct: 64 GGQWLGGRQIRTNWA 78
Score = 33.9 bits (77), Expect = 0.019
Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFVHHTVAATALAAM 66
++VG+L +T + + A F+ G + +V+++ + Y F+ F + A A+ M
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 67 NKRVFLEKEMKVNWAS 82
+ ++++ NWA+
Sbjct: 64 GGQWLGGRQIRTNWAT 79
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 124 bits (314), Expect = 2e-31
Identities = 74/269 (27%), Positives = 120/269 (44%), Gaps = 32/269 (11%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAA 65
+LYVG+LD VTE L LF GPV +V R+ Y ++ F + A AL
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC 125
MN + K +++ W+ + + N IFV +L ++ + L + F+ FG I +C
Sbjct: 62 MNFKRLGGKPIRIMWSQRDPSLRRSGVGN---IFVKNLDKSVDNKALFDTFSKFGNILSC 118
Query: 126 RIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKR 185
++ D + KS+GY FV F K+ A+ AI +NG L + + + R
Sbjct: 119 KVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEV------YVGRFIKKHE-R 170
Query: 186 QNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE---- 241
+ + K T +Y +NE+ + ++F+ FG I V K+
Sbjct: 171 EAAPLKKFT-------------NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGR 217
Query: 242 -KGYAFVKFTTKETATHAIESIHNTDING 269
+G+AFV F E A A+E ++ I
Sbjct: 218 SRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
Score = 113 bits (284), Expect = 2e-27
Identities = 97/406 (23%), Positives = 157/406 (38%), Gaps = 57/406 (14%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIR-EPGNDP-YAFLEFVHHTVAATALAA 65
++V NLD SV + L FS+ G + CKV E G Y F+ F A A+
Sbjct: 89 GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC 125
+N + +KE+ V + +++V +L P + L+E FA FGEI++
Sbjct: 149 VNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSA 208
Query: 126 RIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI-------RTNWSTRKPPA 178
+++D +S+G+AFV+F K +A A+ MNG+ +G R +
Sbjct: 209 AVMKDGSG-RSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAE 267
Query: 179 MTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV 238
+ RK + E ++ N +Y + +E + ++FS G I +V
Sbjct: 268 L--RRKFEELQ------QERKMKAQGVN--LYVKNLDDTVTDEKLRELFSECGEITSAKV 317
Query: 239 F-----KEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWG-KESENNSTL------ 286
+G+ FV F+ E A A+ +H + G + ++ + + L
Sbjct: 318 MLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQ 377
Query: 287 AQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYV 346
QP P + Q Y Q PQQ + G P G+
Sbjct: 378 LQPRMRQLPMGS----PMGGAMGQPPYY------------GQGPQQQFN----GQPLGWP 417
Query: 347 GMVGRQVPGWQGIPGAQPTAQQMA--VAQAQPSMMAAYAMQQFPTQ 390
M +P G PG +A A PS A A Q+ P Q
Sbjct: 418 RM--SMMPTPMG-PGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQ 460
Score = 100 bits (251), Expect = 4e-23
Identities = 58/185 (31%), Positives = 88/185 (47%), Gaps = 36/185 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VGDL P++ L + F PFG + + R+ RD T +S GY +V+F A+AE A+ M
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
N + LG + IR WS R P R+ S N F K+
Sbjct: 63 NFKRLGGKPIRIMWSQRDPSL----RR-----------------SGVGNI------FVKN 95
Query: 218 LNEELVSKV----FSPFGTIVDIRVF-----KEKGYAFVKFTTKETATHAIESIHNTDIN 268
L++ + +K FS FG I+ +V K +GY FV F +E+A AI+ ++ +N
Sbjct: 96 LDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLN 155
Query: 269 GHTVK 273
V
Sbjct: 156 DKEVY 160
Score = 48.6 bits (116), Expect = 3e-06
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG--NDPYAFLEFVHHTVAATA 62
+Q LYV NLD +VT+E L LFS+ G + KV+ + + + F+ F + A A
Sbjct: 283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRA 342
Query: 63 LAAMNKRVFLEKEMKVNWA 81
+ M+ R+ K + V A
Sbjct: 343 VTEMHGRMLGGKPLYVALA 361
Score = 48.3 bits (115), Expect = 4e-06
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIES 261
++Y G D+ E + +F PFG ++ +RV ++ GY +V F A A+E+
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61
Query: 262 IHNTDINGHTVKCFW 276
++ + G ++ W
Sbjct: 62 MNFKRLGGKPIRIMW 76
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM3
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 73
Score = 107 bits (269), Expect = 3e-29
Identities = 44/73 (60%), Positives = 57/73 (78%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
CTVYCGG L E+L+ + FSPFG I++IRVF EKGY+F++F+T E+A HAI S++ T
Sbjct: 1 CTVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTT 60
Query: 267 INGHTVKCFWGKE 279
I GH VKC+WGKE
Sbjct: 61 IEGHVVKCYWGKE 73
Score = 42.3 bits (99), Expect = 2e-05
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++ G ++ + Q +++ F+PFG+I R+ KGY+F+ F A +AI ++
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRV------FPEKGYSFIRFSTHESAAHAIVSV 56
Query: 158 NGQWLGSRSIRTNW 171
NG + ++ W
Sbjct: 57 NGTTIEGHVVKCYW 70
Score = 36.2 bits (83), Expect = 0.002
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
T+Y G + +TE+L+ FS G + +V E G Y+F+ F H AA A+ ++N
Sbjct: 2 TVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKG---YSFIRFSTHESAAHAIVSVNG 58
Query: 69 RVFLEKEMKVNWA 81
+K W
Sbjct: 59 TTIEGHVVKCYWG 71
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 106 bits (265), Expect = 2e-28
Identities = 41/75 (54%), Positives = 54/75 (72%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+IFVGDLSPE+ TL AF+ F S+ R++ D ++ +S+GY FVSF + +AENAI
Sbjct: 1 NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60
Query: 157 MNGQWLGSRSIRTNW 171
MNG+WLGSR IR NW
Sbjct: 61 MNGKWLGSRPIRCNW 75
Score = 45.6 bits (108), Expect = 1e-06
Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
++ G ++ + + FS F + D RV + +GY FV F +++ A +AI +
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 263 HNTDINGHTVKCFW 276
+ + ++C W
Sbjct: 62 NGKWLGSRPIRCNW 75
Score = 36.3 bits (84), Expect = 0.002
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI------REPGNDPYAFLEFVHHTVAATAL 63
++VG+L VT+ L A FS +V+ R G Y F+ F A A+
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRG---YGFVSFRSQQDAENAI 58
Query: 64 AAMNKRVFLEKEMKVNW 80
MN + + ++ NW
Sbjct: 59 NEMNGKWLGSRPIRCNW 75
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 102 bits (254), Expect = 5e-27
Identities = 42/74 (56%), Positives = 57/74 (77%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
CTVYCGG L E+L+ + FSPFG I+++RVF +KGY+FV+F + E+A HAI S++ T
Sbjct: 1 CTVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTT 60
Query: 267 INGHTVKCFWGKES 280
I GH VKC+WGKE+
Sbjct: 61 IEGHVVKCYWGKET 74
Score = 45.1 bits (106), Expect = 2e-06
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++ G ++ + Q +++ F+PFG+I R+ D KGY+FV F A +AI ++
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56
Query: 158 NGQWLGSRSIRTNW 171
NG + ++ W
Sbjct: 57 NGTTIEGHVVKCYW 70
Score = 35.0 bits (80), Expect = 0.006
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
T+Y G + +TE+L+ FS G + +V + G Y+F+ F H AA A+ ++N
Sbjct: 2 TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKG---YSFVRFNSHESAAHAIVSVNG 58
Query: 69 RVFLEKEMKVNWA 81
+K W
Sbjct: 59 TTIEGHVVKCYWG 71
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM1 of nucleolysin TIAR, also termed TIA-1-related
protein, and a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 81
Score = 98.6 bits (245), Expect = 1e-25
Identities = 50/80 (62%), Positives = 57/80 (71%), Gaps = 1/80 (1%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE-PGNDPYAFLEFVHHTVAATALAAMN 67
TLYVGNL VTE L+ LFSQIGP K CK+I E NDPY F+EF H AA ALAAMN
Sbjct: 1 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60
Query: 68 KRVFLEKEMKVNWASSPGNQ 87
R L KE+KVNWA++P +Q
Sbjct: 61 GRKILGKEVKVNWATTPSSQ 80
Score = 44.7 bits (105), Expect = 3e-06
Identities = 20/76 (26%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+LS ++ + + F+ G +C+++ + + + Y FV F + +A A+ AM
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAM 59
Query: 158 NGQWLGSRSIRTNWST 173
NG+ + + ++ NW+T
Sbjct: 60 NGRKILGKEVKVNWAT 75
Score = 35.9 bits (82), Expect = 0.003
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG----YAFVKFTTKETATHAIESIH 263
T+Y G +D+ E L+ ++FS G ++ E Y FV+F A A+ +++
Sbjct: 1 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60
Query: 264 NTDINGHTVKCFWG 277
I G VK W
Sbjct: 61 GRKILGKEVKVNWA 74
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 102 bits (254), Expect = 1e-24
Identities = 45/207 (21%), Positives = 80/207 (38%), Gaps = 3/207 (1%)
Query: 73 EKEMKVNWASSPGNQPKQDTSNHYH--IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD 130
KE + S + + S + +FVG+L ++ + L+E F FG + R+VRD
Sbjct: 91 TKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD 150
Query: 131 PQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHT 190
+T KS+G+AFV F + AE AI +NG+ L R +R + + ++
Sbjct: 151 RETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASF 210
Query: 191 KTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFT 250
+ +Y G EE ++ +F G IV + K K
Sbjct: 211 A-KKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSR 269
Query: 251 TKETATHAIESIHNTDINGHTVKCFWG 277
+ + +++ + G
Sbjct: 270 SFVGNEASKDALESNSRGNKKKILGRG 296
Score = 74.6 bits (182), Expect = 5e-15
Identities = 41/188 (21%), Positives = 75/188 (39%), Gaps = 22/188 (11%)
Query: 1 MCDESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHT 57
+ + TL+VGNL VTEE L LF + GPVK +++R+ +AF+EF
Sbjct: 109 QKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEE 168
Query: 58 VAATALAAMNKRVFLEKEMKVNWA---------------SSPGNQPKQDTSNHYH----I 98
A A+ +N + + ++V A +S + + + +
Sbjct: 169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNL 228
Query: 99 FVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
+VG+L + + L + F G+I + K +FV +A + + N
Sbjct: 229 YVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALESNSRGN 288
Query: 159 GQWLGSRS 166
+ + R
Sbjct: 289 KKKILGRG 296
Score = 65.4 bits (158), Expect = 7e-12
Identities = 25/115 (21%), Positives = 53/115 (46%), Gaps = 8/115 (6%)
Query: 174 RKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTI 233
T E + + + + +S N T++ G D+ EE + ++F FG +
Sbjct: 85 DGERGYTKEFEEELFRSSES--PKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPV 142
Query: 234 VDIRV------FKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESEN 282
+R+ K +G+AFV+F ++E+A AIE ++ ++ G ++ + +
Sbjct: 143 KRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ 197
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 95.1 bits (236), Expect = 2e-24
Identities = 46/74 (62%), Positives = 53/74 (71%), Gaps = 1/74 (1%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE-PGNDPYAFLEFVHHTVAATALAAMN 67
TLYVGNL VTE L+ LFSQIGP K CK+I + GNDPY F+EF H AA +LAAMN
Sbjct: 1 TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60
Query: 68 KRVFLEKEMKVNWA 81
R + KE+KVNWA
Sbjct: 61 GRKIMGKEVKVNWA 74
Score = 47.3 bits (112), Expect = 3e-07
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+LS ++ + + F+ G +C+++ D T + Y FV F + A ++ AM
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59
Query: 158 NGQWLGSRSIRTNWS 172
NG+ + + ++ NW+
Sbjct: 60 NGRKIMGKEVKVNWA 74
Score = 36.9 bits (85), Expect = 0.001
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG----YAFVKFTTKETATHAIESIH 263
T+Y G +D+ E L+ ++FS G ++ + Y FV+F A ++ +++
Sbjct: 1 TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMN 60
Query: 264 NTDINGHTVKCFWG 277
I G VK W
Sbjct: 61 GRKIMGKEVKVNWA 74
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 94.2 bits (235), Expect = 4e-24
Identities = 31/71 (43%), Positives = 50/71 (70%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L P+ + L+E F+ FG++ + R+VRD +T KSKG+AFV F + +AE A+ A+
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61
Query: 158 NGQWLGSRSIR 168
NG+ L R ++
Sbjct: 62 NGKELDGRPLK 72
Score = 76.5 bits (189), Expect = 1e-17
Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 6/73 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIES 261
T++ G D EE + ++FS FG + +R+ ++ KG+AFV+F ++E A A+E+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 262 IHNTDINGHTVKC 274
++ +++G +K
Sbjct: 61 LNGKELDGRPLKV 73
Score = 73.0 bits (180), Expect = 2e-16
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 3/73 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVAATALAA 65
TL+VGNL TEE L LFS+ G V+ +++R+ +AF+EF A AL A
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 66 MNKRVFLEKEMKV 78
+N + + +KV
Sbjct: 61 LNGKELDGRPLKV 73
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 87.6 bits (218), Expect = 9e-22
Identities = 34/71 (47%), Positives = 50/71 (70%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L P+ + LK+ F+ FG I + RIVRD +T +SKG+AFV F + +AE A+ A+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 158 NGQWLGSRSIR 168
NG+ LG R +R
Sbjct: 60 NGKELGGRELR 70
Score = 74.2 bits (183), Expect = 8e-17
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIH 263
++ G D EE + +FS FG I IR+ ++ KG+AFV+F +E A A+E+++
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 264 NTDINGHTVK 273
++ G ++
Sbjct: 61 GKELGGRELR 70
Score = 66.8 bits (164), Expect = 3e-14
Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG--NDPYAFLEFVHHTVAATALAAMN 67
L+VGNL TEE L LFS+ GP++ +++R+ + +AF+EF A AL A+N
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 68 KRVFLEKEMK 77
+ +E++
Sbjct: 61 GKELGGRELR 70
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 84.7 bits (210), Expect = 1e-20
Identities = 33/71 (46%), Positives = 47/71 (66%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L P+ + L+E F+ FGEI + RIVRD KSKG+AFV F +AE A+ A+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDG-KSKGFAFVEFESPEDAEKALEAL 59
Query: 158 NGQWLGSRSIR 168
NG+ L R ++
Sbjct: 60 NGKELDGRKLK 70
Score = 69.6 bits (171), Expect = 3e-15
Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIH 263
++ G D EE + ++FS FG I +R+ ++ KG+AFV+F + E A A+E+++
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 264 NTDINGHTVKC 274
+++G +K
Sbjct: 61 GKELDGRKLKV 71
Score = 67.7 bits (166), Expect = 1e-14
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAMN 67
L+VGNL TEE L LFS+ G ++ +++R+ +AF+EF A AL A+N
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 68 KRVFLEKEMKVN 79
+ +++KV+
Sbjct: 61 GKELDGRKLKVS 72
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 89.6 bits (222), Expect = 2e-19
Identities = 54/199 (27%), Positives = 88/199 (44%), Gaps = 17/199 (8%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI------REPGNDPYAFLEFVHH 56
E T++V L + E L FS++G V+ + I R G A++EF
Sbjct: 85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKG---VAYVEFYDV 141
Query: 57 TVAATALAAMNKRVFLEKEMKV-------NWASSPGNQPKQDTSNHYHIFVGDLSPEIET 109
ALA + L + + V N A+ D N ++VG+L I
Sbjct: 142 ESVIKALALTGQM-LLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITE 200
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRT 169
Q L++ F PFG+I + ++ RDP+T +SKG+ F+ F EA+ A+ MNG L R I+
Sbjct: 201 QELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV 260
Query: 170 NWSTRKPPAMTNERKRQNS 188
++ + ++
Sbjct: 261 GYAQDSTYLLDAANTFEDI 279
Score = 76.9 bits (189), Expect = 3e-15
Identities = 47/200 (23%), Positives = 88/200 (44%), Gaps = 20/200 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV L+ + + L E F+ G++ + + ++D + +SKG A+V F A+ A+
Sbjct: 92 VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-AL 150
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
GQ L R I S E+ R D P +Y G +
Sbjct: 151 TGQMLLGRPIIVQSSQA-------EKNRAAKAATHQPGD------IPNFLKLYVGNLHFN 197
Query: 218 LNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHT 271
+ E+ + ++F PFG I D+++ ++ KG+ F++F E A A+E ++ ++ G
Sbjct: 198 ITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRP 257
Query: 272 VKCFWGKESENNSTLAQPSA 291
+K + ++S A
Sbjct: 258 IKVGYAQDSTYLLDAANTFE 277
Score = 33.3 bits (76), Expect = 0.22
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 136 SKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
S G ++ F A A A+NG++ G + I
Sbjct: 409 SAGKIYLKFSSVDAALAAFQALNGRYFGGKMI 440
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 89.4 bits (221), Expect = 3e-19
Identities = 59/203 (29%), Positives = 92/203 (45%), Gaps = 22/203 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG +S E+ T++ AF PFG I + + DP T K KG+AFV + A+ A+ M
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
NGQ LG R+I+ + P A D V ++ N +Y D
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQP-------------IIDMVQEEAKKFN-RIYVASVHPD 215
Query: 218 LNEELVSKVFSPFGTIV------DIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHT 271
L+E + VF FG IV KGY F+++ ++ + AI S++ D+ G
Sbjct: 216 LSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQY 275
Query: 272 VKCFWGKESENNSTLAQPSAPTT 294
++ GK L QP+ +
Sbjct: 276 LRV--GKCVTPPDALLQPATVSA 296
Score = 77.8 bits (191), Expect = 2e-15
Identities = 48/179 (26%), Positives = 82/179 (45%), Gaps = 9/179 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFVHHTVAATALAAM 66
+YVG++ + E+ + F GP+K + +P + +AF+E+ A AL M
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169
Query: 67 NKRVFLEKEMKVNWASS-PGNQP-----KQDTSNHYHIFVGDLSPEIETQTLKEAFAPFG 120
N ++ + +KV S+ P QP +++ I+V + P++ +K F FG
Sbjct: 170 NGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFG 229
Query: 121 EISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAM 179
EI C++ R P KGY F+ + AI +MN LG + +R P A+
Sbjct: 230 EIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDAL 288
Score = 44.3 bits (104), Expect = 8e-05
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 6/101 (5%)
Query: 179 MTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV 238
+ + Q + + Q+ C VY G +L E+ + + F PFG I I +
Sbjct: 80 LKQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINM 139
Query: 239 ------FKEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
K KG+AFV++ E A A+E ++ + G +K
Sbjct: 140 SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIK 180
Score = 28.5 bits (63), Expect = 8.2
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSI 167
FV F E + A A++G++ G R++
Sbjct: 569 FVEFSDSMEVDRAKAALDGRFFGGRTV 595
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 79.2 bits (196), Expect = 1e-18
Identities = 31/75 (41%), Positives = 46/75 (61%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
N + IFVGDL E+ + L AF+ + ++VRD +T KSKGY FVSF + A
Sbjct: 5 NDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKA 64
Query: 154 ITAMNGQWLGSRSIR 168
+ MNG+++G+R I+
Sbjct: 65 MKEMNGKYVGNRPIK 79
Score = 38.7 bits (91), Expect = 3e-04
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKF 249
++ G G ++ +E++++ FS + + +V K KGY FV F
Sbjct: 9 IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSF 55
Score = 31.4 bits (72), Expect = 0.12
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
++VG+L VT+E+L FS+ + KV+R+ Y F+ F A+ M
Sbjct: 9 IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68
Query: 67 N 67
N
Sbjct: 69 N 69
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 78.0 bits (193), Expect = 3e-18
Identities = 24/71 (33%), Positives = 42/71 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV LS + L+ F+ FG + +++DP+T +S+G+ FV+F +A+ AI +
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 158 NGQWLGSRSIR 168
NG+ L R I+
Sbjct: 64 NGKELEGRVIK 74
Score = 54.9 bits (133), Expect = 6e-10
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATH 257
++ G E+ + +FS FG + ++ + K+ G+ FV F + E A
Sbjct: 1 GNK--LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADA 58
Query: 258 AIESIHNTDINGHTVK 273
AI ++ ++ G +K
Sbjct: 59 AIRDLNGKELEGRVIK 74
Score = 48.8 bits (117), Expect = 8e-08
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAA 60
L+V L TE+ L ALFS+ G V+ ++++P G + F+ F A
Sbjct: 1 GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRG---FGFVTFESVEDAD 57
Query: 61 TALAAMNKRVFLEKEMKV 78
A+ +N + + +KV
Sbjct: 58 AAIRDLNGKELEGRVIKV 75
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 77.7 bits (192), Expect = 5e-18
Identities = 25/73 (34%), Positives = 43/73 (58%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L + + LK+ F FGE+++ R++ D +T +S+G+ FV EA AI +
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61
Query: 158 NGQWLGSRSIRTN 170
NG G R++ N
Sbjct: 62 NGTDFGGRTLTVN 74
Score = 53.8 bits (130), Expect = 1e-09
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIES 261
+Y G ++ EE + +F FG + RV + +G+ FV+ T E A AIE
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 262 IHNTDINGHTVK 273
++ TD G T+
Sbjct: 61 LNGTDFGGRTLT 72
Score = 52.6 bits (127), Expect = 4e-09
Identities = 30/76 (39%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATALAA 65
LYVGNL +VTEE L LF Q G V +VI RE G + F+E A A+
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 66 MNKRVFLEKEMKVNWA 81
+N F + + VN A
Sbjct: 61 LNGTDFGGRTLTVNEA 76
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 76.9 bits (190), Expect = 8e-18
Identities = 30/73 (41%), Positives = 45/73 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L+ E++ + L AF PFG+I + +I D +T K +G+AFV F + +A AI M
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 158 NGQWLGSRSIRTN 170
N L R+IR N
Sbjct: 61 NESELFGRTIRVN 73
Score = 67.6 bits (166), Expect = 2e-14
Identities = 23/72 (31%), Positives = 45/72 (62%), Gaps = 6/72 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETATHAIESI 262
+Y GG ++++E+++ F PFG I DI++ K +G+AFV+F E A AI+++
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 263 HNTDINGHTVKC 274
+ +++ G T++
Sbjct: 61 NESELFGRTIRV 72
Score = 45.3 bits (108), Expect = 1e-06
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
LYVG L V E++L A F G +K ++ + +AF+EF AA A+ M
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 67 NKRVFLEKEMKVN 79
N+ + ++VN
Sbjct: 61 NESELFGRTIRVN 73
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 83
Score = 77.3 bits (191), Expect = 8e-18
Identities = 32/79 (40%), Positives = 53/79 (67%), Gaps = 1/79 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEI-SNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G+L PE++ + L + F+ FG I +I+RDP T SKG+AF+S+ ++ AI A
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 157 MNGQWLGSRSIRTNWSTRK 175
MNGQ+L +R I +++ +K
Sbjct: 64 MNGQYLCNRPITVSYAFKK 82
Score = 46.5 bits (111), Expect = 6e-07
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGP-VKGCKVIREPGNDP---YAFLEFVHHTVAATALAA 65
L++GNLD V E+LL FS G ++ K++R+P +AF+ + + A+ A
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 66 MNKRVFLEKEMKVNWA 81
MN + + + V++A
Sbjct: 64 MNGQYLCNRPITVSYA 79
Score = 40.7 bits (96), Expect = 7e-05
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIV-------DIRVFKEKGYAFVKFTTKETATHAIES 261
++ G +++E+L+ FS FG I+ D KG+AF+ + + E + AIE+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 262 IHNTDING 269
++ +
Sbjct: 64 MNGQYLCN 71
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 76.9 bits (190), Expect = 9e-18
Identities = 32/79 (40%), Positives = 49/79 (62%), Gaps = 1/79 (1%)
Query: 96 YHIFVGDLSPEIETQTLKEAF-APFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+ IFVGDL+P++ L+E F A + + ++V DP T +SKGY FV F + E + A+
Sbjct: 2 HSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL 61
Query: 155 TAMNGQWLGSRSIRTNWST 173
T MNG + SR +R + +T
Sbjct: 62 TEMNGVYCSSRPMRVSPAT 80
Score = 36.1 bits (84), Expect = 0.003
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 12/82 (14%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGP-VKGCKVIREPGNDP-------YAFLEFVHHTVAA 60
+++VG+L VT+ +L F P V+G KV+ DP Y F+ F
Sbjct: 3 SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVV----MDPVTGRSKGYGFVRFGDEDERD 58
Query: 61 TALAAMNKRVFLEKEMKVNWAS 82
AL MN + M+V+ A+
Sbjct: 59 RALTEMNGVYCSSRPMRVSPAT 80
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 82.7 bits (204), Expect = 2e-17
Identities = 57/220 (25%), Positives = 98/220 (44%), Gaps = 37/220 (16%)
Query: 105 PEIETQ-TLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLG 163
P+ TQ ++ F GEI +C++VRD T +S GY FV++V+ +AE A+ ++NG L
Sbjct: 12 PQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQ 71
Query: 164 SRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELV 223
+++I+ +++ R +S S +Y G K + + +
Sbjct: 72 NKTIKVSYA------------RPSS-------------DSIKGANLYVSGLPKTMTQHEL 106
Query: 224 SKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGH----TVK 273
+FSPFG I+ R+ + KG F++F ++ A AI++++ T +G TVK
Sbjct: 107 ESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVK 166
Query: 274 CFWGKESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMG 313
F S +NS P +T I
Sbjct: 167 -FANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGI 205
Score = 79.6 bits (196), Expect = 2e-16
Identities = 49/156 (31%), Positives = 82/156 (52%), Gaps = 8/156 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
T L V L ++T+E + +LF+ IG ++ CK++R+ Y F+ +V A A+
Sbjct: 4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63
Query: 65 AMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
++N K +KV++A +P D+ +++V L + L+ F+PFG+I
Sbjct: 64 SLNGLRLQNKTIKVSYA-----RPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIIT 118
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
RI+ D T SKG F+ F K+ EA+ AI +NG
Sbjct: 119 SRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGT 154
Score = 78.8 bits (194), Expect = 3e-16
Identities = 36/92 (39%), Positives = 51/92 (55%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
G Q Y IFV +LSP+ + L + F PFG + N +I+RD T + KGY FVS
Sbjct: 259 GAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSM 318
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
EA AI ++NG LG+R ++ ++ T K
Sbjct: 319 TNYDEAAMAILSLNGYTLGNRVLQVSFKTNKA 350
Score = 40.7 bits (95), Expect = 8e-04
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGH 270
D +E ++ ++F PFG + ++++ ++ KGY FV T + A AI S++ +
Sbjct: 280 DTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNR 339
Query: 271 TVK 273
++
Sbjct: 340 VLQ 342
Score = 38.8 bits (90), Expect = 0.004
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
++V NL E +L LF G V+ K+IR+ + Y F+ ++ AA A+ ++
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 67 NKRVFLEKEMKVNWASS 83
N + ++V++ ++
Sbjct: 332 NGYTLGNRVLQVSFKTN 348
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM1 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 76
Score = 74.3 bits (183), Expect = 6e-17
Identities = 27/75 (36%), Positives = 46/75 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+LS ++ + LK F FG + R++ D +T +S+G+ +V F +A+ AI AM
Sbjct: 2 LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61
Query: 158 NGQWLGSRSIRTNWS 172
+G+ L R I ++S
Sbjct: 62 DGKELDGRPINVDFS 76
Score = 53.9 bits (130), Expect = 1e-09
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIES 261
T++ G +++E + F FGT+V RV + +G+ +V F + E A AIE+
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 262 IHNTDINGHTVKC 274
+ +++G +
Sbjct: 61 MDGKELDGRPINV 73
Score = 49.7 bits (119), Expect = 4e-08
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAA 65
TL+VGNL SV +E L A F + G V G +VI + + +++F A A+ A
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 66 MNKRVFLEKEMKVNWA 81
M+ + + + V+++
Sbjct: 61 MDGKELDGRPINVDFS 76
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 79.7 bits (196), Expect = 1e-16
Identities = 51/154 (33%), Positives = 80/154 (51%), Gaps = 8/154 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVAATALA 64
T L V L +T+ L ALF IGP+ C+++R+ YAF++F + A+
Sbjct: 108 TNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIK 167
Query: 65 AMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+N K +KV++A PG + +DT+ ++V +L I L F +G+I
Sbjct: 168 NLNGITVRNKRLKVSYA-RPGGESIKDTN----LYVTNLPRTITDDQLDTIFGKYGQIVQ 222
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
I+RD T +G AFV F K+ EA+ AI+A+N
Sbjct: 223 KNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 256
Score = 66.2 bits (161), Expect = 5e-12
Identities = 52/212 (24%), Positives = 91/212 (42%), Gaps = 31/212 (14%)
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAP 118
+A L +M + +N S G+ ++ ++ V L ++ + L F
Sbjct: 71 SACGLGSMGNMANMASTNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRT 130
Query: 119 FGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
G I+ CRI+RD +T S GYAFV F +A+++ AI +NG + R+ R S +P
Sbjct: 131 IGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNG--ITVRNKRLKVSYARPGG 188
Query: 179 MTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV 238
TN +Y + + ++ + +F +G IV +
Sbjct: 189 ---------------------ESIKDTN--LYVTNLPRTITDDQLDTIFGKYGQIVQKNI 225
Query: 239 FKEK------GYAFVKFTTKETATHAIESIHN 264
++K G AFV+F +E A AI +++N
Sbjct: 226 LRDKLTGTPRGVAFVRFNKREEAQEAISALNN 257
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammals, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 73.7 bits (182), Expect = 1e-16
Identities = 31/78 (39%), Positives = 46/78 (58%)
Query: 99 FVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
+VGDL P++ L E F+P G + + R+ RD T +S GYA+V+F A+AE A+ +N
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62
Query: 159 GQWLGSRSIRTNWSTRKP 176
+ + IR WS R P
Sbjct: 63 FDVIKGKPIRIMWSQRDP 80
Score = 58.3 bits (142), Expect = 4e-11
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAATAL 63
LYVG+L VTE +L +FS GPV +V R+ G YA++ F + A AL
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLG---YAYVNFQNPADAERAL 58
Query: 64 AAMNKRVFLEKEMKVNWAS 82
+N V K +++ W+
Sbjct: 59 DTLNFDVIKGKPIRIMWSQ 77
Score = 46.8 bits (112), Expect = 5e-07
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 210 YCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIH 263
Y G D+ E ++ ++FSP G ++ IRV ++ GYA+V F A A+++++
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62
Query: 264 NTDINGHTVKCFW 276
I G ++ W
Sbjct: 63 FDVIKGKPIRIMW 75
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 72.7 bits (179), Expect = 3e-16
Identities = 28/64 (43%), Positives = 41/64 (64%), Gaps = 2/64 (3%)
Query: 107 IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGS-- 164
+ L+EAFAPFGEI + +V+D QT +SKG A+V F K + A A+ MNG+ LG
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73
Query: 165 RSIR 168
+ ++
Sbjct: 74 KPLK 77
Score = 57.0 bits (138), Expect = 1e-10
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 215 GKDLNEELVSKVFSPFGTIVDIRVFK------EKGYAFVKFTTKETATHAIESIHNTDIN 268
GK + E+ + + F+PFG I DI V K KG A+VKF +A A+E ++ +
Sbjct: 11 GKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLG 70
Query: 269 GHT--VKCF 275
G T +K
Sbjct: 71 GDTKPLKVL 79
Score = 34.6 bits (80), Expect = 0.009
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 18 SVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAMNKRV 70
SVTE+ L F+ G ++ V+++ A+++F + AA A+ MN +
Sbjct: 13 SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKC 68
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 74.3 bits (182), Expect = 5e-16
Identities = 29/81 (35%), Positives = 52/81 (64%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS + +L++AFA FG++ + +++ D +T +S+G+ FV+F + A AI+ M
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96
Query: 158 NGQWLGSRSIRTNWSTRKPPA 178
+G+ L R IR N + +P A
Sbjct: 97 DGKELNGRHIRVNPANDRPSA 117
Score = 40.8 bits (95), Expect = 2e-04
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 14/90 (15%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
++ GG ++ + F+ FG +VD +V + +G+ FV F + AT AI +
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96
Query: 263 HNTDINGHTVKCFWGKESENNSTLAQPSAP 292
++NG ++ N +PSAP
Sbjct: 97 DGKELNGRHIRV--------NPANDRPSAP 118
Score = 32.3 bits (73), Expect = 0.20
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATALA 64
T L++G L + L F+ G V KVI RE G + F+ F A A++
Sbjct: 35 TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94
Query: 65 AMNKRVFLEKEMKVNWASSPGNQPK 89
M+ + + ++VN A+ + P+
Sbjct: 95 EMDGKELNGRHIRVNPANDRPSAPR 119
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 71.6 bits (176), Expect = 8e-16
Identities = 29/72 (40%), Positives = 45/72 (62%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+ IFV +L P+ + L + F+PFG ++N +++RD T K KGY FV+ EA +AI
Sbjct: 2 WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61
Query: 156 AMNGQWLGSRSI 167
++NG LG R +
Sbjct: 62 SLNGYRLGGRVL 73
Score = 41.9 bits (99), Expect = 2e-05
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
VY D +E L+ ++FSPFG + +++V ++ KGY FV T E A AI S+
Sbjct: 6 VY--NLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63
Query: 263 HNTDINGHT 271
+ + G
Sbjct: 64 NGYRLGGRV 72
Score = 38.5 bits (90), Expect = 4e-04
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATAL 63
++V NL E LL LFS G V KVIR+ + Y F+ ++ A +A+
Sbjct: 1 GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60
Query: 64 AAMNKRVFLEKEMKV 78
A++N + ++V
Sbjct: 61 ASLNGYRLGGRVLQV 75
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein 3
(RBM3) and similar proteins. This subfamily corresponds
to the RRM domain of two structurally related
heterogenous nuclear ribonucleoproteins, CIRBP (also
termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL),
both of which belong to a highly conserved cold shock
proteins family. The cold shock proteins can be induced
after exposure to a moderate cold-shock and other
cellular stresses such as UV radiation and hypoxia.
CIRBP and RBM3 may function in posttranscriptional
regulation of gene expression by binding to different
transcripts, thus allowing the cell to response rapidly
to environmental signals. However, the kinetics and
degree of cold induction are different between CIRBP and
RBM3. Tissue distribution of their expression is
different. CIRBP and RBM3 may be differentially
regulated under physiological and stress conditions and
may play distinct roles in cold responses of cells.
CIRBP, also termed glycine-rich RNA-binding protein
CIRP, is localized in the nucleus and mediates the
cold-induced suppression of cell cycle progression.
CIRBP also binds DNA and possibly serves as a chaperone
that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore, RBM3
may be essential for cell proliferation and mitosis.
Both, CIRBP and RBM3, contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), that is
involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 70.6 bits (173), Expect = 2e-15
Identities = 27/73 (36%), Positives = 50/73 (68%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS + Q+L++ F+ +G+IS +V+D +T +S+G+ FV+F +A++A+ AM
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 158 NGQWLGSRSIRTN 170
NG+ + R IR +
Sbjct: 63 NGKSVDGRQIRVD 75
Score = 46.8 bits (111), Expect = 5e-07
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ GG D NE+ + +VFS +G I ++ V K+ +G+ FV F + A A+ ++
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 263 HNTDINGHTVK 273
+ ++G ++
Sbjct: 63 NGKSVDGRQIR 73
Score = 35.6 bits (82), Expect = 0.005
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
L++G L E+ L +FS+ G + V+++ + F+ F + A A+ AM
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 67 NKRVFLEKEMKVNWA 81
N + ++++V+ A
Sbjct: 63 NGKSVDGRQIRVDQA 77
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed in
all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. The family also
includes yeast ortholog mRNA 3'-end-processing protein
RNA15 and similar proteins. RNA15 is a core subunit of
cleavage factor IA (CFIA), an essential transcriptional
3'-end processing factor from Saccharomyces cerevisiae.
RNA recognition by CFIA is mediated by an N-terminal
RRM, which is contained in the RNA15 subunit of the
complex. The RRM of RNA15 has a strong preference for
GU-rich RNAs, mediated by a binding pocket that is
entirely conserved in both yeast and vertebrate RNA15
orthologs.
Length = 75
Score = 70.0 bits (172), Expect = 2e-15
Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG++ + + L E F+ G + + R+V D T K KGY F F A +AI +
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 158 NGQWLGSRSIRTNWS 172
NG R++R +++
Sbjct: 61 NGYEFNGRALRVDFA 75
Score = 49.9 bits (120), Expect = 3e-08
Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 11 YVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATALAAMN 67
+VGN+ TEE L +FS++GPV +++ R+ G Y F EF AA+A+ +N
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 68 KRVFLEKEMKVNWA 81
F + ++V++A
Sbjct: 62 GYEFNGRALRVDFA 75
Score = 43.4 bits (103), Expect = 6e-06
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIR-VF-----KEKGYAFVKFTTKETATHAIESI 262
V+ G D EE + ++FS G +V R V K KGY F +F ETA AI ++
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 263 HNTDINGHTVKC 274
+ + NG ++
Sbjct: 61 NGYEFNGRALRV 72
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 70.4 bits (173), Expect = 3e-15
Identities = 26/70 (37%), Positives = 39/70 (55%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG LS + +TL+E F+ +G+I R+VRD T SKGYAFV + + +A A
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65
Query: 158 NGQWLGSRSI 167
+ + I
Sbjct: 66 HKLVIDGSEI 75
Score = 49.9 bits (120), Expect = 5e-08
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAI 259
T++ G EE + +VFS +G I +R+ ++ KGYAFV++ + A A
Sbjct: 3 YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62
Query: 260 ESIHNTDINGHTV 272
H I+G +
Sbjct: 63 RDAHKLVIDGSEI 75
Score = 45.3 bits (108), Expect = 2e-06
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE--PGNDP-YAFLEFVHHTVAATALAA 65
TL+VG L + TEE L +FS+ G ++ +++R+ G YAF+E+ H A A
Sbjct: 5 TLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64
Query: 66 MNKRV 70
+K V
Sbjct: 65 AHKLV 69
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 69.1 bits (170), Expect = 4e-15
Identities = 24/71 (33%), Positives = 44/71 (61%), Gaps = 2/71 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V +L P + + L+E F+P+G++ R+VR+ + +G+AFV F +AE A+ +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58
Query: 158 NGQWLGSRSIR 168
NG L R++R
Sbjct: 59 NGLVLDGRTLR 69
Score = 59.9 bits (146), Expect = 9e-12
Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK----GYAFVKFTTKETATHAIESIHN 264
+Y + EE + + FSP+G + +R+ + K G+AFV+F + E A A++ ++
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 265 TDINGHTVK 273
++G T++
Sbjct: 61 LVLDGRTLR 69
Score = 52.9 bits (128), Expect = 3e-09
Identities = 26/63 (41%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVHHTVAATALAAMNK 68
LYV NL SVTEE L FS G V+G +++R +AF+EF A AL +N
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 69 RVF 71
V
Sbjct: 61 LVL 63
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 69.5 bits (171), Expect = 4e-15
Identities = 24/61 (39%), Positives = 35/61 (57%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+ +L + + LKE F+ FGE+ RIV+D T SKG AFV F K A+ + A
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62
Query: 158 N 158
+
Sbjct: 63 D 63
Score = 43.0 bits (102), Expect = 1e-05
Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAA 65
T+++ NL TEE L LFSQ G VK +++++ AF++F A L A
Sbjct: 2 TVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61
Query: 66 MNKRVFLE 73
+
Sbjct: 62 ADNAEDSG 69
Score = 37.6 bits (88), Expect = 0.001
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 6/51 (11%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIES 261
D EE + ++FS FG + R+ K+ KG AFVKF TKE+A +E+
Sbjct: 11 DATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 69.6 bits (171), Expect = 4e-15
Identities = 25/76 (32%), Positives = 42/76 (55%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ VG+L E + +E +PFG + C +V T +SKGY FV + KA A A +
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 158 NGQWLGSRSIRTNWST 173
+G+ +G R ++ +W+
Sbjct: 62 DGKQIGGRKLQVDWAD 77
Score = 48.8 bits (117), Expect = 8e-08
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAA 65
L VGNL + T+E L S G V+ C ++ Y F+E+ A A
Sbjct: 1 LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60
Query: 66 MNKRVFLEKEMKVNWA 81
++ + ++++V+WA
Sbjct: 61 LDGKQIGGRKLQVDWA 76
Score = 48.0 bits (115), Expect = 2e-07
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 10/68 (14%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVF--------KEKGYAFVKFTTKETATHAIESIHNTDIN 268
+ +E ++ SPFG + R F + KGY FV++ +K +A A + I
Sbjct: 10 EFTDEQFRELVSPFGAVE--RCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIG 67
Query: 269 GHTVKCFW 276
G ++ W
Sbjct: 68 GRKLQVDW 75
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Although the
cellular function of RBM23 remains unclear, it shows
high sequence homology to RBM39 and contains two RRMs.
It may possibly function as a pre-mRNA splicing factor.
.
Length = 73
Score = 69.2 bits (170), Expect = 5e-15
Identities = 28/73 (38%), Positives = 42/73 (57%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L I L+ F PFGEI ++ RDP+T +SKGY F+ F +A+ A+ +
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 158 NGQWLGSRSIRTN 170
NG L R I+
Sbjct: 61 NGFELAGRPIKVG 73
Score = 46.5 bits (111), Expect = 6e-07
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 6/70 (8%)
Query: 210 YCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIH 263
Y G ++ E+ + +F PFG I +++ ++ KGY F++F E A A+E ++
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61
Query: 264 NTDINGHTVK 273
++ G +K
Sbjct: 62 GFELAGRPIK 71
Score = 44.2 bits (105), Expect = 4e-06
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
LYVGNL ++TE+ L +F G ++ ++ R+P Y F++F A AL +
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 67 NKRVFLEKEMKVN 79
N + +KV
Sbjct: 61 NGFELAGRPIKVG 73
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 69.5 bits (170), Expect = 5e-15
Identities = 30/79 (37%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 96 YHIFVGDLSPEIETQTLKEAFA-PFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
Y IFVGDLSPE+ L F F + +I+ DP T S+GY FV F + + + A+
Sbjct: 2 YSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRAL 61
Query: 155 TAMNGQWLGSRSIRTNWST 173
M G + G R +R + +T
Sbjct: 62 IEMQGVYCGGRPMRISTAT 80
Score = 32.1 bits (73), Expect = 0.077
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGP-VKGCKVIREP---GNDPYAFLEFVHHTVAATALA 64
+++VG+L V E L +LF P K K++ +P + Y F+ F AL
Sbjct: 3 SIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALI 62
Query: 65 AMNKRVFLEKEMKVNWAS 82
M + M+++ A+
Sbjct: 63 EMQGVYCGGRPMRISTAT 80
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 69.2 bits (170), Expect = 6e-15
Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 2/78 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++GDL P ++ + AFA GE+++ +I+R+ QT KS GY FV F AE A+ ++
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61
Query: 158 NGQWLGSRSI--RTNWST 173
NG+ + + R NW+
Sbjct: 62 NGKPIPNTQQRFRLNWAN 79
Score = 44.6 bits (106), Expect = 3e-06
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 21/89 (23%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIR------EPGNDPYAFLEFVHHTVAATA 62
TL++G+L+ + E + + F++ G V K+IR G Y F+EF H A A
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAG---YGFVEFATHEAAEQA 57
Query: 63 LAAMN-------KRVFLEKEMKVNWASSP 84
L ++N ++ F ++NWA+
Sbjct: 58 LQSLNGKPIPNTQQRF-----RLNWANFG 81
Score = 41.9 bits (99), Expect = 2e-05
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIES 261
T++ G ++E + F+ G + +++ + K GY FV+F T E A A++S
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60
Query: 262 I 262
+
Sbjct: 61 L 61
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 68.2 bits (167), Expect = 1e-14
Identities = 29/73 (39%), Positives = 46/73 (63%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG +S E+ T+++AF+PFG I + + DP T+K KG+AFV + A+ A+ M
Sbjct: 3 VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62
Query: 158 NGQWLGSRSIRTN 170
NG LG R+I+
Sbjct: 63 NGVMLGGRNIKVG 75
Score = 53.6 bits (129), Expect = 2e-09
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETATHAIE 260
C VY G +L E+ + + FSPFG I I + K KG+AFV++ E A A+E
Sbjct: 1 CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60
Query: 261 SIHNTDINGHTVK 273
++ + G +K
Sbjct: 61 QMNGVMLGGRNIK 73
Score = 33.2 bits (76), Expect = 0.029
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
+YVG++ + E+ + FS GP+K + +P +AF+E+ A AL M
Sbjct: 3 VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62
Query: 67 NKRVFLEKEMKVN 79
N + + +KV
Sbjct: 63 NGVMLGGRNIKVG 75
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the RRM
of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or
splicing component, 35 kDa (splicing factor SC35 or
SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of pre-mRNA.
It is also involved in transcription elongation by
directly or indirectly mediating the recruitment of
elongation factors to the C-terminal domain of
polymerase II. SRSF2 is exclusively localized in the
nucleus and is restricted to nuclear processes. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory elements
on the pre-mRNA. The RS domain modulates SRSF2 activity
through phosphorylation, directly contacts RNA, and
promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 66.9 bits (164), Expect = 2e-14
Identities = 26/69 (37%), Positives = 41/69 (59%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
V +L+ L+ F +GE+ + I RD T +S+G+AFV F K +AE+A+ AM+G
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 160 QWLGSRSIR 168
+ L R +R
Sbjct: 63 KELDGRELR 71
Score = 44.2 bits (105), Expect = 3e-06
Identities = 13/59 (22%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+ + +VF +G + D+ + +++ G+AFV+F K A A++++ +++G
Sbjct: 9 RTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDG 67
Score = 30.0 bits (68), Expect = 0.33
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
L V NL T + L +F + G V + R+ +AF+ F A A+ AM
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Query: 67 NKRVFLEKEMKV 78
+ + +E++V
Sbjct: 61 DGKELDGRELRV 72
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 67.0 bits (163), Expect = 3e-14
Identities = 32/78 (41%), Positives = 48/78 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFV +LSPE + L + F PFG ++N +++RD T K KG+ FV+ EA AI ++
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 158 NGQWLGSRSIRTNWSTRK 175
NG LG R ++ ++ T K
Sbjct: 64 NGYRLGDRVLQVSFKTSK 81
Score = 34.7 bits (79), Expect = 0.010
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
++V NL E +L LF G V KVIR+ + + F+ ++ AA A+A++
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 67 NKRVFLEKEMKVNWASS 83
N ++ ++V++ +S
Sbjct: 64 NGYRLGDRVLQVSFKTS 80
Score = 33.9 bits (77), Expect = 0.020
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 6/61 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ + +E ++ ++F PFG + +++V ++ KG+ FV T + A AI S+
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 263 H 263
+
Sbjct: 64 N 64
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 66.6 bits (163), Expect = 3e-14
Identities = 30/74 (40%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG L P + L+ F PFGEI +I P KG FV FV +A AE AI +
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKI---P---PGKGCGFVQFVHRAAAEAAIQQL 57
Query: 158 NGQWLGSRSIRTNW 171
G +G IR +W
Sbjct: 58 QGTIIGGSRIRLSW 71
Score = 57.7 bits (140), Expect = 6e-11
Identities = 25/72 (34%), Positives = 39/72 (54%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNT 265
N TV+ GG + E+ + +F PFG IV +++ KG FV+F + A AI+ + T
Sbjct: 1 NTTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGT 60
Query: 266 DINGHTVKCFWG 277
I G ++ WG
Sbjct: 61 IIGGSRIRLSWG 72
Score = 40.0 bits (94), Expect = 1e-04
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 19/81 (23%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPV--------KGCKVIREPGNDPYAFLEFVHHTVA 59
TT++VG LD +VTE+ L +LF G + KGC F++FVH A
Sbjct: 2 TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGC-----------GFVQFVHRAAA 50
Query: 60 ATALAAMNKRVFLEKEMKVNW 80
A+ + + ++++W
Sbjct: 51 EAAIQQLQGTIIGGSRIRLSW 71
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the RRM
of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). This family
also includes yeast eIF3-p33, a homolog of vertebrate
eIF-3G, plays an important role in the initiation phase
of protein synthesis in yeast. It binds both, mRNA and
rRNA, fragments due to an RRM near its C-terminus. .
Length = 77
Score = 66.4 bits (163), Expect = 6e-14
Identities = 25/60 (41%), Positives = 39/60 (65%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
V +LS + + L+E F PFG IS + +D +T +S+G+AFV+F + +AE AI +NG
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
Score = 39.1 bits (92), Expect = 2e-04
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 15/62 (24%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVF--------KEKGYAFVKFTTKETATHAIESIHNTDIN 268
D +E+ + ++F PFG I RV+ + +G+AFV F T+E A AIE +N
Sbjct: 10 DADEDDLRELFRPFGPI--SRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK-----LN 62
Query: 269 GH 270
G
Sbjct: 63 GF 64
Score = 37.9 bits (89), Expect = 6e-04
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFVHHTVAATALAA 65
T+ V NL E+ L LF GP+ + ++ + +AF+ F A A+
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
Query: 66 MNKRVFLEKEMKVNWA 81
+N + + V WA
Sbjct: 61 LNGFGYDNLILSVEWA 76
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 86
Score = 66.7 bits (162), Expect = 6e-14
Identities = 31/78 (39%), Positives = 48/78 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFV +LSP+ + L + F PFG ++N +++RD T K KG+ FV+ EA AI ++
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 158 NGQWLGSRSIRTNWSTRK 175
NG LG R ++ ++ T K
Sbjct: 66 NGYRLGDRVLQVSFKTNK 83
Score = 35.1 bits (80), Expect = 0.007
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHA 258
T ++ D +E ++ ++F PFG + +++V ++ KG+ FV T + A A
Sbjct: 2 TGWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMA 61
Query: 259 IESIH 263
I S++
Sbjct: 62 IASLN 66
Score = 33.1 bits (75), Expect = 0.039
Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
++V NL E +L LF G V KVIR+ + + F+ ++ AA A+A++
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 67 NKRVFLEKEMKVNWASSPGNQ 87
N ++ ++V++ ++ ++
Sbjct: 66 NGYRLGDRVLQVSFKTNKTHK 86
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 66.0 bits (162), Expect = 8e-14
Identities = 24/62 (38%), Positives = 35/62 (56%)
Query: 99 FVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
FVG L + ++ F +G I I+RD T +SKG AFV F + EA+ AI A++
Sbjct: 3 FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALH 62
Query: 159 GQ 160
G+
Sbjct: 63 GK 64
Score = 54.9 bits (133), Expect = 7e-10
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 212 GGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNT 265
G K EE V +F +G I ++ + ++ KG AFVKF+++E A AIE++H
Sbjct: 5 GQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGK 64
Score = 39.1 bits (92), Expect = 2e-04
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPY---AFLEFVHHTVAATALAAM 66
L+VG L + TEE + ALF + G ++ +IR+ AF++F A A+ A+
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61
Query: 67 NKRVFLE 73
+ +V +
Sbjct: 62 HGKVTMP 68
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM2 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 73
Score = 65.5 bits (160), Expect = 9e-14
Identities = 26/71 (36%), Positives = 44/71 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+LS + + ++ EAF +GEIS+ R+ DP + + KG+ +V F + A+ A+ A+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 158 NGQWLGSRSIR 168
G L R +R
Sbjct: 61 GGTDLLGRPVR 71
Score = 41.2 bits (97), Expect = 3e-05
Identities = 18/71 (25%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ G D +E+ + + F +G I +R+ + KG+ +V+F+++E A A++++
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 263 HNTDINGHTVK 273
TD+ G V+
Sbjct: 61 GGTDLLGRPVR 71
Score = 30.4 bits (69), Expect = 0.25
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN-DPYAF--LEFVHHTVAATALAAM 66
L+VGNL E+ + F + G + ++ +P + P F +EF A AL A+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 67 NK 68
Sbjct: 61 GG 62
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 65.7 bits (161), Expect = 1e-13
Identities = 20/70 (28%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V +L +++ + LKE F +G+I++ ++++D KSKG+ FV+F A+ A+ +
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62
Query: 158 NGQWLGSRSI 167
NG+ + + +
Sbjct: 63 NGKEVNGKKL 72
Score = 52.2 bits (126), Expect = 6e-09
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 7/73 (9%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-----KEKGYAFVKFTTKETATHAI 259
TN VY G+D+++E + ++F +G I +V K KG+ FV F E A A+
Sbjct: 2 TN--VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAV 59
Query: 260 ESIHNTDINGHTV 272
E ++ ++NG +
Sbjct: 60 EELNGKEVNGKKL 72
Score = 43.7 bits (104), Expect = 5e-06
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAA 65
T +YV NL + +E L LF + G + KV+++ + F+ F +H A A+
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61
Query: 66 MNKRVFLEKEMKV 78
+N + K++ V
Sbjct: 62 LNGKEVNGKKLYV 74
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 65.4 bits (160), Expect = 1e-13
Identities = 25/71 (35%), Positives = 40/71 (56%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+ L E Q L + FAPFG + + ++ D T +SK + FVS+ A+ AI AM
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 158 NGQWLGSRSIR 168
NG +G + ++
Sbjct: 61 NGFQVGGKRLK 71
Score = 41.5 bits (98), Expect = 3e-05
Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDING 269
+ ++ + ++F+PFG ++ +VF + K + FV + E+A AI++++ + G
Sbjct: 8 NEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGG 67
Query: 270 HTVK 273
+K
Sbjct: 68 KRLK 71
Score = 28.8 bits (65), Expect = 1.1
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 3/73 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP---GNDPYAFLEFVHHTVAATALAAM 66
L++ +L T++ L LF+ G V KV + + + F+ + + A A+ AM
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 67 NKRVFLEKEMKVN 79
N K +KV
Sbjct: 61 NGFQVGGKRLKVQ 73
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 65.5 bits (159), Expect = 1e-13
Identities = 30/78 (38%), Positives = 48/78 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFV +L+P+ + L + F PFG ++N +++RD T K KG+ FV+ EA AI ++
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 158 NGQWLGSRSIRTNWSTRK 175
NG LG R ++ ++ T K
Sbjct: 66 NGYRLGDRVLQVSFKTNK 83
Score = 37.0 bits (85), Expect = 0.002
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHA 258
T ++ D +E ++ ++F PFG + +++V ++ KG+ FV T + A A
Sbjct: 2 TGWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMA 61
Query: 259 IESIH 263
I S++
Sbjct: 62 IASLN 66
Score = 33.1 bits (75), Expect = 0.037
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
++V NL E +L +F G V KVIR+ + + F+ ++ AA A+A++
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 67 NKRVFLEKEMKVNWASS 83
N ++ ++V++ ++
Sbjct: 66 NGYRLGDRVLQVSFKTN 82
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 64.9 bits (159), Expect = 2e-13
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IF+ +L I+ + L + F+ FG I +C++ D SKGY FV F + A AI +
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENG-GSKGYGFVHFETEEAAVRAIEKV 63
Query: 158 NGQWLGSRSI 167
NG L + +
Sbjct: 64 NGMLLNDKKV 73
Score = 44.1 bits (105), Expect = 4e-06
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 9/68 (13%)
Query: 214 FGKDLNEELVSKV----FSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIHN 264
F K+L++ + +K FS FG I+ +V + KGY FV F T+E A AIE ++
Sbjct: 6 FIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVNG 65
Query: 265 TDINGHTV 272
+N V
Sbjct: 66 MLLNDKKV 73
Score = 40.6 bits (96), Expect = 7e-05
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAMN 67
+++ NLD S+ + L FS G + CKV + Y F+ F A A+ +N
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64
Query: 68 KRVFLEKEMKVN 79
+ +K++ V
Sbjct: 65 GMLLNDKKVFVG 76
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 64.6 bits (158), Expect = 3e-13
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 103 LSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWL 162
LS + L+E F+ +G I ++V D +T +S+G+ FV F +A+ A +NG +
Sbjct: 7 LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEI 66
Query: 163 GSRSIRTNWS 172
R IR ++S
Sbjct: 67 DGRRIRVDYS 76
Score = 41.5 bits (98), Expect = 3e-05
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 8/71 (11%)
Query: 212 GGFGKDLN--EELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIH 263
G FG L E + +VFS +G I ++V + +G+ FV F + E A A E ++
Sbjct: 3 GVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLN 62
Query: 264 NTDINGHTVKC 274
+I+G ++
Sbjct: 63 GMEIDGRRIRV 73
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 64.2 bits (157), Expect = 3e-13
Identities = 29/73 (39%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHN-T 265
T+Y GG G+ + E+ + F FG I I V + AFV FTT+E A A E + N
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFNKL 61
Query: 266 DINGHTVKCFWGK 278
ING +K WG+
Sbjct: 62 IINGRRLKLKWGR 74
Score = 42.2 bits (100), Expect = 1e-05
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
++VG L + + L++ F FGEI + +V + AFV+F + AE A
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKA 53
Score = 39.2 bits (92), Expect = 2e-04
Identities = 26/77 (33%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAA-- 65
TTLYVG L VTE+ L F Q G ++ V+ AF+ F T A AA
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQ---CAFVTFT--TREAAEKAAER 56
Query: 66 -MNKRVFLEKEMKVNWA 81
NK + + +K+ W
Sbjct: 57 LFNKLIINGRRLKLKWG 73
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other EJC
components (such as Magoh, Aly/REF, RNPS1, Srm160, and
Upf3), plays critical roles in postsplicing processing,
including nuclear export and cytoplasmic localization of
the mRNA, and the nonsense-mediated mRNA decay (NMD)
surveillance process. RBM8 binds to mRNA 20-24
nucleotides upstream of a spliced exon-exon junction. It
is also involved in spliced mRNA nuclear export, and the
process of nonsense-mediated decay of mRNAs with
premature stop codons. RBM8 forms a specific heterodimer
complex with the EJC protein Magoh which then associates
with Aly/REF, RNPS1, DEK, and SRm160 on the spliced
mRNA, and inhibits ATP turnover by eIF4AIII, thereby
trapping the EJC core onto RNA. RBM8 contains an
N-terminal putative bipartite nuclear localization
signal, one RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
in the central region, and a C-terminal serine-arginine
rich region (SR domain) and glycine-arginine rich region
(RG domain). .
Length = 88
Score = 64.2 bits (157), Expect = 4e-13
Identities = 29/80 (36%), Positives = 45/80 (56%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFV + E + + + + FA FGEI N + D +T KGYA + + K EA+ AI +
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 158 NGQWLGSRSIRTNWSTRKPP 177
NG+ L ++I +W+ K P
Sbjct: 69 NGKELLGQTISVDWAFVKGP 88
Score = 44.5 bits (106), Expect = 3e-06
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 220 EELVSKVFSPFGTIVDI------RVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
EE V F+ FG I ++ R KGYA +++ TK+ A AIE ++ ++ G T+
Sbjct: 20 EEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTIS 79
Query: 274 CFW 276
W
Sbjct: 80 VDW 82
Score = 41.0 bits (97), Expect = 5e-05
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKV--IREPGN-DPYAFLEFVHHTVAATALAAM 66
++V + EE + F++ G +K + R G YA +E+ A A+ +
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 67 NKRVFLEKEMKVNWA 81
N + L + + V+WA
Sbjct: 69 NGKELLGQTISVDWA 83
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 63.5 bits (155), Expect = 5e-13
Identities = 23/59 (38%), Positives = 40/59 (67%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G LS E +LK F+ +GEI++C +++DP T +S+G+ FV+F +E + A+ A
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Score = 40.0 bits (94), Expect = 1e-04
Identities = 20/60 (33%), Positives = 29/60 (48%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L++G L T++ L FSQ G + C V+++P FV A+ AAMN R
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61
Score = 33.5 bits (77), Expect = 0.025
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 212 GGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHA 258
GG + ++ + FS +G I D V K+ +G+ FV F + A
Sbjct: 5 GGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAA 57
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 63.4 bits (155), Expect = 5e-13
Identities = 25/68 (36%), Positives = 44/68 (64%), Gaps = 1/68 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V +L I+ + L+E F+PFG I++ +++ D + +SKG+ FV F EA A+T M
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAVTEM 62
Query: 158 NGQWLGSR 165
NG+ +G +
Sbjct: 63 NGRIIGGK 70
Score = 47.2 bits (113), Expect = 3e-07
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAMN 67
LYV NLD S+ +E L FS G + KV+ + + F+ F A A+ MN
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63
Query: 68 KRVFLEKEMKVNWA 81
R+ K + V A
Sbjct: 64 GRIIGGKPLYVALA 77
Score = 46.8 bits (112), Expect = 4e-07
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 10/61 (16%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIHNTDINGHT 271
+++E + + FSPFGTI +V + KG+ FV F++ E AT A+ T++NG
Sbjct: 12 SIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAV-----TEMNGRI 66
Query: 272 V 272
+
Sbjct: 67 I 67
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM2 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 73
Score = 63.3 bits (155), Expect = 6e-13
Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L +IE + L++ F G++ RIVRD +T KG+ +V F K ++ +
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLF-KTKDSVALALKL 60
Query: 158 NGQWLGSRSIR 168
NG L R IR
Sbjct: 61 NGIKLKGRKIR 71
Score = 42.1 bits (100), Expect = 2e-05
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 12/77 (15%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAATA 62
+++VGNL + EE L F G V+ +++R+ G + ++ F T + A
Sbjct: 1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKG---FGYVLF--KTKDSVA 55
Query: 63 LA-AMNKRVFLEKEMKV 78
LA +N ++++V
Sbjct: 56 LALKLNGIKLKGRKIRV 72
Score = 37.5 bits (88), Expect = 7e-04
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIE 260
+V+ G D+ EE + K F G + +R+ ++ KG+ +V F TK++ A++
Sbjct: 1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK 59
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. It interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20, and may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM11 is a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. It is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. Both, RBM7 and RBM11, contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 63.1 bits (154), Expect = 7e-13
Identities = 28/72 (38%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAM 66
TL+VGNLD VTEE+L LF Q GP++G K+ ++P P +AF+ F H A+ +
Sbjct: 3 TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLL 62
Query: 67 NKRVFLEKEMKV 78
N +E+++
Sbjct: 63 NGIRLFGRELRI 74
Score = 48.5 bits (116), Expect = 9e-08
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L + + L E F G + +I +DP K K +AFV+F + AI +
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQLL 62
Query: 158 NGQWLGSRSIR 168
NG L R +R
Sbjct: 63 NGIRLFGRELR 73
Score = 43.1 bits (102), Expect = 9e-06
Identities = 15/73 (20%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIE 260
+ T++ G + EE++ ++F G + +++ K+ K +AFV F + + +AI+
Sbjct: 1 DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60
Query: 261 SIHNTDINGHTVK 273
++ + G ++
Sbjct: 61 LLNGIRLFGRELR 73
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 63.1 bits (154), Expect = 8e-13
Identities = 28/66 (42%), Positives = 40/66 (60%), Gaps = 2/66 (3%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
T+Y G+G L EE++ K FSPFG I++I + KEK FV F E+A AI ++ T +
Sbjct: 6 TLYVHGYG--LTEEILKKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNGTTV 63
Query: 268 NGHTVK 273
G +K
Sbjct: 64 QGVQLK 69
Score = 41.5 bits (98), Expect = 4e-05
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 10/73 (13%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQW 161
L+ EI LK+AF+PFG I N + ++ K FV+F K A+ AI +NG
Sbjct: 13 GLTEEI----LKKAFSPFGNIINISMEKE------KNCGFVTFEKMESADRAIAELNGTT 62
Query: 162 LGSRSIRTNWSTR 174
+ ++ + + +
Sbjct: 63 VQGVQLKVSLARK 75
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 61.9 bits (151), Expect = 2e-12
Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L + LK+ F+PFG + I R P K KG+AFV F KA+AE AI +
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGV 60
Query: 158 NGQWLGSRSIRTNWS 172
NG+ + R + +W+
Sbjct: 61 NGKKIKGRPVAVDWA 75
Score = 48.4 bits (116), Expect = 1e-07
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 219 NEELVSKVFSPFGTIVDI-----RVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
E + K+FSPFG + ++ K+KG+AFV+FT+K A AI+ ++ I G V
Sbjct: 12 TEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVA 71
Query: 274 CFW 276
W
Sbjct: 72 VDW 74
Score = 39.2 bits (92), Expect = 2e-04
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAMN 67
L V NL TE L LFS G V + R+P +AF++F A A+ +N
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61
Query: 68 KRVFLEKEMKVNWA 81
+ + + V+WA
Sbjct: 62 GKKIKGRPVAVDWA 75
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 61.1 bits (149), Expect = 3e-12
Identities = 20/59 (33%), Positives = 39/59 (66%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G LS + ++L+E F+ +GE+ +C I++DP T +S+G+ FV+F + + + A
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59
Score = 41.4 bits (98), Expect = 3e-05
Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 210 YCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIH 263
+ GG D EE + + FS +G +VD + K+ G+ FV F + + +
Sbjct: 2 FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61
Query: 264 NTDINGHTVKC 274
+ ++G +
Sbjct: 62 HV-LDGREIDP 71
Score = 28.7 bits (65), Expect = 1.0
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 9/62 (14%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAATAL 63
L++G L TEE L FS+ G V C ++++P G + F+ F + L
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRG---FGFVTFADPSSVDKVL 57
Query: 64 AA 65
AA
Sbjct: 58 AA 59
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise role
of PPIase remains unclear. PPIase contains a conserved
N-terminal peptidyl-prolyl cistrans isomerase (PPIase)
motif, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 61.1 bits (149), Expect = 4e-12
Identities = 25/75 (33%), Positives = 41/75 (54%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV L+P + L+ F+ FG+I +C ++RD +T S YAF+ F K + E A M
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65
Query: 158 NGQWLGSRSIRTNWS 172
+ + R I ++S
Sbjct: 66 DNVLIDDRRIHVDFS 80
Score = 38.4 bits (90), Expect = 4e-04
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE--PGND-PYAFLEFVHHTVAATAL 63
L+V L+ T+E L +FS+ G +K C+VIR+ G+ YAF+EF A
Sbjct: 3 ENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAY 62
Query: 64 AAMNKRVFLEKEMKVNWASS 83
M+ + ++ + V+++ S
Sbjct: 63 FKMDNVLIDDRRIHVDFSQS 82
Score = 33.8 bits (78), Expect = 0.020
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 226 VFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHA 258
+FS FG I V ++K YAF++F TKE A
Sbjct: 23 IFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 60.9 bits (148), Expect = 4e-12
Identities = 25/65 (38%), Positives = 42/65 (64%), Gaps = 1/65 (1%)
Query: 105 PEIETQ-TLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLG 163
P+ TQ ++ F+ GEI +C+++RD T +S GY FV++V +AE AI +NG L
Sbjct: 10 PQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQ 69
Query: 164 SRSIR 168
+++I+
Sbjct: 70 NKTIK 74
Score = 41.3 bits (97), Expect = 4e-05
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
T L V L ++T++ + +LFS IG ++ CK+IR+ Y F+ +V A A+
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61
Query: 65 AMNKRVFLEKEMKVNWA 81
+N K +KV++A
Sbjct: 62 TLNGLRLQNKTIKVSYA 78
Score = 34.3 bits (79), Expect = 0.011
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDINGHT 271
+ ++ + +FS G I ++ ++K GY FV + E A AI +++ + T
Sbjct: 13 MTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKT 72
Query: 272 VK 273
+K
Sbjct: 73 IK 74
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing
factor Cwc2 and similar proteins. This subfamily
corresponds to the RRM of yeast protein Cwc2, also
termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and an intervening loop, also termed
RNA-binding loop or RB loop, between ZnF and RRM, all of
which are necessary and sufficient for RNA binding. The
ZnF is also responsible for mediating protein-protein
interaction. The C-terminal flexible region of Cwc2
interacts with the WD40 domain of Prp19.
Length = 78
Score = 60.7 bits (148), Expect = 6e-12
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 206 NCTVYCGGFGKDLN----EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
N T+Y GG EE++ + F +G I DIRV KG AFV++ + +A A E+
Sbjct: 1 NRTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYKYRASAEFAKEA 60
Query: 262 IHNTDINGHTV 272
+ + ++G V
Sbjct: 61 MADQSLDGGEV 71
Score = 43.4 bits (103), Expect = 7e-06
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
I G +IE + L+ F +G+I + R+ L SKG AFV + +A AE A
Sbjct: 7 GGIKAGSALKQIE-EILRRHFGEWGDIEDIRV------LPSKGIAFVRYKYRASAEFAKE 59
Query: 156 AMNGQWLGSRSI 167
AM Q L +
Sbjct: 60 AMADQSLDGGEV 71
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM1 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 60.2 bits (146), Expect = 6e-12
Identities = 30/74 (40%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEFVHHTVAATALAAMN 67
LYVGNLD VTE++L +F GPV+ K+I + Y F+E+ A AL +N
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60
Query: 68 KRVFLEKEMKVNWA 81
R E++VNWA
Sbjct: 61 GRQIENNEIRVNWA 74
Score = 50.2 bits (120), Expect = 2e-08
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L P + LK+ F G + N +I+ D + K Y FV + + +AE A+ +
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59
Query: 158 NGQWLGSRSIRTNWS 172
NG+ + + IR NW+
Sbjct: 60 NGRQIENNEIRVNWA 74
Score = 32.9 bits (75), Expect = 0.037
Identities = 13/73 (17%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRV-----FKEKGYAFVKFTTKETATHAIESIH 263
+Y G + E+++ ++F G + ++++ K Y FV++ A A+++++
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60
Query: 264 NTDINGHTVKCFW 276
I + ++ W
Sbjct: 61 GRQIENNEIRVNW 73
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 60.8 bits (148), Expect = 6e-12
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 96 YHIFVGDLSPEIETQTLKEAF-APFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+ +FVGDL+P+++ L E F + ++V D Q S+GY FV F ++E + A+
Sbjct: 2 FSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRAL 60
Query: 155 TAMNG-QWLGSRSIR 168
T M G LG + IR
Sbjct: 61 TEMQGASGLGGKPIR 75
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP complex,
which is one of the key factors facilitating the
splicing of pre-mRNA via interaction at the 5' splice
site, and is involved in regulation of polyadenylation
of some viral and cellular genes, enhancing or
inhibiting efficient poly(A) site usage. U1-70K plays an
essential role in targeting the U1 snRNP to the 5'
splice site through protein-protein interactions with
regulatory RNA-binding splicing factors, such as the RS
protein ASF/SF2. Moreover, U1-70K protein can
specifically bind to stem-loop I of the U1 small nuclear
RNA (U1 snRNA) contained in the U1 snRNP complex. It
also mediates the binding of U1C, another U1-specific
protein, to the U1 snRNP complex. U1-70K contains a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by an adjacent glycine-rich region at the
N-terminal half, and two serine/arginine-rich (SR)
domains at the C-terminal half. The RRM is responsible
for the binding of stem-loop I of U1 snRNA molecule.
Additionally, the most prominent immunodominant region
that can be recognized by auto-antibodies from
autoimmune patients may be located within the RRM. The
SR domains are involved in protein-protein interaction
with SR proteins that mediate 5' splice site
recognition. For instance, the first SR domain is
necessary and sufficient for ASF/SF2 Binding. The family
also includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but its
SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 60.7 bits (148), Expect = 8e-12
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV L+ + L+ F +G I R+VRD +T K +GYAF+ F + + + A
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63
Query: 158 NGQWLGSRSI-------RT--NWSTRK 175
+G+ + R + RT W R+
Sbjct: 64 DGKKIDGRRVLVDVERGRTVKGWLPRR 90
Score = 41.8 bits (99), Expect = 3e-05
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHH 56
TL+V L+ TE L F + GP+K +++R+ YAF+EF H
Sbjct: 3 TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHE 53
Score = 31.4 bits (72), Expect = 0.13
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKF 249
T++ D E + + F +G I IR+ K +GYAF++F
Sbjct: 3 TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEF 50
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic
RNA-binding protein RBM24, RBM38 and similar proteins.
This subfamily corresponds to the RRM of RBM24 and RBM38
from vertebrate, SUPpressor family member SUP-12 from
Caenorhabditis elegans and similar proteins. Both, RBM24
and RBM38, are preferentially expressed in cardiac and
skeletal muscle tissues. They regulate myogenic
differentiation by controlling the cell cycle in a
p21-dependent or -independent manner. RBM24, also termed
RNA-binding region-containing protein 6, interacts with
the 3'-untranslated region (UTR) of myogenin mRNA and
regulates its stability in C2C12 cells. RBM38, also
termed CLL-associated antigen KW-5, or HSRNASEB, or
RNA-binding region-containing protein 1(RNPC1), or
ssDNA-binding protein SEB4, is a direct target of the
p53 family. It is required for maintaining the stability
of the basal and stress-induced p21 mRNA by binding to
their 3'-UTRs. It also binds the AU-/U-rich elements in
p63 3'-UTR and regulates p63 mRNA stability and
activity. SUP-12 is a novel tissue-specific splicing
factor that controls muscle-specific splicing of the
ADF/cofilin pre-mRNA in C. elegans. All family members
contain a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 59.9 bits (146), Expect = 8e-12
Identities = 25/57 (43%), Positives = 33/57 (57%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
IFVG L +L++ F+ FGEI ++ D QT KS+GY FV+F K AE A
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59
Score = 45.3 bits (108), Expect = 1e-06
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIE 260
++ GG ++ + K FS FG I + V K +GY FV F KE+A A +
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 261 SIHNTDINGHTVKCFW 276
+ I+G
Sbjct: 61 DPNPI-IDGRKANVNL 75
Score = 40.7 bits (96), Expect = 7e-05
Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 4/77 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATALA 64
T ++VG L T++ L FSQ G ++ VI R+ G Y F+ F A A
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 65 AMNKRVFLEKEMKVNWA 81
N + ++ VN A
Sbjct: 61 DPNP-IIDGRKANVNLA 76
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to the
RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a TRBP-interacting
domain. RBM4 is a ubiquitously expressed splicing factor
with two isoforms, RBM4A (also known as Lark homolog)
and RBM4B (also known as RBM30), which are very similar
in structure and sequence. RBM4 may also function as a
translational regulator of stress-associated mRNAs as
well as play a role in micro-RNA-mediated gene
regulation. RBM4 contains two N-terminal RRMs, a
CCHC-type zinc finger, and three alanine-rich regions
within their C-terminal regions. This family also
includes Drosophila RNA-binding protein lark (Dlark), a
homolog of human RBM4. It plays an important role in
embryonic development and in the circadian regulation of
adult eclosion. Dlark shares high sequence similarity
with RBM4 at the N-terminal region. However, Dlark has
three proline-rich segments instead of three
alanine-rich segments within the C-terminal region. .
Length = 66
Score = 59.5 bits (145), Expect = 9e-12
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 9/69 (13%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L ++ L+ F +G ++ C +V++ Y FV ++ +AE+AI A+
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53
Query: 158 NG-QWLGSR 165
NG +++G R
Sbjct: 54 NGYEFMGKR 62
Score = 45.7 bits (109), Expect = 9e-07
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L+VGNL + T E L ALF + G V C V++ Y F+ A A+ A+N
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-----YGFVHMEEEEDAEDAIKALNGY 56
Query: 70 VFLEKEMKV 78
F+ K + V
Sbjct: 57 EFMGKRINV 65
Score = 39.5 bits (93), Expect = 1e-04
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+EEL +F +GT+ + V K Y FV +E A AI++++ + G +
Sbjct: 13 SEEL-RALFEKYGTVTECDVVKN--YGFVHMEEEEDAEDAIKALNGYEFMGKRIN 64
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 59.6 bits (145), Expect = 1e-11
Identities = 25/68 (36%), Positives = 37/68 (54%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L + L+E F FGEIS + D +T +SKG+AFVSF+ A A + +
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 158 NGQWLGSR 165
+G R
Sbjct: 62 DGSIFQGR 69
Score = 39.6 bits (93), Expect = 1e-04
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 220 EELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDING 269
EE + ++F FG I ++ + + KG+AFV F E A A + + G
Sbjct: 13 EEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQG 68
Score = 34.6 bits (80), Expect = 0.007
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI------REPGNDPYAFLEFVHHTVAATAL 63
L+V NL + TEE L LF G + + R G +AF+ F+ A A
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKG---FAFVSFMFPEHAVKAY 58
Query: 64 AAMNKRVF 71
+ ++ +F
Sbjct: 59 SELDGSIF 66
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to the
RRM1 of hnRNP A0 which is a low abundance hnRNP protein
that has been implicated in mRNA stability in mammalian
cells. It has been identified as the substrate for
MAPKAP-K2 and may be involved in the lipopolysaccharide
(LPS)-induced post-transcriptional regulation of tumor
necrosis factor-alpha (TNF-alpha), cyclooxygenase 2
(COX-2) and macrophage inflammatory protein 2 (MIP-2).
hnRNP A0 contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 79
Score = 59.8 bits (145), Expect = 1e-11
Identities = 19/60 (31%), Positives = 36/60 (60%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG L+ + L+ F +G+++ C ++ DP T +S+G+ F++F EA+ A+ A
Sbjct: 5 LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ 64
Score = 30.9 bits (70), Expect = 0.19
Identities = 14/73 (19%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIE 260
C ++ GG ++ + + F+ +G + + V + +G+ F+ F++ + A A+E
Sbjct: 3 CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62
Query: 261 SIHNTDINGHTVK 273
I+G+ ++
Sbjct: 63 -AQPHSIDGNQIE 74
Score = 29.4 bits (66), Expect = 0.72
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEFVHHTVAATALAAM 66
L+VG L++ ++ L F++ G + C V+ +P + + F+ F A A+ A
Sbjct: 5 LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ 64
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 59.7 bits (144), Expect = 2e-11
Identities = 27/78 (34%), Positives = 46/78 (58%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IF+ +L + + L + F PFG ++N +++RD T K KG+ FV+ EA AI ++
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 158 NGQWLGSRSIRTNWSTRK 175
NG LG + ++ ++ T K
Sbjct: 64 NGYRLGDKILQVSFKTSK 81
Score = 40.4 bits (94), Expect = 9e-05
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 6/61 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ G+D +E ++ ++F PFG + +++V ++ KG+ FV T E A AI S+
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 263 H 263
+
Sbjct: 64 N 64
Score = 32.0 bits (72), Expect = 0.091
Identities = 20/81 (24%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
+++ NL E +L +F G V KVIR+ + + F+ ++ AA A+A++
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 67 NKRVFLEKEMKVNWASSPGNQ 87
N +K ++V++ +S ++
Sbjct: 64 NGYRLGDKILQVSFKTSKSHK 84
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 59.2 bits (144), Expect = 2e-11
Identities = 25/72 (34%), Positives = 41/72 (56%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
I+V + P++ +K F FG+I +C + DP+T K KGY F+ + A++AI +
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61
Query: 157 MNGQWLGSRSIR 168
MN LG + +R
Sbjct: 62 MNLFDLGGQQLR 73
Score = 43.4 bits (103), Expect = 7e-06
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIV------DIRVFKEKGYAFVKFTTKETATHAIESI 262
+Y DL+E+ + VF FG I D K KGY F+++ ++A AI S+
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62
Query: 263 HNTDING 269
+ D+ G
Sbjct: 63 NLFDLGG 69
Score = 42.3 bits (100), Expect = 2e-05
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIR--EPGNDP-YAFLEFVHHTVAATALAAM 66
+YV ++ ++E+ + ++F G +K C + E G Y F+E+ + A A+A+M
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62
Query: 67 N 67
N
Sbjct: 63 N 63
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 59.4 bits (144), Expect = 2e-11
Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG LS + ++ FAPFG I C ++RD Q +S+G AFV+F + A NAI AM
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQCALNAIKAM 62
Query: 158 NGQ 160
+
Sbjct: 63 HHS 65
Score = 49.8 bits (119), Expect = 4e-08
Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIH 263
++ G K NE V +F+PFG+I + V ++ +G AFV F +++ A +AI+++H
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63
Query: 264 NTDI 267
++
Sbjct: 64 HSQT 67
Score = 30.6 bits (69), Expect = 0.29
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPY--AFLEFVHHTVAATALAAMN 67
L+VG L E + +F+ G ++ C V+R+ AF+ F A A+ AM+
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63
Query: 68 KRVFLE 73
+E
Sbjct: 64 HSQTME 69
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, being highly expressed
throughout the brain and in glandular tissues,
moderately expressed in heart, skeletal muscle, and
liver, is also known as bruno-like protein 4 (BRUNOL-4),
or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4
also contain three highly conserved RRMs. The splicing
activation or repression activity of CELF-4 on some
specific substrates is mediated by its RRM1/RRM2. On the
other hand, both RRM1 and RRM2 of CELF-4 can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
being strongly expressed in kidney, brain, and testis,
is also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in a muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element, MSE2.
CELF-6 also promotes skipping of exon 11 of insulin
receptor, a known target of CELF activity that is
expressed in kidney. In addition to three highly
conserved RRMs, CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 58.6 bits (142), Expect = 3e-11
Identities = 28/62 (45%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG LS + ++ F PFG I C I+R P SKG AFV F AEA+ AI A+
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDG-NSKGCAFVKFSSHAEAQAAINAL 62
Query: 158 NG 159
+G
Sbjct: 63 HG 64
Score = 46.7 bits (111), Expect = 6e-07
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 210 YCGGFGKDLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTKETATHAIESIH 263
+ G K E+ V ++F PFGTI + + + KG AFVKF++ A AI ++H
Sbjct: 5 FVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63
Score = 36.6 bits (85), Expect = 0.002
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP-GNDP-YAFLEFVHHTVAATALAAMN 67
L+VG L TE+ + LF G ++ C ++R P GN AF++F H A A+ A++
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 58.6 bits (142), Expect = 3e-11
Identities = 24/72 (33%), Positives = 38/72 (52%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
TVY G + + +F FG I++ R ++G+AFVK T E A AI + +
Sbjct: 2 TVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPV 61
Query: 268 NGHTVKCFWGKE 279
+G ++C WGK+
Sbjct: 62 HGRPLRCGWGKD 73
Score = 44.0 bits (104), Expect = 4e-06
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG++ P L F FG I R D +G+AFV +A AI +
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56
Query: 158 NGQWLGSRSIRTNW 171
G + R +R W
Sbjct: 57 QGFPVHGRPLRCGW 70
Score = 34.8 bits (80), Expect = 0.007
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TT+YVGN+ T+ L LF G + R + +AF++ H AA A+ +
Sbjct: 1 TTVYVGNIPPYTTQADLIPLFQNFGYILE---FRHQPDRGFAFVKLDTHEQAAMAIVQLQ 57
Query: 68 KRVFLEKEMKVNW 80
+ ++ W
Sbjct: 58 GFPVHGRPLRCGW 70
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes. Since
the Hu proteins share high homology with the Drosophila
embryonic lethal abnormal vision (ELAV) protein, the Hu
family is sometimes referred to as the ELAV family.
Drosophila ELAV is exclusively expressed in neurons and
is required for the correct differentiation and survival
of neurons in flies. The neuronal members of the Hu
family include Hu-antigen B (HuB or ELAV-2 or Hel-N1),
Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D
(HuD or ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Moreover, HuR has an anti-apoptotic
function during early cell stress response. It binds to
mRNAs and enhances the expression of several
anti-apoptotic proteins, such as p21waf1, p53, and
prothymosin alpha. HuR also has pro-apoptotic function
by promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 79
Score = 58.5 bits (142), Expect = 3e-11
Identities = 25/63 (39%), Positives = 36/63 (57%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V L + Q L+ F+P+G I RI+ D T S+G F+ F K+ EAE AI A+
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 158 NGQ 160
NG
Sbjct: 63 NGT 65
Score = 44.6 bits (106), Expect = 3e-06
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
+Y G K + ++ + +FSP+G I+ R+ + +G F++F + A AI+++
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 263 HNTDINGHTVK 273
+ T G T
Sbjct: 63 NGTIPPGATEP 73
Score = 30.3 bits (69), Expect = 0.32
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
LYV L ++T++ L ALFS G + +++ + F+ F A A+ A+
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 67 NKRV 70
N +
Sbjct: 63 NGTI 66
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 58.3 bits (142), Expect = 3e-11
Identities = 20/65 (30%), Positives = 34/65 (52%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ VG L+ + LKE F+ +G + + + D + +GYA+V F +AE AI M
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 158 NGQWL 162
+G +
Sbjct: 61 DGGQI 65
Score = 42.9 bits (102), Expect = 9e-06
Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 6/64 (9%)
Query: 216 KDLNEELVSKVFSPFGTIVDI------RVFKEKGYAFVKFTTKETATHAIESIHNTDING 269
+++N++ + ++FS +GT+ D+ V +GYA+V+F + E A AI+ + I+G
Sbjct: 8 RNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDG 67
Query: 270 HTVK 273
V
Sbjct: 68 QEVT 71
Score = 40.2 bits (95), Expect = 8e-05
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPG-NDPYAFLEFVHHTVAATALAAM 66
L+VG L +V ++ L +FS G VK + RE YA++EF A A+ M
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 67 N 67
+
Sbjct: 61 D 61
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 57.9 bits (141), Expect = 3e-11
Identities = 19/55 (34%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 223 VSKVFSPFGTIVDIRVFKEK-GYAFVKFTTKETATHAIESIHNTDINGHTVKCFW 276
+ K+FSPFG + I++ K+K G+AFV+F+T+E A A++ ++ G ++ +
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
Score = 56.0 bits (136), Expect = 1e-10
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
L + F+PFG + ++++ K G+AFV F + AE A+ +NG G R +R ++
Sbjct: 1 LYKLFSPFGNVEKIKLLK-----KKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
Query: 172 S 172
S
Sbjct: 56 S 56
Score = 47.5 bits (114), Expect = 1e-07
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 24 LCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKRVFLEKEMKVNWA 81
L LFS G V+ K++++ +AF+EF A A+ +N +F + ++V+++
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPG--FAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 58.4 bits (142), Expect = 3e-11
Identities = 21/78 (26%), Positives = 41/78 (52%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L + + L+E F+ G I C +V+D + K +G+ +V+F + +A+ A+
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 158 NGQWLGSRSIRTNWSTRK 175
G R I ++ +K
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
Score = 50.3 bits (121), Expect = 2e-08
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAA 65
TL+V NL T+E L FS++GP+K C V+++ G+ + ++ F A AL
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60
Query: 66 MNKRVFLEKEMKVNWA 81
K F +++ V +A
Sbjct: 61 KKKTKFGGRKIHVEFA 76
Score = 39.5 bits (93), Expect = 2e-04
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIES 261
T++ D +E + + FS G I V K+K G+ +V F +E A A+E
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60
Query: 262 IHNTDINGHTVK 273
T G +
Sbjct: 61 KKKTKFGGRKIH 72
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 58.0 bits (141), Expect = 4e-11
Identities = 29/73 (39%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
+YVGNLD VTEELL LF Q GPV + ++ Y F+EF+ A A+ M
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 67 NKRVFLEKEMKVN 79
N K ++VN
Sbjct: 61 NMIKLYGKPIRVN 73
Score = 52.6 bits (127), Expect = 4e-09
Identities = 25/73 (34%), Positives = 39/73 (53%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L ++ + L E F G + N I +D T +GY FV F+ + +A+ AI M
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 158 NGQWLGSRSIRTN 170
N L + IR N
Sbjct: 61 NMIKLYGKPIRVN 73
Score = 42.2 bits (100), Expect = 2e-05
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 6/72 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
VY G + + EEL+ ++F G +V++ + K++ GY FV+F ++E A +AI+ +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 263 HNTDINGHTVKC 274
+ + G ++
Sbjct: 61 NMIKLYGKPIRV 72
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 58.0 bits (141), Expect = 4e-11
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++VG+L P + L++ F +G + + + R+P G+AFV F +AE+A+ A
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRA 55
Query: 157 MNGQWLGSRSIRTNWSTR 174
++G+ + +R S
Sbjct: 56 LDGRRICGNRVRVELSRG 73
Score = 43.4 bits (103), Expect = 5e-06
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVHHTVAATALAAMNK 68
+YVGNL T+ L F + GP++ V R P P +AF+EF A A+ A++
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP---PGFAFVEFEDPRDAEDAVRALDG 58
Query: 69 RVFLEKEMKV 78
R ++V
Sbjct: 59 RRICGNRVRV 68
Score = 42.6 bits (101), Expect = 1e-05
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRV-FKEKGYAFVKFTTKETATHAIESIHNTDI 267
VY G G + + F +G + + V G+AFV+F A A+ ++ I
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRRI 61
Query: 268 NGHTVK 273
G+ V+
Sbjct: 62 CGNRVR 67
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 77
Score = 56.9 bits (137), Expect = 1e-10
Identities = 26/73 (35%), Positives = 40/73 (54%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
+ +L P Q +E PFG + C +V T SKGY FV ++KK A A + + G
Sbjct: 4 IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63
Query: 160 QWLGSRSIRTNWS 172
+ LGSR++ +W+
Sbjct: 64 KQLGSRTLYVHWT 76
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 56.9 bits (138), Expect = 1e-10
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIV---RDPQTLKSKGYAFVSFVKKAEAENAI 154
+++G+L + L + F+ +G+I + P + +GY FV+F K EAE A+
Sbjct: 2 LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61
Query: 155 TAMNGQWLGSRSIRTNW 171
++NG+ + + W
Sbjct: 62 KSLNGKTALGKKLVVRW 78
Score = 56.1 bits (136), Expect = 3e-10
Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGC-----KVIREPGND-PYAFLEFVHHTVAATA 62
L++GNLD +TE L LFS+ G +K K G Y F+ F A A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 63 LAAMNKRVFLEKEMKVNWAS 82
L ++N + L K++ V WA
Sbjct: 61 LKSLNGKTALGKKLVVRWAH 80
Score = 46.1 bits (110), Expect = 7e-07
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 9/65 (13%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDI-----RVFKEKG----YAFVKFTTKETATHA 258
++ G L E + K+FS +G I + KG Y FV F TKE A A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 259 IESIH 263
++S++
Sbjct: 61 LKSLN 65
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is
a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 75
Score = 56.7 bits (137), Expect = 1e-10
Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+F+G LS + + L+E F+ FGEI C ++RDP T +S+G+ FV+F A +
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVD 54
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 56.7 bits (136), Expect = 2e-10
Identities = 26/76 (34%), Positives = 46/76 (60%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L + + LK F GEI +C++VRD T +S GY FV+++ +AE AI
Sbjct: 6 NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65
Query: 157 MNGQWLGSRSIRTNWS 172
+NG L +++I+ +++
Sbjct: 66 LNGLRLQTKTIKVSYA 81
Score = 40.5 bits (94), Expect = 9e-05
Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAA 60
E T L V L ++T+E L +LF IG ++ CK++R+ Y F+ ++ A
Sbjct: 1 EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60
Query: 61 TALAAMNKRVFLEKEMKVNWA 81
A+ +N K +KV++A
Sbjct: 61 KAINTLNGLRLQTKTIKVSYA 81
Score = 27.4 bits (60), Expect = 3.8
Identities = 14/69 (20%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+++ +E + +F G I ++ ++K GY FV + + A AI +++ +
Sbjct: 14 QNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT 73
Query: 270 HTVKCFWGK 278
T+K + +
Sbjct: 74 KTIKVSYAR 82
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 77
Score = 56.5 bits (137), Expect = 2e-10
Identities = 23/70 (32%), Positives = 37/70 (52%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IF+G L + +KE FG++ +V+D T SKGYAF ++ + + AI +
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62
Query: 158 NGQWLGSRSI 167
NG LG + +
Sbjct: 63 NGMQLGDKKL 72
Score = 37.2 bits (87), Expect = 0.001
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIESI 262
++ GG L+E+ V ++ FG + D KGYAF ++ AI +
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62
Query: 263 HNTDINGHTVKC 274
+ + +
Sbjct: 63 NGMQLGDKKLTV 74
Score = 31.8 bits (73), Expect = 0.093
Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
+++G L ++E+ + L G +K ++++ YAF E++ +V A+A +
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62
Query: 67 NKRVFLEKEMKV 78
N +K++ V
Sbjct: 63 NGMQLGDKKLTV 74
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. This family also includes the sex-lethal
protein (SXL) from Drosophila melanogaster. SXL governs
sexual differentiation and X chromosome dosage
compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own pre-mRNA
and promotes female-specific alternative splicing. It
contains an N-terminal Gly/Asn-rich domain that may be
responsible for the protein-protein interaction, and
tandem RRMs that show high preference to bind
single-stranded, uridine-rich target RNA transcripts. .
Length = 77
Score = 55.8 bits (135), Expect = 3e-10
Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIR 168
L+ F G I +C+IVRD T +S GY FV +V + +A+ AI +NG + ++ ++
Sbjct: 17 LRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLK 73
Score = 50.4 bits (121), Expect = 2e-08
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIR--EPGND-PYAFLEFVHHTVAATALA 64
T L V L +T+E L +LF IGP++ CK++R G Y F+++V A A+
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60
Query: 65 AMNKRVFLEKEMKVNWA 81
+N K +KV++A
Sbjct: 61 TLNGFEIRNKRLKVSYA 77
Score = 33.9 bits (78), Expect = 0.015
Identities = 14/63 (22%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDINGH 270
D+ +E + +F G I ++ +++ GY FV + + A AI +++ +I
Sbjct: 11 DMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNK 70
Query: 271 TVK 273
+K
Sbjct: 71 RLK 73
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type
and RNA-binding motif-containing protein 1 (ZCRB1) and
similar proteins. This subfamily corresponds to the RRM
of ZCRB1, also termed MADP-1, or U11/U12 small nuclear
ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or
U11/U12-31K), a novel multi-functional nuclear factor,
which may be involved in morphine dependence, cold/heat
stress, and hepatocarcinoma. It is located in the
nucleoplasm, but outside the nucleolus. ZCRB1 is one of
the components of U11/U12 snRNPs that bind to U12-type
pre-mRNAs and form a di-snRNP complex, simultaneously
recognizing the 5' splice site and branchpoint sequence.
ZCRB1 is characterized by an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 55.4 bits (134), Expect = 3e-10
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIE 260
TVY L + K+FS +G +V + + K+K G AF+ F +E A ++
Sbjct: 2 STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61
Query: 261 SIHNTDINGHTVKC 274
+++N ++ G T+KC
Sbjct: 62 ALNNKELFGRTLKC 75
Score = 54.2 bits (131), Expect = 1e-09
Identities = 18/53 (33%), Positives = 34/53 (64%)
Query: 116 FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIR 168
F+ +G++ IV+D +T KSKG AF+ F+ + +A + A+N + L R+++
Sbjct: 22 FSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLK 74
Score = 34.6 bits (80), Expect = 0.010
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
+T+YV NL S+T L +FS+ G V ++++ AF+ F+ A +
Sbjct: 2 STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61
Query: 65 AMNKRVFLEKEMKVNWA 81
A+N + + +K + A
Sbjct: 62 ALNNKELFGRTLKCSIA 78
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 55.7 bits (135), Expect = 3e-10
Identities = 20/84 (23%), Positives = 50/84 (59%), Gaps = 6/84 (7%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIV---RDPQTLKSKGYAFVSFVKKA 148
T+N ++VG+L+P++ + L + F FG +++ +I+ + + +++ FV+F+ +A
Sbjct: 1 TTN---LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRA 57
Query: 149 EAENAITAMNGQWLGSRSIRTNWS 172
+AE A+ ++G+ + ++ W
Sbjct: 58 DAERALDELDGKDVMGYELKLGWG 81
Score = 55.3 bits (134), Expect = 5e-10
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 10/84 (11%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--------REPGNDPYAFLEFVHHTVA 59
T LYVGNL+ VTEE+LC F + GP+ K++ R N F+ F++ A
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRN--CGFVAFMNRADA 59
Query: 60 ATALAAMNKRVFLEKEMKVNWASS 83
AL ++ + + E+K+ W +
Sbjct: 60 ERALDELDGKDVMGYELKLGWGKA 83
Score = 37.2 bits (87), Expect = 0.001
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV---------FKEKGYAFVKFTTKETA 255
TN +Y G + EE++ + F FG + +++ + + FV F + A
Sbjct: 2 TN--LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADA 59
Query: 256 THAIESIHNTDINGHTVKCFWGK 278
A++ + D+ G+ +K WGK
Sbjct: 60 ERALDELDGKDVMGYELKLGWGK 82
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM2 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed
BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-1 is strongly expressed in all adult
and fetal tissues tested. Human CELF-1 is a nuclear and
cytoplasmic RNA-binding protein that regulates multiple
aspects of nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic dystrophy
protein kinase) gene; it preferentially targets UGU-rich
mRNA elements. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
binds specifically to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contains three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it preferentially binds
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contains three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are also
important for localization in the cytoplasm. The
splicing activation or repression activity of CELF-2 on
some specific substrates is mediated by RRM1/RRM2. Both,
RRM1 and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 55.4 bits (133), Expect = 5e-10
Identities = 26/61 (42%), Positives = 40/61 (65%), Gaps = 1/61 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G +S + ++ F+PFG+I CRI+R P L S+G AFV+F +A A+ AI AM
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGL-SRGCAFVTFTTRAMAQTAIKAM 62
Query: 158 N 158
+
Sbjct: 63 H 63
Score = 42.4 bits (99), Expect = 2e-05
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTKETATHAIESIH 263
++ G K NE + +FSPFG I + R+ + +G AFV FTT+ A AI+++H
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63
Query: 264 NT 265
Sbjct: 64 QA 65
Score = 35.4 bits (81), Expect = 0.005
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG--NDPYAFLEFVHHTVAATALAAMN 67
L++G + E + +FS G ++ C+++R P + AF+ F +A TA+ AM+
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63
Query: 68 KRVFLE 73
+ +E
Sbjct: 64 QAQTME 69
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 55.2 bits (133), Expect = 5e-10
Identities = 22/78 (28%), Positives = 44/78 (56%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L+ + + L + F+ I + +V DP+T +S+GY FV+F +A+ A+ +
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 158 NGQWLGSRSIRTNWSTRK 175
+ L R +R + + R+
Sbjct: 62 KNKKLHGRILRLDIAERR 79
Score = 53.7 bits (129), Expect = 1e-09
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAA 65
TL+V NL SVT+E L FS + P+K V+ +P Y F+ F A ALA
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60
Query: 66 MNKRVFLEKEMKVNWA 81
+ + + ++++ A
Sbjct: 61 LKNKKLHGRILRLDIA 76
Score = 32.1 bits (73), Expect = 0.077
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGH 270
+ +E ++ FS I V + +GY FV F E A A+ + N ++G
Sbjct: 10 SVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGR 69
Query: 271 TVKCFWGK 278
++ +
Sbjct: 70 ILRLDIAE 77
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 55.0 bits (133), Expect = 5e-10
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVHHTVAATALAA 65
+++VG L VT+E L FS+ G + +I+ + +AF++F AA A+ +
Sbjct: 3 KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62
Query: 66 MNKRVFLEKEMKV 78
N + K M V
Sbjct: 63 ENHSMLKNKTMHV 75
Score = 53.1 bits (128), Expect = 3e-09
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
Y IFVG LSP++ + L E F+ G+I +++ + +AF+ F ++ A A+
Sbjct: 4 YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVE 61
Query: 156 AMNGQWLGSRSIR 168
+ N L ++++
Sbjct: 62 SENHSMLKNKTMH 74
Score = 42.7 bits (101), Expect = 1e-05
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATHAIES 261
+++ G D+ +E +++ FS G I+++ + K +AF+KF ++ A A+ES
Sbjct: 5 SIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 77
Score = 54.6 bits (132), Expect = 7e-10
Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+LS E L+E F GE+ + RI +D +SKG+ V F + A+ A
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDG-RSKGFGHVEFATEEGAQKA-LEK 59
Query: 158 NGQWLGSRSIR 168
+G+ L R IR
Sbjct: 60 SGEELLGREIR 70
Score = 40.8 bits (96), Expect = 6e-05
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-----KEKGYAFVKFTTKETATHAIESI 262
T++ G ++ + + F G +VD+R+ + KG+ V+F T+E A A+E
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE-K 59
Query: 263 HNTDINGHTVKC 274
++ G ++
Sbjct: 60 SGEELLGREIRV 71
Score = 31.1 bits (71), Expect = 0.15
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 3/77 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAM 66
TL+VGNL S ++ L F + G V ++ ++ + +EF A AL
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EK 59
Query: 67 NKRVFLEKEMKVNWASS 83
+ L +E++V+ A+
Sbjct: 60 SGEELLGREIRVDLATE 76
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 54.5 bits (131), Expect = 7e-10
Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG++S + L+ F FG + C V K YAFV ++ EA AI A+
Sbjct: 3 IFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIEAL 54
Query: 158 NGQWLGSRSI 167
NG+ + R I
Sbjct: 55 NGKEVKGRRI 64
Score = 42.2 bits (99), Expect = 1e-05
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
++VGN+ + T + L LF + G V C +++ YAF+ A A+ A+N
Sbjct: 1 WKIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-----YAFVHMEREEEALAAIEALN 55
Query: 68 KRVFLEKEMKV 78
+ + + V
Sbjct: 56 GKEVKGRRINV 66
Score = 38.3 bits (89), Expect = 4e-04
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 225 KVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDING 269
+F FG +V+ K YAFV +E A AIE+++ ++ G
Sbjct: 19 GLFEEFGRVVECDKVK--DYAFVHMEREEEALAAIEALNGKEVKG 61
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM1 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1). Musashi-1 has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover, it
represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 77
Score = 54.6 bits (131), Expect = 8e-10
Identities = 25/70 (35%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS + + L+E F FGE+ C ++RDP T +S+G+ FV+F+ +A + + A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK-VLAQ 61
Query: 158 NGQWLGSRSI 167
+ L S++I
Sbjct: 62 SRHELDSKTI 71
Score = 30.7 bits (69), Expect = 0.22
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP---GNDPYAFLEFVHHTVAATALA 64
+++G L T+E L F Q G VK C V+R+P + + F+ F+ LA
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. This
subfamily also includes some p54nrb/PSF/PSP1 homologs
from invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 54.2 bits (131), Expect = 9e-10
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L +I + KE F+ +GE+S + ++ KG+ F+ + AE A +
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAEL 57
Query: 158 NGQWLGSRSIR 168
+G R +R
Sbjct: 58 DGIMRKGRQLR 68
Score = 52.3 bits (126), Expect = 4e-09
Identities = 17/67 (25%), Positives = 34/67 (50%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
C ++ G D+ EE ++FS +G + ++ + KEKG+ F++ T+ A A +
Sbjct: 2 CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIM 61
Query: 267 INGHTVK 273
G ++
Sbjct: 62 RKGRQLR 68
Score = 36.9 bits (86), Expect = 0.001
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L+VGNL +TEE LFS+ G V + +E G + F+ T A A A ++
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKG---FGFIRLDTRTNAEKAKAELDGI 60
Query: 70 VFLEKEMKV 78
+ ++++V
Sbjct: 61 MRKGRQLRV 69
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation
factor (ACF). hnRNP R is a ubiquitously expressed
nuclear RNA-binding protein that specifically bind
mRNAs with a preference for poly(U) stretches and has
been implicated in mRNA processing and mRNA transport,
and also acts as a regulator to modify binding to
ribosomes and RNA translation. hnRNP Q is also a
ubiquitously expressed nuclear RNA-binding protein. It
has been identified as a component of the spliceosome
complex, as well as a component of the apobec-1
editosome, and has been implicated in the regulation of
specific mRNA transport. ACF is an RNA-binding subunit
of a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. This
family also includes two functionally unknown
RNA-binding proteins, RBM46 and RBM47. All members
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains).
Length = 72
Score = 53.8 bits (130), Expect = 1e-09
Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
LYV NL +S TEE L LFS+ G V+ K I++ YAF+ F A A+ MN +
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-----YAFVHFEERDDAVKAMEEMNGK 58
Query: 70 VFLEKEMKVNWA 81
++V+ A
Sbjct: 59 ELEGSPIEVSLA 70
Score = 50.3 bits (121), Expect = 2e-08
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 10/79 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V +L + L+E F+ +GE+ + ++D YAFV F ++ +A A+ M
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55
Query: 158 NGQWLGSRSIRTNWSTRKP 176
NG+ L I + + KP
Sbjct: 56 NGKELEGSPIEVSLA--KP 72
Score = 48.8 bits (117), Expect = 9e-08
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 220 EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGK 278
EE + ++FS +G + RV K K YAFV F ++ A A+E ++ ++ G ++ K
Sbjct: 15 EEQLRELFSEYGEVE--RVKKIKDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAK 71
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 54.2 bits (131), Expect = 1e-09
Identities = 25/71 (35%), Positives = 42/71 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I++G L E+ + F+ +GEI + +VRD +T KSKG+AF+++ + A+ +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71
Query: 158 NGQWLGSRSIR 168
NG L R+IR
Sbjct: 72 NGIKLLGRTIR 82
Score = 43.0 bits (102), Expect = 1e-05
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
+Y GG +L E + VFS +G IVDI + K KG+AF+ + + + A++++
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71
Query: 263 HNTDINGHTVK 273
+ + G T++
Sbjct: 72 NGIKLLGRTIR 82
Score = 30.7 bits (70), Expect = 0.31
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEF 53
+Y+G L +TE + +FSQ G + ++R+ +AFL +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAY 58
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 53.7 bits (130), Expect = 1e-09
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF-VKKAEAENAITA 156
+FVG LSP + L+E F+ FG +S+ I++ +G+A++ +A+ + +
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61
Query: 157 MNG-QWLGSR 165
+NG +W GS
Sbjct: 62 LNGTKWKGSV 71
Score = 37.5 bits (88), Expect = 7e-04
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK------EKGYAFVKFTTKETATH-AIES 261
++ GG + E + + FS FGT+ D+ + K ++G+A++ T E +
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61
Query: 262 IHNTDINGHTVKC 274
++ T G +K
Sbjct: 62 LNGTKWKGSVLKI 74
Score = 37.2 bits (87), Expect = 0.001
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEF 53
L+VG L SVTE L FS+ G V ++I++ P +A+++
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDL 48
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM2 of the sex-lethal protein (SXL) which
governs sexual differentiation and X chromosome dosage
compensation in Drosophila melanogaster. It induces
female-specific alternative splicing of the transformer
(tra) pre-mRNA by binding to the tra uridine-rich
polypyrimidine tract at the non-sex-specific 3' splice
site during the sex-determination process. SXL binds
also to its own pre-mRNA and promotes female-specific
alternative splicing. SXL contains an N-terminal
Gly/Asn-rich domain that may be responsible for the
protein-protein interaction, and tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), that show high
preference to bind single-stranded, uridine-rich target
RNA transcripts. .
Length = 79
Score = 53.7 bits (129), Expect = 2e-09
Identities = 21/63 (33%), Positives = 39/63 (61%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++V +L ++ L++ F +G I C ++RD T +G AFV + K+ EA+ AI++
Sbjct: 2 NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61
Query: 157 MNG 159
+NG
Sbjct: 62 LNG 64
Score = 43.7 bits (103), Expect = 5e-06
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
+Y + L E+ + K+F +G IV + ++K G AFV++ +E A AI S+
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 263 HNTDINGHT 271
+ T G T
Sbjct: 63 NGTIPPGST 71
Score = 28.7 bits (64), Expect = 1.3
Identities = 18/59 (30%), Positives = 28/59 (47%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
T LYV NL +TE+ L +F G + C ++R+ + FV + A AA+
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAI 59
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM1 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells, as well as the
neurite elongation and morphological differentiation.
HuD specifically binds poly(A) RNA. Like other Hu
proteins, HuD contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 83
Score = 53.6 bits (128), Expect = 2e-09
Identities = 24/76 (31%), Positives = 45/76 (59%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L + + + F GEI +C++VRD T +S GY FV+++ +AE AI
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 157 MNGQWLGSRSIRTNWS 172
+NG L +++I+ +++
Sbjct: 64 LNGLRLQTKTIKVSYA 79
Score = 35.5 bits (81), Expect = 0.006
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
T L V L ++T+E +LF IG ++ CK++R+ Y F+ ++ A A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 65 AMNKRVFLEKEMKVNWA 81
+N K +KV++A
Sbjct: 63 TLNGLRLQTKTIKVSYA 79
Score = 27.8 bits (61), Expect = 2.8
Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+++ +E +F G I ++ ++K GY FV + + A AI +++ +
Sbjct: 12 QNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT 71
Query: 270 HTVKCFWGKES 280
T+K + + S
Sbjct: 72 KTIKVSYARPS 82
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 53.5 bits (128), Expect = 2e-09
Identities = 20/59 (33%), Positives = 38/59 (64%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G LS E ++L+ F +G +++C ++RDP T +S+G+ FV++ E + A+ A
Sbjct: 5 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63
Score = 36.6 bits (84), Expect = 0.002
Identities = 21/64 (32%), Positives = 30/64 (46%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAA 65
Q L++G L T+E L + F Q G + C V+R+P FV ++ AA
Sbjct: 1 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60
Query: 66 MNKR 69
MN R
Sbjct: 61 MNAR 64
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 53.2 bits (127), Expect = 2e-09
Identities = 22/59 (37%), Positives = 40/59 (67%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G LS E +L+E F +G +++C ++RDPQT +S+G+ FV++ E + A++A
Sbjct: 5 LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63
Score = 29.7 bits (66), Expect = 0.50
Identities = 18/64 (28%), Positives = 29/64 (45%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAA 65
Q L++G L T++ L F + G + C V+R+P FV ++ AA
Sbjct: 1 QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60
Query: 66 MNKR 69
M+ R
Sbjct: 61 MSAR 64
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 2 (Musashi-2 ) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 76
Score = 52.8 bits (126), Expect = 3e-09
Identities = 21/57 (36%), Positives = 36/57 (63%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+F+G LS + +L++ F+ FGEI C ++RDP T +S+G+ FV+F A + +
Sbjct: 2 MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 75
Score = 52.7 bits (126), Expect = 3e-09
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG LS + + LK+ F FGE+++C I DP T +S+G+ F+ F K A + +
Sbjct: 2 MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILF-KDASSVEKVLEQ 60
Query: 158 NGQWLGSRSI 167
L R I
Sbjct: 61 KEHRLDGRLI 70
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the RRM
of SLIRP, a widely expressed small steroid receptor RNA
activator (SRA) binding protein, which binds to STR7, a
functional substructure of SRA. SLIRP is localized
predominantly to the mitochondria and plays a key role
in modulating several nuclear receptor (NR) pathways. It
functions as a co-repressor to repress SRA-mediated
nuclear receptor coactivation. It modulates SHARP- and
SKIP-mediated co-regulation of NR activity. SLIRP
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is required for SLIRP's corepression activities. .
Length = 73
Score = 52.7 bits (127), Expect = 4e-09
Identities = 24/56 (42%), Positives = 36/56 (64%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
+FVG+L + ++ LKE F+ FG++ +C + D +T SKGY FVSF + ENA
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENA 57
Score = 28.4 bits (64), Expect = 1.3
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPG-NDPYAFLEF 53
L+VGNL +V + L FSQ G VK C V +E G + Y F+ F
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSF 48
Score = 27.3 bits (61), Expect = 3.2
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 10/46 (21%)
Query: 227 FSPFGTIVDIRV-F-KE----KGYAFVKFTTKETATHAIESIHNTD 266
FS FG + V F KE KGY FV F++++ +E+
Sbjct: 20 FSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD----GLENALQKQ 61
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM2 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 52.7 bits (126), Expect = 5e-09
Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++++ L + + +++ F+ FG I N R++ D T S+G AF+ F K++EAE AIT+
Sbjct: 2 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61
Query: 157 MNGQ 160
NG
Sbjct: 62 FNGH 65
Score = 38.1 bits (88), Expect = 6e-04
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 11/68 (16%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
+Y G + + ++ V +FS FG I++ RV + +G AF++F + A AI
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAI--- 59
Query: 263 HNTDINGH 270
T NGH
Sbjct: 60 --TSFNGH 65
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 52.4 bits (126), Expect = 5e-09
Identities = 21/70 (30%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG L P++ + KE F+ FG++ + ++++D T +S+G+ FV+F ++ E + +
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVE-RVFSA 60
Query: 158 NGQWLGSRSI 167
LG + +
Sbjct: 61 GMLELGGKQV 70
Score = 35.0 bits (81), Expect = 0.006
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG D+ EE + FS FG +VD ++ ++ G+ FV F + E+A + S
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60
Query: 263 HNTDINGHTV 272
++ G V
Sbjct: 61 GMLELGGKQV 70
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 52.0 bits (125), Expect = 6e-09
Identities = 17/61 (27%), Positives = 28/61 (45%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V L + LK F+ +G + + R T KG+AF+ F EA+ A +
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 158 N 158
N
Sbjct: 62 N 62
Score = 42.0 bits (99), Expect = 2e-05
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETATHAIES 261
TVY K+ E + VFS +GT+V + + KG+AF++F T E A A +
Sbjct: 1 TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60
Query: 262 IHNTD 266
++N
Sbjct: 61 LNNPP 65
Score = 30.0 bits (68), Expect = 0.38
Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP-GNDP--YAFLEFVHHTVAATALAA 65
T+YV L + T E L A+FS+ G V + R D +AF+EF A A
Sbjct: 1 TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60
Query: 66 MNKRVFLEKEMKVNWAS 82
+N E +
Sbjct: 61 LN----NPPETATDKPG 73
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 52.3 bits (125), Expect = 7e-09
Identities = 31/91 (34%), Positives = 48/91 (52%), Gaps = 2/91 (2%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
GN+ D + +F LS + L+E F+ +G I++ IV D Q+ +S+G+AFV F
Sbjct: 1 GNRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
+A+ A NG L R IR ++S K
Sbjct: 59 ENVDDAKEAKERANGMELDGRRIRVDFSITK 89
Score = 37.3 bits (86), Expect = 0.001
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 200 NQSSPT-NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTK 252
N+++P NC + G E + +VFS +G I D+ + + +G+AFV F
Sbjct: 2 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 61
Query: 253 ETATHAIESIHNTDINGHTVK 273
+ A A E + +++G ++
Sbjct: 62 DDAKEAKERANGMELDGRRIR 82
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM2 of polypyrimidine tract-binding protein 1 (PTB or
hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2
or nPTB), regulator of differentiation 1 (Rod1),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), polypyrimidine tract-binding protein homolog
3 (PTBPH3), polypyrimidine tract-binding protein homolog
1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and
RRM3 of PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. Rod1 is a mammalian polypyrimidine tract
binding protein (PTB) homolog of a regulator of
differentiation in the fission yeast Schizosaccharomyces
pombe, where the nrd1 gene encodes an RNA binding
protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. .
Length = 85
Score = 51.8 bits (125), Expect = 8e-09
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVF-KEKGY-AFVKFTTKETATHAIESIHNTDINGHTVKC 274
+ +++ +VFSP+G + I +F K G A V+F + E+A +A ++++ +I
Sbjct: 12 PVTVDVLHQVFSPYGAVEKILIFEKNTGVQALVQFDSVESAENAKKALNGRNIYDGCCTL 71
Score = 32.1 bits (74), Expect = 0.066
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 107 IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGY-AFVSFVKKAEAENAITAMNGQ 160
+ L + F+P+G + I K+ G A V F AENA A+NG+
Sbjct: 13 VTVDVLHQVFSPYGAVEKILIFE-----KNTGVQALVQFDSVESAENAKKALNGR 62
Score = 28.3 bits (64), Expect = 1.9
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 14 NLDVSVTEELLCALFSQIGPVKGCK-VIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
NL VT ++L +FS G V+ K +I E A ++F A A A+N R
Sbjct: 8 NLLYPVTVDVLHQVFSPYGAVE--KILIFEKNTGVQALVQFDSVESAENAKKALNGR 62
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 51.6 bits (124), Expect = 8e-09
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
IFVG LSPE + ++E F FG I + D +T K +G+ F++F ++E +
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF----DSEEPVK 55
Score = 36.2 bits (84), Expect = 0.002
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 9/71 (12%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIES- 261
++ GG + EE + + F FG IV+I + K +G+ F+ F ++E +E+
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61
Query: 262 IHNTDINGHTV 272
H I G V
Sbjct: 62 FHV--IGGKKV 70
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by YNL110C
from Saccharomyces cerevisiae, and localizes to the
nucleoplasm and nucleolus. Nop15p has been identified as
a component of a pre-60S particle. It interacts with RNA
components of the early pre-60S particles. Furthermore,
Nop15p binds directly to a pre-rRNA transcript in vitro
and is required for pre-rRNA processing. It functions as
a ribosome synthesis factor required for the 5' to 3'
exonuclease digestion that generates the 5' end of the
major, short form of the 5.8S rRNA as well as for
processing of 27SB to 7S pre-rRNA. Nop15p also play a
specific role in cell cycle progression. Nop15p contains
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 51.7 bits (124), Expect = 9e-09
Identities = 21/62 (33%), Positives = 32/62 (51%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I++G L + LK+ F+ FG + N R+ R +T SK Y F+ F+ A A +M
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 158 NG 159
N
Sbjct: 62 NN 63
Score = 45.9 bits (109), Expect = 1e-06
Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIR--EPGNDP-YAFLEFVHHTVAATALAA 65
+Y+G+L E+ L FSQ G VK +V R + GN Y F++F++ VAA A +
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60
Query: 66 MNKRVFLEKEMKV 78
MN + + K ++V
Sbjct: 61 MNNYLLMGKVLQV 73
Score = 42.9 bits (101), Expect = 1e-05
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIES 261
+Y G E+ + K FS FGT+ ++RV K Y F++F E A A +S
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60
Query: 262 IHNTDINGHTVK 273
++N + G ++
Sbjct: 61 MNNYLLMGKVLQ 72
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 77
Score = 51.2 bits (123), Expect = 1e-08
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 7/71 (9%)
Query: 107 IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRS 166
Q LK+ F+ FGE+ ++ +DP+T +SKG+ FV F A+ E+ + ++
Sbjct: 11 TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRF---ADYEDQVKVLS----QRHM 63
Query: 167 IRTNWSTRKPP 177
I W K P
Sbjct: 64 IDGRWCDVKIP 74
Score = 32.4 bits (74), Expect = 0.059
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTD 266
E+ + FS FG ++ ++V K+ KG+ FV+F E + H D
Sbjct: 10 KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHMID 65
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 51.2 bits (123), Expect = 1e-08
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TTL++G+L VTEE L LF + G ++ +I G A++ A AL +
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRG---CAYVCMETRQDAHRALQKLR 59
Query: 68 KRVFLEKEMKVNWASSPG 85
K++KV WA + G
Sbjct: 60 NVKLAGKKIKVAWAPNKG 77
Score = 43.1 bits (102), Expect = 7e-06
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G LS ++ + LK F +GEI + + + +G A+V + +A A+ +
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDM------IPPRGCAYVCMETRQDAHRALQKL 58
Query: 158 NGQWLGSRSIRTNWSTRK 175
L + I+ W+ K
Sbjct: 59 RNVKLAGKKIKVAWAPNK 76
Score = 41.6 bits (98), Expect = 3e-05
Identities = 19/69 (27%), Positives = 35/69 (50%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
T++ G K + EE + +F +G I I + +G A+V T++ A A++ + N +
Sbjct: 4 TLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRNVKL 63
Query: 268 NGHTVKCFW 276
G +K W
Sbjct: 64 AGKKIKVAW 72
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 51.4 bits (124), Expect = 1e-08
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 6/73 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETATHAIES 261
VY G E + K FS FGT+ +R+ K KGYAFV+F + E A E+
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60
Query: 262 IHNTDINGHTVKC 274
++N + +KC
Sbjct: 61 MNNYLLFERLLKC 73
Score = 49.1 bits (118), Expect = 5e-08
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 108 ETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
E + L++ F+ FG ++ R+ R +T KSKGYAFV F A+ MN L R +
Sbjct: 13 EPE-LRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLL 71
Query: 168 RT 169
+
Sbjct: 72 KC 73
Score = 44.1 bits (105), Expect = 3e-06
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP--GNDP-YAFLEFVHHTVAATALAA 65
+Y+G+L E L FSQ G V ++ R G YAF+EF VA
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60
Query: 66 MNKRVFLEKEMKV 78
MN + E+ +K
Sbjct: 61 MNNYLLFERLLKC 73
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 51.0 bits (122), Expect = 1e-08
Identities = 24/57 (42%), Positives = 34/57 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+FVG LS + + LKE F+ FGE+ +C I DP T +S+G+ FV F A E +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVL 57
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 51.1 bits (123), Expect = 1e-08
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 4/73 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRI---VRDPQTLKSKGYAFVSFVKKAEAENAI 154
I+V +L +++ L+ F+ FGE+ + RI + Q + G+AFV+F + AENA+
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62
Query: 155 TAMNGQWLGSRSI 167
+NG LG R I
Sbjct: 63 -QLNGTELGGRKI 74
Score = 44.6 bits (106), Expect = 2e-06
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 10/61 (16%)
Query: 218 LNEELVSKVFSPFGTIVDIRV---FKEK------GYAFVKFTTKETATHAIESIHNTDIN 268
L+E+ + +FS FG + IR+ EK G+AFV F +A +A++ ++ T++
Sbjct: 12 LDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ-LNGTELG 70
Query: 269 G 269
G
Sbjct: 71 G 71
Score = 35.3 bits (82), Expect = 0.005
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPV------KGCKVIREPGNDPYAFLEFVHHTVAATAL 63
+YV NLD + E+ L +FS+ G V K + N+ +AF+ F + A AL
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62
Query: 64 AAMNKRVFLEKEMKVN 79
+N +++ V+
Sbjct: 63 -QLNGTELGGRKISVS 77
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 51.1 bits (123), Expect = 2e-08
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 15/74 (20%)
Query: 214 FGKDLN----EELVSKVFSPFGTIVDIRVFKEK-----------GYAFVKFTTKETATHA 258
F K+LN EE + K F G + + + K+K GY FV+F +KE A A
Sbjct: 4 FVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKA 63
Query: 259 IESIHNTDINGHTV 272
++ + T ++GH +
Sbjct: 64 LKRLQGTVLDGHAL 77
Score = 49.9 bits (120), Expect = 4e-08
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--------YAFLEFVHHTVA 59
TTL+V NL+ TEE L F + G V+ + ++ Y F+EF A
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60
Query: 60 ATALAAMN 67
AL +
Sbjct: 61 QKALKRLQ 68
Score = 48.8 bits (117), Expect = 1e-07
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVR-----DPQTLKSKGYAFVSFVKKAEAEN 152
+FV +L+ + +TLK+ F G + + I + P L S GY FV F K A+
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 153 AITAMNG 159
A+ + G
Sbjct: 63 ALKRLQG 69
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. Also included in this subfamily is the
sex-lethal protein (SXL) from Drosophila melanogaster.
SXL governs sexual differentiation and X chromosome
dosage compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 51.1 bits (122), Expect = 2e-08
Identities = 24/64 (37%), Positives = 38/64 (59%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++V L + + L++ F+ +G I RI+RD T S+G F+ F K+ EAE AI
Sbjct: 2 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61
Query: 157 MNGQ 160
+NGQ
Sbjct: 62 LNGQ 65
Score = 34.5 bits (79), Expect = 0.011
Identities = 15/69 (21%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
+Y G K + ++ + ++FS +G I+ R+ +++ G F++F + A AI+ +
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 263 HNTDINGHT 271
+ G +
Sbjct: 63 NGQKPEGAS 71
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 50.8 bits (122), Expect = 2e-08
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+ +FVG+L + + L F G + R++ D +T KSKG AFV F AEA
Sbjct: 1 FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEF-DTAEAMTKAL 59
Query: 156 AMNGQWLGSRSI 167
++ L R I
Sbjct: 60 KLHHTLLKGRKI 71
Score = 34.2 bits (79), Expect = 0.013
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIES 261
++ G D E + F G +R+ K KG AFV+F T E T A+
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-K 60
Query: 262 IHNTDING 269
+H+T + G
Sbjct: 61 LHHTLLKG 68
Score = 28.9 bits (65), Expect = 0.90
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 14/64 (21%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEF-----------V 54
L+VGNL T E L A F G +++ + AF+EF +
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61
Query: 55 HHTV 58
HHT+
Sbjct: 62 HHTL 65
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 50.5 bits (121), Expect = 2e-08
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK--GYAFVKFTTKETATHAIESIHNT 265
TVY G F V ++F G + + + +AF+ F E A AIE+++
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60
Query: 266 DINGHTVK 273
++G+ +K
Sbjct: 61 SVDGNCIK 68
Score = 40.1 bits (94), Expect = 8e-05
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 4/71 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++ G +K F G + ++ + + +AF++F A+ AI +
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETL 57
Query: 158 NGQWLGSRSIR 168
NG + I+
Sbjct: 58 NGASVDGNCIK 68
Score = 33.6 bits (77), Expect = 0.020
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
T+Y G S + LF GPV+ ++ P+AF+ F + A A+ +N
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRT-VQPHAFITFENLEAAQLAIETLNG 59
Query: 69 RVFLEKEMKV 78
+KV
Sbjct: 60 ASVDGNCIKV 69
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM2
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the 35
S pre-rRNA. MRD1 contains 5 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which may play an
important structural role in organizing specific rRNA
processing events. .
Length = 79
Score = 50.5 bits (121), Expect = 2e-08
Identities = 20/63 (31%), Positives = 37/63 (58%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L + L++ F+ FGE+S + D ++ KSKG+A+V F+ +A A +
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 158 NGQ 160
+G+
Sbjct: 65 DGK 67
Score = 33.1 bits (76), Expect = 0.027
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 220 EELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHA 258
E+ + K+FS FG + ++ V K KG+A+V F E A A
Sbjct: 16 EDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60
Score = 32.0 bits (73), Expect = 0.067
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAM 66
L+V NL S E+ L LFS+ G + V + + +A++ F+ A A +
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 67 NKRVF 71
+ +VF
Sbjct: 65 DGKVF 69
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 77
Score = 50.0 bits (120), Expect = 3e-08
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 98 IFVGDLSPEIETQTLKEAF-APFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ V +L + LKE F GEI++ +++R KS+ AF+ + + EA+ A
Sbjct: 3 LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDG-KSRRIAFIGYKTEEEAQKAKDY 61
Query: 157 MNGQWLGSRSIRTNWS 172
N ++ + I ++
Sbjct: 62 FNNTYINTSKISVEFA 77
Score = 37.2 bits (87), Expect = 0.001
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 216 KDLNEELVSKVFS-PFGTIVDIRV-FKEKG----YAFVKFTTKETATHAIESIHNTDING 269
L E + + FS G I D+++ E G AF+ + T+E A A + +NT IN
Sbjct: 10 ASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNNTYINT 69
Query: 270 HTVKCFW 276
+ +
Sbjct: 70 SKISVEF 76
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition, steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway. It binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 76
Score = 49.9 bits (119), Expect = 3e-08
Identities = 19/49 (38%), Positives = 34/49 (69%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+F+G L+ E +L+E F FGE+++C ++RD T +S+G+ F++F K
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49
Score = 32.2 bits (73), Expect = 0.074
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG---NDPYAFLEF 53
+++G L+ T++ L F Q G V C V+R+ + + FL F
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTF 47
Score = 31.0 bits (70), Expect = 0.15
Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ GG + ++ + + F FG + D V ++ +G+ F+ F ++ ++
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60
Query: 263 HNTD 266
H D
Sbjct: 61 HILD 64
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 49.9 bits (119), Expect = 3e-08
Identities = 23/57 (40%), Positives = 31/57 (54%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+FVG+L E + L F G I RIVRDP+T KG+A+V F + E A+
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL 58
Score = 29.8 bits (67), Expect = 0.51
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAI 259
V+ G G + EE + +VF G I +R+ ++ KG+A+V+F + A+
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL 58
Score = 29.1 bits (65), Expect = 0.91
Identities = 13/47 (27%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEF 53
++VGNL EE L +F + G ++ +++R+P + +A+++F
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQF 48
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM1 of HuR,
also termed ELAV-like protein 1 (ELAV-1), a ubiquitously
expressed Hu family member. It has a variety of
biological functions mostly related to the regulation of
cellular response to DNA damage and other types of
stress. HuR has an anti-apoptotic function during early
cell stress response; it binds to mRNAs and enhances the
expression of several anti-apoptotic proteins, such as
p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also
has pro-apoptotic function by promoting apoptosis when
cell death is unavoidable. Furthermore, HuR may be
important in muscle differentiation, adipogenesis,
suppression of inflammatory response and modulation of
gene expression in response to chronic ethanol exposure
and amino acid starvation. Like other Hu proteins, HuR
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 50.1 bits (119), Expect = 4e-08
Identities = 23/76 (30%), Positives = 43/76 (56%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L + L+ F+ GE+ + +++RD S GY FV++V +AE AI
Sbjct: 3 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62
Query: 157 MNGQWLGSRSIRTNWS 172
+NG L S++I+ +++
Sbjct: 63 LNGLRLQSKTIKVSYA 78
Score = 36.6 bits (84), Expect = 0.002
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE--PGND-PYAFLEFVHHTVAATALA 64
T L V L ++T++ L +LFS IG V+ K+IR+ G+ Y F+ +V+ A A+
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61
Query: 65 AMNKRVFLEKEMKVNWA 81
+N K +KV++A
Sbjct: 62 TLNGLRLQSKTIKVSYA 78
Score = 31.2 bits (70), Expect = 0.14
Identities = 14/71 (19%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+++ ++ + +FS G + ++ ++K GY FV + + A AI +++ +
Sbjct: 11 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQS 70
Query: 270 HTVKCFWGKES 280
T+K + + S
Sbjct: 71 KTIKVSYARPS 81
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-4, can activate cardiac troponin T (cTNT)
exon 5 inclusion. CELF-5, expressed in brain, is also
known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein 6
(BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent manner
and can activate inclusion via multiple copies of a
single element, MSE2. CELF-6 also promotes skipping of
exon 11 of insulin receptor, a known target of CELF
activity that is expressed in kidney. In addition to
three highly conserved RRMs, CELF-6 also possesses
numerous potential phosphorylation sites, a potential
nuclear localization signal (NLS) at the C terminus, and
an alanine-rich region within the divergent linker
region. .
Length = 79
Score = 49.9 bits (119), Expect = 4e-08
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++F+ L E L + F PFG + + ++ D T +SK + FVSF A A+ AI A
Sbjct: 6 NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65
Query: 157 MNGQWLGSRSIR 168
MNG +G + ++
Sbjct: 66 MNGFQIGMKRLK 77
Score = 33.3 bits (76), Expect = 0.032
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATH 257
P C ++ ++ + + ++F PFG ++ +VF + K + FV F +A
Sbjct: 2 PEGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQA 61
Query: 258 AIESIHNTDI 267
AI++++ I
Sbjct: 62 AIQAMNGFQI 71
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 50.0 bits (120), Expect = 4e-08
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
IFVG + P+ + L++ F+ FG + + +I+ D + SKGY FV+F + +AE +
Sbjct: 5 IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKIL 60
Score = 46.9 bits (112), Expect = 4e-07
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIES 261
++ GG D EE + FS FG++ D+++ + KGY FV F T+E A +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM 62
Score = 36.9 bits (86), Expect = 0.001
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEFVHHTVAATALA 64
P ++VG + TEE L FS+ G VK K+I R + Y F+ F A +
Sbjct: 2 PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTF-ETQEDAEKIL 60
Query: 65 AMNKRVFLEKEMKV 78
AM F K++ +
Sbjct: 61 AMGNLNFRGKKLNI 74
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 54.5 bits (131), Expect = 4e-08
Identities = 65/319 (20%), Positives = 111/319 (34%), Gaps = 58/319 (18%)
Query: 10 LYVGNLDVSVTEELLCALFSQI-----------GPVKGCKVIREPGNDPYAFLEF--VHH 56
LYVG + EE + F+ + G I + N +AFLEF V
Sbjct: 178 LYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKN--FAFLEFRTVEE 235
Query: 57 TVAATALAAMN-KRVFLEKEMKVNWASSPGNQPK--QDTSNHY----------------- 96
A AL ++ VFL+ ++ P P+ Q +
Sbjct: 236 ATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSK 295
Query: 97 -HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
I++G+L + +KE FG++ +++D T SKGYAF + + + AI
Sbjct: 296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIA 355
Query: 156 AMNGQWLGSRSIRTNWST--RKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYC-- 211
A+NG+ G + + + + Q V
Sbjct: 356 ALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLT 415
Query: 212 -GGFGKDLN-----EELVSKV---FSPFGTIVDIRVFKEK---------GYAFVKFTTKE 253
G DL EE+ V FS +G +++I + + G F+++
Sbjct: 416 NLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVR 475
Query: 254 TATHAIESIHNTDINGHTV 272
+A A+E ++ N V
Sbjct: 476 SAEKAMEGMNGRKFNDRVV 494
Score = 54.1 bits (130), Expect = 6e-08
Identities = 46/200 (23%), Positives = 74/200 (37%), Gaps = 39/200 (19%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATAL 63
+Y+GNL + + E+ + L G +K +I G YAF E+ +V A+
Sbjct: 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQPKQDTSN----------------------------- 94
AA+N + + ++ V A NQ DTSN
Sbjct: 355 AALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQL 414
Query: 95 HYHIFVGDLSPEIE----TQTLKEAFAPFGEISNCRIVRDPQTLKSK---GYAFVSFVKK 147
+ DL + E + +K F+ +G + N I R S G F+ +
Sbjct: 415 TNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADV 474
Query: 148 AEAENAITAMNGQWLGSRSI 167
AE A+ MNG+ R +
Sbjct: 475 RSAEKAMEGMNGRKFNDRVV 494
Score = 37.2 bits (86), Expect = 0.013
Identities = 44/245 (17%), Positives = 86/245 (35%), Gaps = 34/245 (13%)
Query: 81 ASSPGNQPKQDTSNHYH-IFVGDLSPEIETQTLKEAF-----------APFGEISNCRIV 128
P +Q + ++VG + PE + + + F A G+ + +
Sbjct: 160 TPLPVLPYQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI 219
Query: 129 RDPQTLKSKGYAFVSFVKKAEAENAIT----AMNGQWLGSRSIRTNWSTRKPPAMTNE-- 182
K K +AF+ F EA A+ + +L R ++ P +T E
Sbjct: 220 N-----KEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRP-HDYI--PVPQITPEVS 271
Query: 183 RKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE- 241
+K + + K + + +Y G L E+ + ++ FG + + K+
Sbjct: 272 QKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI 331
Query: 242 -----KGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESENNSTLAQ--PSAPTT 294
KGYAF ++ AI +++ D + + N +T+ AP T
Sbjct: 332 ATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVT 391
Query: 295 PQPNS 299
+
Sbjct: 392 LLAKA 396
Score = 29.9 bits (67), Expect = 2.4
Identities = 21/108 (19%), Positives = 40/108 (37%), Gaps = 15/108 (13%)
Query: 209 VYCGGFGKDLNEELVSKVFS------------PFGTIVDIRVFKEKGYAFVKFTTKETAT 256
+Y GG + EE V F+ + + + KEK +AF++F T E AT
Sbjct: 178 LYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEAT 237
Query: 257 HAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNSTAPQF 304
A+ ++ + + +K + + + P+ A
Sbjct: 238 FAM-ALDSIIYSNVFLK--IRRPHDYIPVPQITPEVSQKNPDDNAKNV 282
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 49.6 bits (118), Expect = 4e-08
Identities = 24/73 (32%), Positives = 42/73 (57%)
Query: 103 LSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWL 162
LS + L+E F+ +G ++ +V D +T +S+G+AFV F + +++ A+ NG L
Sbjct: 7 LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66
Query: 163 GSRSIRTNWSTRK 175
R IR ++S K
Sbjct: 67 DGRRIRVDYSITK 79
Score = 33.0 bits (75), Expect = 0.031
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 212 GGFGKDL--NEELVSKVFSPFG------TIVDIRVFKEKGYAFVKFTTKETATHAIESIH 263
G FG L E + +VFS +G + D R + +G+AFV F + + A+E +
Sbjct: 3 GVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHAN 62
Query: 264 NTDINGHTVK 273
+++G ++
Sbjct: 63 GMELDGRRIR 72
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed
in the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 49.7 bits (119), Expect = 5e-08
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATAL 63
+ L+V L SVT+E L LF + G VK +++ P A++E+ + + A+ A+
Sbjct: 1 EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAV 60
Query: 64 AAMNKRVFLEKEMKVNWASSP 84
M+ EK + V ++ P
Sbjct: 61 LKMDGTEIKEKTISVAISNPP 81
Score = 46.6 bits (111), Expect = 6e-07
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-----KEKGYAFVKFTTKETATHAIESI 262
++ G + +E + K+F G + +R+ K KG A+V++ + +A+ A+ +
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63
Query: 263 HNTDINGHTVK 273
T+I T+
Sbjct: 64 DGTEIKEKTIS 74
Score = 42.0 bits (99), Expect = 2e-05
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV L + + L++ F G + + R+V + ++ K KG A+V + ++ A A+ M
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVLKM 63
Query: 158 NGQWLGSRSIRTNWSTRKPP 177
+G + ++I S PP
Sbjct: 64 DGTEIKEKTISVAIS--NPP 81
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM2 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B), and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possess mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also termed one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 49.7 bits (119), Expect = 5e-08
Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP--GNDPYAFLEFVHHTVAATALAAM 66
TL+VGNL++++TEE L F + G V+ + R P + YAF++F++ +A A AM
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63
Query: 67 NKRVFLEKEMKVNW 80
+ + ++K+ +
Sbjct: 64 SGQYIGRNQIKIGY 77
Score = 48.9 bits (117), Expect = 7e-08
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L I + L+ AF +G + + I R P+ + YAFV F+ A A AM
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRG-QGNAYAFVKFLNLDMAHRAKVAM 63
Query: 158 NGQWLGSRSIRTNW 171
+GQ++G I+ +
Sbjct: 64 SGQYIGRNQIKIGY 77
Score = 30.4 bits (69), Expect = 0.29
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDI---RVFKEKG--YAFVKFTTKETATHAIESI 262
T++ G + EE + + F +G + D+ R + +G YAFVKF + A A ++
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63
Query: 263 HNTDINGHTVKCFWGK 278
I + +K +GK
Sbjct: 64 SGQYIGRNQIKIGYGK 79
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM1
of hnRNP A2/B1 which is an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Moreover, the
overexpression of hnRNP A2/B1 has been described in many
cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 81
Score = 49.3 bits (117), Expect = 6e-08
Identities = 19/59 (32%), Positives = 39/59 (66%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G LS E ++L+ + +G++++C ++RDP + +S+G+ FV+F E + A+ A
Sbjct: 5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63
Score = 33.5 bits (76), Expect = 0.021
Identities = 19/60 (31%), Positives = 27/60 (45%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L++G L TEE L + Q G + C V+R+P + FV + AAM R
Sbjct: 5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAAR 64
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation factor
64 kDa subunit (CstF64), is the vertebrate conterpart of
yeast mRNA 3'-end-processing protein RNA15. It is
expressed in all somatic tissues and is one of three
cleavage stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. .
Length = 75
Score = 49.0 bits (117), Expect = 6e-08
Identities = 24/73 (32%), Positives = 41/73 (56%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG++ E + LK+ F+ G + + R+V D +T K KGY F + + A +A+ +
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 158 NGQWLGSRSIRTN 170
NG L R +R +
Sbjct: 61 NGYELNGRQLRVD 73
Score = 42.1 bits (99), Expect = 2e-05
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
V+ G + EE + +FS G +V R+ K KGY F ++ +ETA A+ ++
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 263 HNTDINGHTVK 273
+ ++NG ++
Sbjct: 61 NGYELNGRQLR 71
Score = 39.8 bits (93), Expect = 1e-04
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATALAAM 66
++VGN+ TEE L +FS++GPV +++ RE G Y F E+ A +A+ +
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 67 NKRVFLEKEMKVNWA 81
N ++++V+ A
Sbjct: 61 NGYELNGRQLRVDNA 75
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 48.9 bits (117), Expect = 7e-08
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVHHTVAATALAAMN 67
T++VG +D S++E+ L FS G V ++ + + +AF+EF A +AL+A+N
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFAD---AESALSALN 58
Query: 68 K 68
Sbjct: 59 L 59
Score = 46.6 bits (111), Expect = 5e-07
Identities = 28/77 (36%), Positives = 42/77 (54%), Gaps = 7/77 (9%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I VG + + LKE F+ GE++ R+ D Q S +AFV F A+AE+A++A+
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEF---ADAESALSAL 57
Query: 158 N--GQWLGSRSIRTNWS 172
N G LG +R + S
Sbjct: 58 NLSGTLLGGHPLRVSPS 74
Score = 36.6 bits (85), Expect = 0.002
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGY----AFVKFTTKETATHAIE 260
T++ GG L+E+ + + FS G + +R+ ++ + AFV+F E+A A+
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALN 58
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate
RNA-binding protein 7 (RBM7). This subfamily
corresponds to the RRM of RBM7, a ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. RBM7 interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20. It may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM7 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
.
Length = 75
Score = 48.7 bits (116), Expect = 7e-08
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAM 66
TL+VGNLD VTEEL+ LF Q GPV K+ ++ P +AF+ F H A+ +
Sbjct: 3 TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLL 62
Query: 67 N 67
N
Sbjct: 63 N 63
Score = 38.0 bits (88), Expect = 5e-04
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L P++ + + E F G + +I +D K K +AFV+F + A+ +
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDG-KPKQFAFVNFKHEVSVPYAMNLL 62
Query: 158 NGQWLGSRSIR 168
NG L R +
Sbjct: 63 NGIKLYGRPLN 73
Score = 29.5 bits (66), Expect = 0.57
Identities = 15/71 (21%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESI 262
T++ G + EEL+ ++F G ++ +++ K+ K +AFV F + + +A+ +
Sbjct: 3 TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLL 62
Query: 263 HNTDINGHTVK 273
+ + G +
Sbjct: 63 NGIKLYGRPLN 73
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and
similar proteins. PABPs are highly conserved proteins
that bind to the poly(A) tail present at the 3' ends of
most eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. ePABP-2 is
predominantly located in the cytoplasm and PABP-2 is
located in the nucleus. In contrast to the type I PABPs
containing four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), the type II PABPs contains
a single highly-conserved RRM. This subfamily also
includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C)
gene encoding cytoplasmic mRNA-binding protein Rbp29
that binds preferentially to poly(A). Although not
essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 48.8 bits (117), Expect = 7e-08
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG++ + L+E F G I+ I+ D T + KG+A++ F+ K+ ENA+ +
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60
Query: 158 NGQWLGSRSI 167
N R I
Sbjct: 61 NESEFRGRQI 70
Score = 37.3 bits (87), Expect = 8e-04
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 11 YVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAMN 67
+VGN+D T E L F G + ++ + +A++EF+ + AL +N
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61
Query: 68 KRVFLEKEMKV 78
+ F +++KV
Sbjct: 62 ESEFRGRQIKV 72
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subfamily corresponds to the
RRM2 of SREK1, also termed
serine/arginine-rich-splicing regulatory protein 86-kDa
(SRrp86), or splicing factor arginine/serine-rich 12
(SFRS12), or splicing regulatory protein 508 amino acid
(SRrp508). SREK1 belongs to a family of proteins
containing regions rich in serine-arginine dipeptides
(SR proteins family), which is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. It is a unique SR family member and it may play
a crucial role in determining tissue specific patterns
of alternative splicing. SREK1 can alter splice site
selection by both positively and negatively modulating
the activity of other SR proteins. For instance, SREK1
can activate SRp20 and repress SC35 in a dose-dependent
manner both in vitro and in vivo. In addition, SREK1
contains two (some contain only one) RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains)
separated by an unusual glutamic acid-lysine (EK) rich
region. The RRM and SR domains are highly conserved
among other members of the SR superfamily. However, the
EK domain is unique to SREK1. It plays a modulatory
role controlling SR domain function by involvement in
the inhibition of both constitutive and alternative
splicing and in the selection of splice-site. .
Length = 85
Score = 49.2 bits (118), Expect = 8e-08
Identities = 28/72 (38%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG-NDPYAFLEFVHHTVAATALAAMN 67
T+YVGNLD + T + L FSQ G VK ++ + YAF+EF T AL +N
Sbjct: 6 TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINAL-KLN 64
Query: 68 KRVFLEKEMKVN 79
+F + +KVN
Sbjct: 65 GAMFGGRPLKVN 76
Score = 43.1 bits (102), Expect = 9e-06
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I+VG+L P L E F+ GE+ R+ D + YAFV F ++ NA+ +
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDET--QPTRYAFVEFAEQTSVINALK-L 63
Query: 158 NGQWLGSRSIRTNWST 173
NG G R ++ N S
Sbjct: 64 NGAMFGGRPLKVNHSN 79
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 48.8 bits (117), Expect = 8e-08
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I V +L + L+E F GE+++ +++R KS+ + FV F + +A+ A+
Sbjct: 3 IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDG-KSRRFGFVGFKSEEDAQQAVKYF 61
Query: 158 NGQWLGSRSI 167
N ++ + I
Sbjct: 62 NKTFIDTSKI 71
Score = 35.3 bits (82), Expect = 0.005
Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEKG-----YAFVKFTTKETATHAIESIHNTDIN 268
K + E+ + + F G + D++V + + + FV F ++E A A++ + T I+
Sbjct: 10 KYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNKTFID 67
Score = 33.3 bits (77), Expect = 0.024
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 2/63 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAA 65
+ + V NL VTE+ L F G V KV+R + F+ F A A+
Sbjct: 1 SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60
Query: 66 MNK 68
NK
Sbjct: 61 FNK 63
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 48.8 bits (116), Expect = 8e-08
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++F+ L E L + F PFG + + ++ D QT SK + FVS+ A+ AI A
Sbjct: 6 NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65
Query: 157 MNGQWLGSRSIR 168
MNG +G++ ++
Sbjct: 66 MNGFQIGTKRLK 77
Score = 30.7 bits (69), Expect = 0.25
Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG------YAFVKFTTKETATH 257
P C ++ ++ + +++ F PFG ++ +VF +K + FV + ++A
Sbjct: 2 PEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQA 61
Query: 258 AIESIHNTDINGHTVK 273
AI++++ I +K
Sbjct: 62 AIQAMNGFQIGTKRLK 77
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of SXL which governs sexual differentiation
and X chromosome dosage compensation in Drosophila
melanogaster. It induces female-specific alternative
splicing of the transformer (tra) pre-mRNA by binding to
the tra uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 48.9 bits (117), Expect = 8e-08
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRT 169
+ + F G + NC+IVRD +T S G+ FV + +A+ AI +NG L ++ I+
Sbjct: 15 EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKV 74
Query: 170 NWS 172
++
Sbjct: 75 AYA 77
Score = 43.9 bits (104), Expect = 4e-06
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVAATALA 64
T L + L ++T+E +LF +GPVK CK++R+ + F+++ A A+
Sbjct: 1 TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60
Query: 65 AMNKRVFLEKEMKVNWASSPG 85
+N K +KV +A G
Sbjct: 61 TLNGLQLQNKRIKVAYARPGG 81
Score = 30.1 bits (68), Expect = 0.46
Identities = 13/64 (20%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+ L +E +F G + + ++ ++K G+ FV + + E A AI +++ +
Sbjct: 10 QTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQN 69
Query: 270 HTVK 273
+K
Sbjct: 70 KRIK 73
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM1 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 49.0 bits (116), Expect = 9e-08
Identities = 25/76 (32%), Positives = 45/76 (59%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++ V L + + K F GEI +C++VRD T +S GY FV++V +A+ AI
Sbjct: 5 NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64
Query: 157 MNGQWLGSRSIRTNWS 172
+NG L +++I+ +++
Sbjct: 65 LNGLKLQTKTIKVSYA 80
Score = 32.4 bits (73), Expect = 0.060
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
T L V L ++T+E +LF IG ++ CK++R+ Y F+ +V A A+
Sbjct: 4 TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63
Query: 65 AMNKRVFLEKEMKVNWA 81
+N K +KV++A
Sbjct: 64 TLNGLKLQTKTIKVSYA 80
Score = 27.4 bits (60), Expect = 3.7
Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESIHNTDING 269
+++ +E +F G I ++ ++K GY FV + A AI +++ +
Sbjct: 13 QNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQT 72
Query: 270 HTVKCFWGKES 280
T+K + + S
Sbjct: 73 KTIKVSYARPS 83
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of RBM23
remains unclear, it shows high sequence homology to
RBM39 and contains two RRMs. It may possibly function as
a pre-mRNA splicing factor. .
Length = 73
Score = 48.8 bits (117), Expect = 9e-08
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV LS ++ + L E F+ G++ + RI+RD + +SKG A+V F + A+ +
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60
Query: 158 NGQWLGSRSI 167
GQ L + I
Sbjct: 61 TGQRLLGQPI 70
Score = 31.4 bits (72), Expect = 0.12
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIE 260
TV+ + E + + FS G + D+R+ ++ KG A+V+F +E+ A+
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG 59
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 48.6 bits (116), Expect = 9e-08
Identities = 26/57 (45%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATAL 63
T+YV ++D VTEE L ALFS G V C+V +P N +AF+EF A AL
Sbjct: 4 TVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDP-NSVLRFAFIEFTDEEGARAAL 59
Score = 41.3 bits (97), Expect = 4e-05
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V D+ ++ + L F+ G++ +CR+ DP ++ +AF+ F + A A++ +
Sbjct: 5 VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLR--FAFIEFTDEEGARAALS-L 61
Query: 158 NGQWLGSRSIR 168
+G LG +R
Sbjct: 62 SGTMLGFYPVR 72
Score = 36.2 bits (84), Expect = 0.002
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG----YAFVKFTTKETATHAIE 260
TVY + + EE ++ +FS G +VD RV + +AF++FT +E A A+
Sbjct: 3 RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAALS 60
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins.
This subfamily includes the RRM1 and RRM2 of
RNA-binding protein 5 (RBM5 or LUCA15 or H37) and
RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). These RBMs share high sequence homology and may
play an important role in regulating apoptosis. RBM5 is
a known modulator of apoptosis. It may also act as a
tumor suppressor or an RNA splicing factor. RBM6 has
been predicted to be a nuclear factor based on its
nuclear localization signal. Both, RBM6 and RBM5,
specifically bind poly(G) RNA. RBM10 is a paralog of
RBM5. It may play an important role in mRNA generation,
processing and degradation in several cell types. The
rat homolog of human RBM10 is protein S1-1, a
hypothetical RNA binding protein with poly(G) and
poly(U) binding capabilities. All family members
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a
G-patch/D111 domain. .
Length = 84
Score = 48.7 bits (117), Expect = 1e-07
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 12/71 (16%)
Query: 7 PT-TLYVGNLDVSVTEELLCALFSQIG--PVKGCKVIREP------GNDPYAFLEFVHHT 57
PT TL + LD+ TEE + S I P+K ++IR+ G +AF+EF
Sbjct: 1 PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRG---FAFVEFPSLE 57
Query: 58 VAATALAAMNK 68
A + A+N
Sbjct: 58 DATQWMDALNN 68
Score = 48.3 bits (116), Expect = 1e-07
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 103 LSPEIETQTLKEAFAPFG--EISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
L + + +A + I + R++RD T S+G+AFV F +A + A+N
Sbjct: 10 LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68
Score = 43.7 bits (104), Expect = 6e-06
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 12/80 (15%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFG--TIVDIRVFKEK------GYAFVKFTTKETA 255
PTN T+ G EE + + S I D+R+ ++K G+AFV+F + E A
Sbjct: 1 PTN-TLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDA 59
Query: 256 THAIESIHNTD---INGHTV 272
T +++++N D I+G V
Sbjct: 60 TQWMDALNNLDPFVIDGRVV 79
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 48.2 bits (115), Expect = 1e-07
Identities = 26/71 (36%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+LS E L+ F G I R++ + K KG+AFV F E E A A+
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNAL 57
Query: 158 NGQWLGSRSIR 168
G+ L R++R
Sbjct: 58 KGKHLNGRALR 68
Score = 38.6 bits (90), Expect = 3e-04
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
++ G + E+ + F G I +R+ K KG+AFV F E AT+A++
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60
Query: 263 H 263
H
Sbjct: 61 H 61
Score = 33.6 bits (77), Expect = 0.019
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKV 39
L+VGNL TE+ L A F ++G ++ ++
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRM 30
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 48.4 bits (115), Expect = 1e-07
Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT-- 155
+F+G LS + + LK+ F+ FGE+ +C + DP T +S+G+ FV F + + +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 156 --AMNGQ 160
+NG+
Sbjct: 61 EHKLNGK 67
Score = 28.0 bits (62), Expect = 1.6
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
++ GG D ++ + FS FG +VD + + +G+ FV F E+ ++
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 263 HNTDINGHTV 272
+ +NG +
Sbjct: 61 EHK-LNGKVI 69
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 86
Score = 48.6 bits (116), Expect = 1e-07
Identities = 19/58 (32%), Positives = 36/58 (62%), Gaps = 3/58 (5%)
Query: 220 EELVSKVFSPFGTIVDIRVFKE---KGYAFVKFTTKETATHAIESIHNTDINGHTVKC 274
E V++ FS +GT+V ++V ++ + YAFV+FT + A +A+ T ++G ++C
Sbjct: 20 EAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNALAKGQGTILDGRHIRC 77
Score = 41.2 bits (97), Expect = 5e-05
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 98 IFVGDL----SPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
+FV L S + + E F+ +G + +++RD + + YAFV F +A+NA
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNA 61
Query: 154 ITAMNGQWLGSRSIRT 169
+ G L R IR
Sbjct: 62 LAKGQGTILDGRHIRC 77
Score = 40.1 bits (94), Expect = 1e-04
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 10 LYVGNLDVSVTEELLCAL----FSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA 64
++V +L S +++ L A FS+ G + KV+R+ PYAF++F + A ALA
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNALA 63
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a transcription
coactivator of LEF-1 and AML-1 for the TCRalpha enhancer
function. In addition, THOC4 specifically binds to
rhesus (RH) promoter in erythroid, and might be a novel
transcription cofactor for erythroid-specific genes.
SKAR shows high sequence homology with THOC4 and
possesses one RRM as well. SKAR is widely expressed and
localizes to the nucleus. It may be a critical player in
the function of S6K1 in cell and organism growth control
by binding the activated, hyperphosphorylated form of
S6K1 but not S6K2. Furthermore, SKAR functions as a
protein partner of the p50 subunit of DNA polymerase
delta. In addition, SKAR may have particular importance
in pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 48.0 bits (115), Expect = 1e-07
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L ++ + L+E F GE+ +I D + +S+G A V F K+ +AE AI
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQF 61
Query: 158 NGQWLGSRSIR 168
NG L + ++
Sbjct: 62 NGVLLDGQPMQ 72
Score = 42.2 bits (100), Expect = 2e-05
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEFVHHTVAATALAA 65
T L V NL VTEE L LF ++G VK K+ R ++ A + F A A+
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60
Query: 66 MNKRVFLEKEMKVN 79
N + + M+V
Sbjct: 61 FNGVLLDGQPMQVE 74
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to the
RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contain
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. On the other
hand, both RRM1 and RRM2 of CELF-4 can activate cardiac
troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in
brain, is also known as bruno-like protein 5 (BRUNOL-5),
or CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, strongly
expressed in kidney, brain, and testis, is also known as
bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in an muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In additiona to three highly conserved RRMs,
CELF-6 also possesses numerous potential phosphorylation
sites, a potential nuclear localization signal (NLS) at
the C terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 48.6 bits (116), Expect = 1e-07
Identities = 19/68 (27%), Positives = 36/68 (52%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
+ +FVG + +E + L+ F FG+I +++D T KG AF+++ + A
Sbjct: 3 DDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALK 62
Query: 153 AITAMNGQ 160
A +A++ Q
Sbjct: 63 AQSALHEQ 70
Score = 37.0 bits (86), Expect = 0.001
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNT 265
++L E+ + +F FG I ++ V K+ KG AF+ + +E+A A ++H
Sbjct: 15 RNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSALHEQ 70
Score = 29.7 bits (67), Expect = 0.61
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 11/70 (15%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPY-------AFLEFVHH 56
+ L+VG + ++ E+ L LF Q G + V++ D Y AFL +
Sbjct: 2 DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLK----DKYTGMHKGCAFLTYCAR 57
Query: 57 TVAATALAAM 66
A A +A+
Sbjct: 58 ESALKAQSAL 67
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 48.3 bits (115), Expect = 1e-07
Identities = 22/62 (35%), Positives = 39/62 (62%), Gaps = 1/62 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG L+ + + ++E F+P+G + + ++RD +S+G AFV + K A+ AI A+
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60
Query: 158 NG 159
NG
Sbjct: 61 NG 62
Score = 46.4 bits (110), Expect = 7e-07
Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIH 263
++ G K E+ V +VFSP+G + DI + ++ +G AFVK+++KE A AI++++
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61
Query: 264 NTDI 267
Sbjct: 62 GVYT 65
Score = 29.4 bits (66), Expect = 0.58
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAMN 67
L+VG L+ TE+ + +FS G V+ ++R+ AF+++ +A A+ A+N
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 47.8 bits (114), Expect = 1e-07
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 208 TVYCGGFGKD-LNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
T++ GF EE + K+F PFG +V + K +AFV+F E AT A+E++H +
Sbjct: 1 TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--RKTFAFVEFEDSEDATKALEALHGSR 58
Query: 267 INGHTVKCFWGK 278
I+G + + K
Sbjct: 59 IDGSVLTVEFVK 70
Score = 43.2 bits (102), Expect = 7e-06
Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 9/77 (11%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+FV P + +++ F PFG + C I K +AFV F +A A+ A
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEA 53
Query: 157 MNGQWLGSRSIRTNWST 173
++G + + +
Sbjct: 54 LHGSRIDGSVLTVEFVK 70
Score = 38.2 bits (89), Expect = 4e-04
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 9 TLYVGNLDV-SVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TL+V D + EE + LF GP+ C + + +AF+EF A AL A++
Sbjct: 1 TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRK-----TFAFVEFEDSEDATKALEALH 55
Query: 68 KRVFLEKEMKVNWA 81
+ V +
Sbjct: 56 GSRIDGSVLTVEFV 69
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46),
belonging to the Aly/REF family of RNA binding proteins
that have been implicated in coupling transcription
with pre-mRNA splicing and nucleo-cytoplasmic mRNA
transport. SKAR is widely expressed and localizes to
the nucleus. It may be a critical player in the
function of S6K1 in cell and organism growth control by
binding the activated, hyperphosphorylated form of S6K1
but not S6K2. Furthermore, SKAR functions as a protein
partner of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. SKAR contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain).
Length = 69
Score = 47.6 bits (114), Expect = 2e-07
Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
T L V NL SVTE+ + LFS IG +K +++R PG A + +V A TA+ N
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVR-PGV---AEVVYVRKDDALTAIDKYN 56
Query: 68 KRVFLEKEMKVN 79
R + MK
Sbjct: 57 NRELDGQPMKCK 68
Score = 37.2 bits (87), Expect = 9e-04
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 220 EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKC 274
E+ + ++FS G + R+ + G A V + K+ A AI+ +N +++G +KC
Sbjct: 14 EDDIVELFSAIGALKRARLVR-PGVAEVVYVRKDDALTAIDKYNNRELDGQPMKC 67
Score = 35.3 bits (82), Expect = 0.004
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+ V +L P + + E F+ G + R+VR G A V +V+K +A AI
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVR-------PGVAEVVYVRKDDALTAID 53
Query: 156 AMNGQWL 162
N + L
Sbjct: 54 KYNNREL 60
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 47.9 bits (115), Expect = 2e-07
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVR--DPQTLKSKGYAFVSFVKKAEAENAIT 155
++VG+LS + + E F+ G+I RI+ D T G+ FV + + +AENA+
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58
Query: 156 AMNGQWLGSRSIRTNW 171
+NG L R IR +W
Sbjct: 59 YLNGTKLDDRIIRVDW 74
Score = 46.8 bits (112), Expect = 5e-07
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 13/79 (16%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI-------REP-GNDPYAFLEFVHHTVAAT 61
LYVGNL TEE + LFS+ G +K ++I + P G + F+E+ A
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCG---FCFVEYYTREDAEN 55
Query: 62 ALAAMNKRVFLEKEMKVNW 80
A+ +N ++ ++V+W
Sbjct: 56 AVKYLNGTKLDDRIIRVDW 74
Score = 36.4 bits (85), Expect = 0.002
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDI-----RVFKEK-GYAFVKFTTKETATHAIESI 262
+Y G EE + ++FS G I I R K G+ FV++ T+E A +A++ +
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 263 HNTDINGHTVKCFW 276
+ T ++ ++ W
Sbjct: 61 NGTKLDDRIIRVDW 74
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 47.6 bits (113), Expect = 2e-07
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L PE Q ++ F +G++ C I+ K Y FV K A+ AI +
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRNL 54
Query: 158 N 158
+
Sbjct: 55 H 55
Score = 34.8 bits (80), Expect = 0.005
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVH 55
L+VGNL TE+ + +LF Q G V C +I+ G FVH
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYG--------FVH 40
Score = 32.2 bits (73), Expect = 0.055
Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
++ G + E+ + +F +G +++ + K Y FV K A AI ++H+ ++
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--YGFVHMDDKTAADEAIRNLHHYKLH 60
Query: 269 G 269
G
Sbjct: 61 G 61
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions as
a translational regulator that activates translation in
an mRNA-specific manner. DAZAP1 was initially identified
as a binding partner of Deleted in Azoospermia (DAZ). It
also interacts with numerous hnRNPs, including hnRNP U,
hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D,
suggesting DAZAP1 might associate and cooperate with
hnRNP particles to regulate adenylate-uridylate-rich
elements (AU-rich element or ARE)-containing mRNAs.
DAZAP1 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
proline-rich domain. .
Length = 82
Score = 47.9 bits (114), Expect = 2e-07
Identities = 20/47 (42%), Positives = 32/47 (68%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
+FVG LS E +TL+ F+ +GE+ +C I++D T +S+G+ FV F
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48
Score = 31.7 bits (72), Expect = 0.10
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
L+VG L T+E L FSQ G V C ++++ + + F++F T LA
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLA 59
Score = 30.2 bits (68), Expect = 0.41
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG + +E + + FS +G +VD + K+K G+ FVKF +
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61
Query: 263 -HNTDINGHTV 272
H D G T+
Sbjct: 62 PHTLD--GRTI 70
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. It functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 47.4 bits (113), Expect = 2e-07
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFV +L ++ + LKE F G++ I D + KS+G V F EA AI+
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEHPIEAVQAISMF 59
Query: 158 NGQWLGSRSIR 168
NGQ L R +R
Sbjct: 60 NGQMLFDRPMR 70
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2 of
PHIP1. A. thaliana PHIP1 and its homologs represent a
novel class of plant-specific RNA-binding proteins that
may play a unique role in the polarized mRNA transport
to the vicinity of the cell plate. The family members
consist of multiple functional domains, including a
lysine-rich domain (KRD domain) that contains three
nuclear localization motifs (KKKR/NK), two RNA
recognition motifs (RRMs), and three CCHC-type zinc
fingers. PHIP1 is a peripheral membrane protein and is
localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 47.4 bits (113), Expect = 2e-07
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G+L+ +I ++E F EI++ R+ D +T + KG+ V F + + A+ +
Sbjct: 2 VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KL 59
Query: 158 NGQWLGSRSIRTN 170
+G L R IR
Sbjct: 60 DGTVLCGRPIRIA 72
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 47.3 bits (113), Expect = 2e-07
Identities = 18/48 (37%), Positives = 31/48 (64%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFV 145
+FVG L ++ + L+E F+ +G + + IV D +T K +G+AFV+F
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFD 49
Score = 41.1 bits (97), Expect = 4e-05
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG +D+ EE + + FS +G + + + +K G+AFV F + +
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61
Query: 263 HNTDINGHTV 272
++T INGH V
Sbjct: 62 YHT-INGHRV 70
Score = 36.1 bits (84), Expect = 0.003
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGND-PYAFLEFVHH 56
L+VG L VTEE L FSQ G V+ +++ +E G +AF+ F +
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDY 51
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 46.9 bits (112), Expect = 3e-07
Identities = 16/56 (28%), Positives = 32/56 (57%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+ ++ VF FG ++D+ + K Y + K+ +E+A AI ++H ++NG +K
Sbjct: 11 PPDYILEDVFCRFGGLIDVYLVPGKNYGYAKYADRESAERAITTLHGKEVNGVKLK 66
Score = 35.0 bits (81), Expect = 0.005
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
L++ F FG + + +V K Y + + + AE AIT ++G+
Sbjct: 14 YILEDVFCRFGGLIDVYLVPG------KNYGYAKYADRESAERAITTLHGK 58
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional and
post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 46.9 bits (111), Expect = 3e-07
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
+FVG LSP+ + +KE F FGEI N + D +T + +G+ FV++
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTY 48
Score = 34.6 bits (79), Expect = 0.010
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIES 261
V+ GG D EE + + F FG I +D + + +G+ FV +T +E +ES
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 46.9 bits (111), Expect = 4e-07
Identities = 20/47 (42%), Positives = 30/47 (63%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
IFVG L+PE + ++E F FGEI + DP+T K +G+ F++F
Sbjct: 7 IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITF 53
Score = 29.6 bits (66), Expect = 0.52
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIE-S 261
++ GG + EE + + F FG I +D + K +G+ F+ F ++ +E
Sbjct: 7 IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEKK 66
Query: 262 IHN 264
HN
Sbjct: 67 FHN 69
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 47.4 bits (112), Expect = 4e-07
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++F+ L E Q L + F PFG + + ++ D QT SK + FVS+ A+ AI A
Sbjct: 9 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQA 68
Query: 157 MNGQWLGSRSIR 168
MNG +G + ++
Sbjct: 69 MNGFQIGMKRLK 80
Score = 26.6 bits (58), Expect = 7.6
Identities = 16/78 (20%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG------YAFVKFTTKETA 255
P ++ ++ ++ + ++F PFG +V +VF +K + FV + +A
Sbjct: 3 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 62
Query: 256 THAIESIHNTDINGHTVK 273
AI++++ I +K
Sbjct: 63 QAAIQAMNGFQIGMKRLK 80
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 46.8 bits (112), Expect = 4e-07
Identities = 18/52 (34%), Positives = 36/52 (69%), Gaps = 5/52 (9%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIHNT 265
++ + ++FSPFG + +R+ K+ +G+AFV+F TK+ A +A+E++ +T
Sbjct: 13 TKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKST 64
Score = 44.5 bits (106), Expect = 3e-06
Identities = 19/48 (39%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
L+E F+PFG++ + R+ + +G+AFV FV K EA+NA+ A+
Sbjct: 17 LRELFSPFGQVKSVRLPKKFDG-SHRGFAFVEFVTKQEAQNAMEALKS 63
Score = 33.0 bits (76), Expect = 0.031
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP--GNDPYAFLEFVHHTVAATALAA 65
T L V N+ T++ L LFS G VK ++ ++ + +AF+EFV A A+ A
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60
Query: 66 M 66
+
Sbjct: 61 L 61
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 46.3 bits (110), Expect = 6e-07
Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
+Y F D +E + ++FSP+G + ++++ +AFV+F + E+A A +S+H +N
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--NFAFVEFESLESAIRAKDSVHGKVLN 59
Query: 269 GHTVKC 274
+ +
Sbjct: 60 NNPLYV 65
Score = 40.5 bits (95), Expect = 6e-05
Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V P+ ++E F+P+G + +++ +AFV F A A ++
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDSV 53
Query: 158 NGQWL 162
+G+ L
Sbjct: 54 HGKVL 58
Score = 36.6 bits (85), Expect = 0.001
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
LYV +E + +FS G VK K+I +AF+EF A A +++ +
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN-----FAFVEFESLESAIRAKDSVHGK 56
Query: 70 VF 71
V
Sbjct: 57 VL 58
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 46.4 bits (110), Expect = 6e-07
Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIES 261
C V+ G +D+ E+ + +F G I + R+ E +GYAFV +TTKE A AI
Sbjct: 2 CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRI 61
Query: 262 IHNTDI 267
++N +I
Sbjct: 62 LNNYEI 67
Score = 32.9 bits (75), Expect = 0.037
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG + ++ L F G+I R++ + +++GYAFV + K EA+ AI +
Sbjct: 4 VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSG-ENRGYAFVMYTTKEEAQLAIRIL 62
Query: 158 N 158
N
Sbjct: 63 N 63
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 46.1 bits (110), Expect = 6e-07
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 218 LNEELVSK-----VFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTV 272
LN + VSK +FS +G I+ I + K GY FV+F +E A A+ + +I G +
Sbjct: 8 LNTDKVSKEDLEEIFSKYGKILGISLHK--GYGFVQFDNEEDARAAVAGENGREIAGQKL 65
Score = 43.0 bits (102), Expect = 7e-06
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 98 IFVGDLSPEIETQT-LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+FVG+L+ + ++ L+E F+ +G+I + KGY FV F + +A A+
Sbjct: 3 VFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAG 54
Query: 157 MNGQ 160
NG+
Sbjct: 55 ENGR 58
Score = 41.8 bits (99), Expect = 2e-05
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 10 LYVGNLDVS-VTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
++VGNL+ V++E L +FS+ G + G + + Y F++F + A A+A N
Sbjct: 3 VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKG-----YGFVQFDNEEDARAAVAGENG 57
Query: 69 RVFLEKEMKVN 79
R +++ +N
Sbjct: 58 REIAGQKLDIN 68
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM2 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 71
Score = 46.1 bits (110), Expect = 6e-07
Identities = 31/73 (42%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYA-FLEF--VHHTVAATALAA 65
TL V NLD ++++ L +LFSQ G VK IRE P F+EF + A AL A
Sbjct: 3 TLLVFNLDSPISDQELRSLFSQFGEVKD---IRETPLRPSQKFVEFYDIRA--AEAALDA 57
Query: 66 MNKRVFLEKEMKV 78
+N R FL +KV
Sbjct: 58 LNGRPFLGGRLKV 70
Score = 34.9 bits (81), Expect = 0.006
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L I Q L+ F+ FGE+ + +R+ S+ FV F AE A+ A+
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEV---KDIRETPLRPSQ--KFVEFYDIRAAEAALDAL 58
Query: 158 NGQWLGSRSIR 168
NG+ ++
Sbjct: 59 NGRPFLGGRLK 69
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome
proliferator-activated receptor gamma coactivator 1A
(PGC-1alpha) family of regulated coactivators. This
subfamily corresponds to the RRM of PGC-1alpha,
PGC-1beta, and PGC-1-related coactivator (PRC), which
serve as mediators between environmental or endogenous
signals and the transcriptional machinery governing
mitochondrial biogenesis. They play an important
integrative role in the control of respiratory gene
expression through interacting with a number of
transcription factors, such as NRF-1, NRF-2, ERR, CREB
and YY1. All family members are multi-domain proteins
containing the N-terminal activation domain, an LXXLL
coactivator signature, a tetrapeptide motif (DHDY)
responsible for HCF binding, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In contrast to PGC-1alpha
and PRC, PGC-1beta possesses two glutamic/aspartic
acid-rich acidic domains, but lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 89
Score = 46.5 bits (111), Expect = 8e-07
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRV-FKEKG--YAFVKFTTKETATHAIESIHN 264
+Y G D + + F PFG I +I + F++ G Y FV + A AIE ++
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAIEHGND 63
Score = 41.9 bits (99), Expect = 3e-05
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
I+VG + + L++ F PFGEI + Y FV++ +A AI
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN---YGFVTYRYACDAFRAI 58
Score = 33.8 bits (78), Expect = 0.020
Identities = 13/59 (22%), Positives = 23/59 (38%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
+YVG + + T L F G ++ + D Y F+ + + A A+ N
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAIEHGND 63
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 46.3 bits (109), Expect = 8e-07
Identities = 23/64 (35%), Positives = 37/64 (57%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++V L + + L++ F+ +G I RI+ D T S+G F+ F K+ EAE AI
Sbjct: 4 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63
Query: 157 MNGQ 160
+NGQ
Sbjct: 64 LNGQ 67
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 45.7 bits (108), Expect = 9e-07
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-----KEKGYAFVKFTTKETATHAIES 261
C V+ G +D+ E+ + VF G I ++R+ K +GYAFV +T K A A+
Sbjct: 2 CEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRE 61
Query: 262 IHNTDI 267
++N +I
Sbjct: 62 LNNYEI 67
Score = 41.1 bits (96), Expect = 5e-05
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG + ++ L F G I R++ D K++GYAFV + +K EA+ A+ +
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDG-KNRGYAFVMYTQKHEAKRAVREL 62
Query: 158 N 158
N
Sbjct: 63 N 63
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 45.9 bits (109), Expect = 1e-06
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+ L+E F FG+I IV+D T +SKG+ +V F K ++A A+
Sbjct: 15 EDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59
Score = 34.3 bits (79), Expect = 0.011
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIE 260
K EE + + F FG I + + K+ KG+ +VKF A A+E
Sbjct: 10 KSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60
Score = 27.0 bits (60), Expect = 4.0
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 6/62 (9%)
Query: 18 SVTEELLCALFSQIGPVKGCKVIREPGN-DPYAFLEFVHHTVAATALAAMN-----KRVF 71
S TEE L F + G ++ ++++ + F H + A+A N K V
Sbjct: 11 SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCDKSFKAVL 70
Query: 72 LE 73
E
Sbjct: 71 AE 72
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 45.8 bits (108), Expect = 1e-06
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS + + L E + FGE+ +C I DP T +S+G+ FV F K A + + + +
Sbjct: 2 MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLF-KDAASVDKVLEL 60
Query: 158 NGQWLGSRSI 167
L + I
Sbjct: 61 KEHKLDGKLI 70
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 45.3 bits (108), Expect = 1e-06
Identities = 21/58 (36%), Positives = 31/58 (53%)
Query: 103 LSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
L P + L++ PFG+I + + + D +T K KGY FV F A AI +NG+
Sbjct: 8 LPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65
Score = 35.7 bits (83), Expect = 0.003
Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHA 258
TN VY G + +E + K+ PFG I+ + K KGY FV F + E A A
Sbjct: 1 TN--VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKA 58
Query: 259 IESIHNTDINGHT 271
IE ++ +
Sbjct: 59 IEGLNGRGVQAQF 71
Score = 32.2 bits (74), Expect = 0.058
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
T +Y+ L + T+E L L G + K I + + Y F++F A A+
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
Query: 65 AMNKRVF 71
+N R
Sbjct: 61 GLNGRGV 67
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 45.6 bits (108), Expect = 1e-06
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG--YAFVKFTTKETATHAIE 260
PT ++ D+ EE V + G IV+++VF+ G A V+F T+E AT A+
Sbjct: 5 PPTK-MIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEALA 63
Query: 261 SIHNTDINGHTVK 273
H + +NG T++
Sbjct: 64 CKHASSLNGSTIR 76
Score = 27.8 bits (62), Expect = 2.3
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 4/71 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I V +L ++ + + A G I N ++ K A V F + +A A+
Sbjct: 10 IHVSNLPSDVTEEDVINHLAEHGVIVNVKVFE----SNGKKQALVEFATEEQATEALACK 65
Query: 158 NGQWLGSRSIR 168
+ L +IR
Sbjct: 66 HASSLNGSTIR 76
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM2 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 81
Score = 45.4 bits (107), Expect = 1e-06
Identities = 22/64 (34%), Positives = 37/64 (57%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++V L + + +++ F+ +G I RI+ D T S+G F+ F K+ EAE AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62
Query: 157 MNGQ 160
+NGQ
Sbjct: 63 LNGQ 66
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 45.3 bits (107), Expect = 1e-06
Identities = 19/57 (33%), Positives = 29/57 (50%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+FVG L ++ L E F+ FG + ++ D QT K +G+ FV F A+ A
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58
Score = 36.4 bits (84), Expect = 0.002
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHA-IES 261
++ GG D+ E +++ FS FG + V K++G+ FV F ++A A +
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61
Query: 262 IHNTDINGHTVK 273
H INGH V+
Sbjct: 62 FHP--INGHRVE 71
Score = 29.1 bits (65), Expect = 0.76
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATA 62
L+VG L V E L FSQ GPV+ +VI ++ G + F+ F +H A A
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 45.4 bits (108), Expect = 1e-06
Identities = 27/81 (33%), Positives = 46/81 (56%), Gaps = 5/81 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGE-ISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++GDL P ++ +K AFA GE + + +I+R+ T GY FV F +A AE +
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61
Query: 157 MNGQWL-GS---RSIRTNWST 173
+NG+ + GS + + N +T
Sbjct: 62 LNGKPIPGSNPPKRFKLNRAT 82
Score = 29.6 bits (67), Expect = 0.55
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIG-PVKGCKVIREP---GNDPYAFLEFVHHTVAATALA 64
+L++G+L+ + E + F+ +G V K+IR G Y F+EF A L
Sbjct: 1 SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60
Query: 65 AMNKRVF----LEKEMKVNWAS 82
+N + K K+N A+
Sbjct: 61 KLNGKPIPGSNPPKRFKLNRAT 82
Score = 28.5 bits (64), Expect = 1.8
Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFG-TIVDIRVFKEK------GYAFVKFTTKETATHAIE 260
+++ G ++E + + F+ G T++ +++ + K GY FV+F + TA +
Sbjct: 1 SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60
Query: 261 SIHNTDING 269
++ I G
Sbjct: 61 KLNGKPIPG 69
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 44.8 bits (106), Expect = 2e-06
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG++ + + L+ F +G + +C ++R +AFV +A A+ AI +
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54
Query: 158 NGQWLGSRSI 167
NG+ L R +
Sbjct: 55 NGRELHGRKL 64
Score = 43.3 bits (102), Expect = 6e-06
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
++VGN+D ++E L ALF G V C V+R+ +AF+ A A+ +N R
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ-----FAFVHLRGEAAADRAIEELNGR 57
Query: 70 VFLEKEMKV 78
+++ V
Sbjct: 58 ELHGRKLVV 66
Score = 41.3 bits (97), Expect = 3e-05
Identities = 14/64 (21%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
++ G +D ++E + +F +G ++ V ++ +AFV + A AIE ++ +++
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--FAFVHLRGEAAADRAIEELNGRELH 60
Query: 269 GHTV 272
G +
Sbjct: 61 GRKL 64
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM2 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and is highly conserved between
plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 44.8 bits (106), Expect = 2e-06
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE-PGNDPYAFLEFVHHTVAATALAAMN 67
TL V NLD SV+ + L +F G +K IRE P + F+EF A AL A+N
Sbjct: 3 TLVVFNLDPSVSNDDLHQIFGAYGEIKE---IRETPNKRHHKFIEFYDVRSAEAALKALN 59
Query: 68 KRVFLEKEMKV 78
+ K +K+
Sbjct: 60 RSEIAGKRIKL 70
Score = 35.9 bits (83), Expect = 0.003
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L P + L + F +GEI R +T + + F+ F AE A+ A+
Sbjct: 4 LVVFNLDPSVSNDDLHQIFGAYGEIKEIR-----ETPNKRHHKFIEFYDVRSAEAALKAL 58
Query: 158 NGQWLGSRSIR 168
N + + I+
Sbjct: 59 NRSEIAGKRIK 69
Score = 31.3 bits (71), Expect = 0.11
Identities = 14/56 (25%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 219 NEELVSKVFSPFGTIVDIR-VFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
N++L ++F +G I +IR ++ + F++F +A A+++++ ++I G +K
Sbjct: 15 NDDL-HQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSEIAGKRIK 69
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich
splicing factor 10 (SRSF10) and similar proteins. This
subgroup corresponds to the RRM of SRSF10, also termed
40 kDa SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). SRSF10 is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 45.0 bits (106), Expect = 2e-06
Identities = 21/82 (25%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +++ + ++ L+ F +G I + + D T + +G+A+V F +AE+A+ +
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 158 NGQWLGSRSIRTNWST--RKPP 177
+ +W+ R I ++ RK P
Sbjct: 63 DRKWICGRQIEIQFAQGDRKTP 84
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM1 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically binds mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone, and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs);
DND1 harbors only two RRMs. .
Length = 78
Score = 44.9 bits (107), Expect = 2e-06
Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIES 261
C V+ G +DL E+ + +F G I ++R+ + +GYAFV +T KE A A++
Sbjct: 2 CEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQ 61
Query: 262 IHNTDING 269
+HN +I
Sbjct: 62 LHNYEIRP 69
Score = 40.2 bits (95), Expect = 8e-05
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 96 YHIFVG----DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+FVG DL + L F G I R++ D L ++GYAFV++ K A+
Sbjct: 2 CEVFVGKIPRDLFED----ELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQ 56
Query: 152 NAITAMNG 159
A+ ++
Sbjct: 57 RAVKQLHN 64
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 44.5 bits (106), Expect = 2e-06
Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 8/74 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L P L+ F FG I + YA++ + A+ A A+
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYD------PGRNYAYIEYESIEAAQAAKEAL 54
Query: 158 NGQWLGS--RSIRT 169
G LG R +R
Sbjct: 55 RGFPLGGPGRRLRV 68
Score = 39.9 bits (94), Expect = 1e-04
Identities = 14/52 (26%), Positives = 25/52 (48%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
++ GG G + + + F FG I I + YA++++ + E A A E
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKE 52
Score = 36.0 bits (84), Expect = 0.002
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L+VG L + L F + G ++ YA++E+ A A A+
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDP---GRNYAYIEYESIEAAQAAKEALRGF 57
Query: 70 VF--LEKEMKVNWA 81
+ ++V++A
Sbjct: 58 PLGGPGRRLRVDFA 71
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 90
Score = 45.2 bits (106), Expect = 3e-06
Identities = 23/64 (35%), Positives = 37/64 (57%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++V L + + L++ F+ +G I RI+ D T S+G F+ F K+ EAE AI
Sbjct: 7 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66
Query: 157 MNGQ 160
+NGQ
Sbjct: 67 LNGQ 70
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 44.4 bits (106), Expect = 3e-06
Identities = 29/80 (36%), Positives = 41/80 (51%), Gaps = 10/80 (12%)
Query: 9 TLYVGNLDVSVT-EEL---LCALFSQIGPV---KGCKVIREPGNDPYAFLEFVHHTVAAT 61
TLY+ NL+ + +EL L ALFSQ GPV K ++ G AF+ F A
Sbjct: 1 TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQ---AFVVFKDVESATN 57
Query: 62 ALAAMNKRVFLEKEMKVNWA 81
AL A+ F +K M++ +A
Sbjct: 58 ALRALQGFPFYDKPMRIQYA 77
Score = 43.3 bits (103), Expect = 8e-06
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 226 VFSPFGTIVDIRVFKEK---GYAFVKFTTKETATHAIESIHNT 265
+FS FG ++DI K G AFV F E+AT+A+ ++
Sbjct: 23 LFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALRALQGF 65
Score = 37.9 bits (89), Expect = 6e-04
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 98 IFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
+++ +L+ +I+ LK + F+ FG + + + TLK +G AFV F A NA
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATNA 58
Query: 154 ITAMNGQWLGSRSIRTNWS 172
+ A+ G + +R ++
Sbjct: 59 LRALQGFPFYDKPMRIQYA 77
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living cells.
RRM2/3 are implicated in ACF interaction with APOBEC-1.
.
Length = 78
Score = 44.6 bits (105), Expect = 3e-06
Identities = 22/69 (31%), Positives = 40/69 (57%), Gaps = 6/69 (8%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIES 261
C ++ G +DL E+ + + G I ++R+ + +GYAFV F+ K+ A +AI+
Sbjct: 2 CEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQ 61
Query: 262 IHNTDI-NG 269
++N +I NG
Sbjct: 62 LNNYEIRNG 70
Score = 40.0 bits (93), Expect = 1e-04
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IF+G L ++ L G+I R++ D ++GYAFV+F K EA+NAI +
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNG-NNRGYAFVTFSNKQEAKNAIKQL 62
Query: 158 N 158
N
Sbjct: 63 N 63
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate
RNA-binding protein 11 (RBM11). This subfamily
corresponds to the RRM or RBM11, a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. RBM11 is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. RBM11 contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a region
lacking known homology at the C-terminus. The RRM of
RBM11 is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 44.2 bits (104), Expect = 3e-06
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAAM 66
TL+VGNL+ V EE+L LF Q GP+ + ++ P + F+ F H A+A +
Sbjct: 3 TLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALL 62
Query: 67 N 67
N
Sbjct: 63 N 63
Score = 39.2 bits (91), Expect = 2e-04
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L + + L E F G ++ I +D + K K + FV F AI +
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEG-KPKSFGFVCFKHSESVPYAIALL 62
Query: 158 NGQWLGSRSIR 168
NG L R I+
Sbjct: 63 NGIRLYGRPIK 73
Score = 32.6 bits (74), Expect = 0.050
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFG-----TIVDIRVFKEKGYAFVKFTTKETATHAIESI 262
T++ G + EE++ ++F G TI + K K + FV F E+ +AI +
Sbjct: 3 TLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALL 62
Query: 263 HNTDINGHTVK 273
+ + G +K
Sbjct: 63 NGIRLYGRPIK 73
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 44.2 bits (105), Expect = 3e-06
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +++ +E + L+ F FG+I R + K +G+ VS+ A A A+
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDI---RTLYT--ACKHRGFIMVSYYDIRAARRAKRAL 58
Query: 158 NGQWLGSRSI 167
G LG R +
Sbjct: 59 QGTELGGRKL 68
Score = 34.2 bits (79), Expect = 0.014
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVK 35
TL+V N++ +V +E L ALF Q G ++
Sbjct: 3 TLFVRNINSNVEDEELRALFEQFGDIR 29
Score = 30.3 bits (69), Expect = 0.28
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 7/61 (11%)
Query: 217 DLNEELVSKVFSPFGTIVDIR----VFKEKGYAFVKFTTKETATHAIESIHNTDINGHTV 272
++ +E + +F FG DIR K +G+ V + A A ++ T++ G +
Sbjct: 12 NVEDEELRALFEQFG---DIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTELGGRKL 68
Query: 273 K 273
Sbjct: 69 D 69
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 44.3 bits (105), Expect = 3e-06
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 111 TLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTN 170
+L E F+ GEI+ I D +T SKG+A++ F E A+ ++G LG ++ +
Sbjct: 19 SLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVVD 77
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 44.0 bits (104), Expect = 3e-06
Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE-PGNDPYAFLEFVHHTVAATALAAMN 67
TL + NLD +V+ E L ++F G VK +RE P F+EF AA AL AMN
Sbjct: 3 TLVIFNLDPTVSSETLRSIFQVYGDVKE---LRETPCKREQRFVEFFDVRDAAKALRAMN 59
Query: 68 KRVFLEKEMKV 78
+ K + +
Sbjct: 60 GKEISGKPVVI 70
Score = 34.8 bits (80), Expect = 0.007
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
+ +L P + ++TL+ F +G++ R +T + FV F +A A+ AMNG
Sbjct: 6 IFNLDPTVSSETLRSIFQVYGDVKELR-----ETPCKREQRFVEFFDVRDAAKALRAMNG 60
Query: 160 QWLGSRSIR 168
+ + + +
Sbjct: 61 KEISGKPVV 69
Score = 27.5 bits (61), Expect = 2.4
Identities = 12/58 (20%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFK-EKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
++ E + +F +G + ++R ++ FV+F A A+ +++ +I+G V
Sbjct: 12 TVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKEISGKPVV 69
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 78
Score = 44.2 bits (104), Expect = 3e-06
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV LS + +TLKE+F G I RIV D T SKG+ FV F + +A+ A AM
Sbjct: 3 LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59
Query: 158 NGQWLGSRSIRTNWSTRK 175
+ + +++ K
Sbjct: 60 EDGEIDGNKVTLDFAKPK 77
Score = 35.7 bits (82), Expect = 0.004
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTI-----VDIRVFKEKGYAFVKFTTKETATHAIESI 262
T++ G +D EE + + F G+I D KG+ FV F+++E A A E++
Sbjct: 2 TLFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59
Query: 263 HNTDINGHTVKCFWGK 278
+ +I+G+ V + K
Sbjct: 60 EDGEIDGNKVTLDFAK 75
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 44.4 bits (105), Expect = 4e-06
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 14/78 (17%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G+L + L+E FG I +IV++ K AFV F+ A A +T +
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKVVTTL 59
Query: 158 NGQWLGSRSIRTNWSTRK 175
++++R+
Sbjct: 60 --------PCEPDYASRR 69
Score = 39.7 bits (93), Expect = 1e-04
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
VY G + +EE + + FG I I++ KEK AFV F + A + ++ + +
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTL-PCEPD 64
Query: 269 GHTVKCFWGKE 279
+ + F+GK+
Sbjct: 65 YASRRIFYGKD 75
Score = 37.0 bits (86), Expect = 0.001
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 16/76 (21%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM--- 66
+Y+GNL S +EE L + GP+ K+++E + FVH A A+ +
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKN------IAFVHFLSIANAIKVVTTL 59
Query: 67 -------NKRVFLEKE 75
++R+F K+
Sbjct: 60 PCEPDYASRRIFYGKD 75
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 72
Score = 43.8 bits (104), Expect = 4e-06
Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
+FV +L + L++ F+ GEI++ R+V++ + KSKGYA+V F + + A
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA 56
Score = 39.2 bits (92), Expect = 2e-04
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIR-VF----KEKGYAFVKFTTKETATHA 258
TV+ + E+ + K+FS G I D+R V K KGYA+V+F +E+ A
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEA 56
Score = 36.9 bits (86), Expect = 0.001
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALA 64
T++V NLD SV E+ L LFS+ G + ++++ YA++EF + AL
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK 58
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 84
Score = 44.1 bits (104), Expect = 4e-06
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDP------QTLKSKGYAFVSFVKKAEAE 151
+FV +L+ Q L +AF R+ P QTL S G+ FV F K +A+
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTL-SMGFGFVGFKTKEQAQ 61
Query: 152 NAITAMNGQWLGSRSIRTNWSTR 174
A+ AM+G L ++ +S R
Sbjct: 62 AALKAMDGFVLDGHTLVVKFSHR 84
Score = 32.9 bits (75), Expect = 0.047
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 243 GYAFVKFTTKETATHAIESIHNTDINGHTV 272
G+ FV F TKE A A++++ ++GHT+
Sbjct: 48 GFGFVGFKTKEQAQAALKAMDGFVLDGHTL 77
Score = 31.7 bits (72), Expect = 0.11
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 12/83 (14%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP----------YAFLEFVHHTV 58
TL+V NL+ S T + L F + +V +P DP + F+ F
Sbjct: 2 TLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKP--DPKRPGQTLSMGFGFVGFKTKEQ 59
Query: 59 AATALAAMNKRVFLEKEMKVNWA 81
A AL AM+ V + V ++
Sbjct: 60 AQAALKAMDGFVLDGHTLVVKFS 82
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM2
of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Overexpression of hnRNP
A2/B1 has been described in many cancers. It functions
as a nuclear matrix protein involving in RNA synthesis
and the regulation of cellular migration through
alternatively splicing pre-mRNA. It may play a role in
tumor cell differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 80
Score = 43.9 bits (103), Expect = 4e-06
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
+FVG + + E L++ F +G+I I+ D Q+ K +G+ FV+F
Sbjct: 3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49
Score = 33.1 bits (75), Expect = 0.030
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
++ GG +D E + F +G I I + K++G+ FV F + +
Sbjct: 3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQK 62
Query: 263 HNTDINGHTVK 273
++T INGH +
Sbjct: 63 YHT-INGHNAE 72
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 43.9 bits (104), Expect = 5e-06
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRT 169
L++ F FG I + I+ + + SKG+ FV+F A+A+ A ++G + R I
Sbjct: 15 PDLRQMFGQFGPILDVEIIFNER--GSKGFGFVTFANSADADRAREKLHGTVVEGRKIEV 72
Query: 170 NWST 173
N +T
Sbjct: 73 NNAT 76
Score = 38.9 bits (91), Expect = 3e-04
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 227 FSPFGTIVDIR-VFKE---KGYAFVKFTTKETATHAIESIHNTDING 269
F FG I+D+ +F E KG+ FV F A A E +H T + G
Sbjct: 21 FGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHGTVVEG 67
Score = 31.6 bits (72), Expect = 0.092
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI-REPGNDPYAFLEFVHHTVAATALAAMNK 68
L+V N+ + L +F Q GP+ ++I E G+ + F+ F + A A ++
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHG 62
Query: 69 RVFLEKEMKVNWAS 82
V ++++VN A+
Sbjct: 63 TVVEGRKIEVNNAT 76
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 44.2 bits (104), Expect = 5e-06
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVA 59
D+ L++GNLD +V+E L F + G ++ VI+ P YAFL+F + +A
Sbjct: 4 DQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKFQNLDMA 62
Query: 60 ATALAAMNKRVFLEKEMKVNWA 81
A AM+ RV +K+ +
Sbjct: 63 HRAKVAMSGRVIGRNPIKIGYG 84
Score = 40.7 bits (95), Expect = 9e-05
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 1/84 (1%)
Query: 88 PKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKK 147
P+ D ++F+G+L + L+ AF +G I I R P + YAF+ F
Sbjct: 1 PEDDQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKR-PARGQGGAYAFLKFQNL 59
Query: 148 AEAENAITAMNGQWLGSRSIRTNW 171
A A AM+G+ +G I+ +
Sbjct: 60 DMAHRAKVAMSGRVIGRNPIKIGY 83
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 43.8 bits (104), Expect = 5e-06
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L I+ L++ F FG I++ ++ K + + FV + + EA+ A+
Sbjct: 3 LIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDG-KFRKFGFVGYKTEEEAQKALKHF 61
Query: 158 NGQWLGSRSIR 168
N ++ + I
Sbjct: 62 NNSFIDTSKIT 72
Score = 39.2 bits (92), Expect = 2e-04
Identities = 18/58 (31%), Positives = 35/58 (60%), Gaps = 5/58 (8%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRV-FKEKG----YAFVKFTTKETATHAIESIHNTDIN 268
K + E+ + K+F FGTI D+++ + + G + FV + T+E A A++ +N+ I+
Sbjct: 10 KGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFID 67
Score = 31.1 bits (71), Expect = 0.14
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 2/73 (2%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGC--KVIREPGNDPYAFLEFVHHTVAATALAA 65
+ L V NL + E+ L LF G + K ++ + F+ + A AL
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60
Query: 66 MNKRVFLEKEMKV 78
N ++ V
Sbjct: 61 FNNSFIDTSKITV 73
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 43.7 bits (104), Expect = 5e-06
Identities = 18/44 (40%), Positives = 25/44 (56%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
N +++ FS FGTIV+I+V A V+F+T E A A S
Sbjct: 14 NNITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAYRS 57
Score = 28.3 bits (64), Expect = 1.2
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 6/43 (13%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
L E F+ FG I N ++ + A V F EA+ A
Sbjct: 19 LNEHFSKFGTIVNIQV------NYNPESALVQFSTSEEAKKAY 55
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 43.8 bits (103), Expect = 5e-06
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L +I + K+ F +GE S I RD +G+ F+ + AE A +
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 57
Query: 158 NGQWLGSRSIR 168
+G L +R +R
Sbjct: 58 DGTILKNRPLR 68
Score = 34.1 bits (78), Expect = 0.011
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETA 255
C ++ G D+ EE K+F +G ++ + +++G+ F++ ++ A
Sbjct: 2 CRLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLA 50
Score = 32.2 bits (73), Expect = 0.058
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L+VGNL +TEE LF + G + R+ G + F+ T+A A A ++
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRG---FGFIRLESRTLAEIAKAELDGT 60
Query: 70 VFLEKEMKVNW 80
+ + +++ +
Sbjct: 61 ILKNRPLRIRF 71
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 43.5 bits (103), Expect = 6e-06
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKS-KGYAFVSFVKKAEAENAITA 156
I V ++ E + L+E F+ FGE+ R+ + S +G+ FV F+ K +A+ A A
Sbjct: 3 ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKA 62
Query: 157 M 157
+
Sbjct: 63 L 63
Score = 39.7 bits (93), Expect = 2e-04
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 8/55 (14%)
Query: 223 VSKVFSPFGTIVDIRVFKE-------KGYAFVKFTTKETATHAIESI-HNTDING 269
+ ++FS FG + +R+ K+ +G+ FV F TK+ A A +++ H+T + G
Sbjct: 17 LRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHLYG 71
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 43.5 bits (102), Expect = 6e-06
Identities = 18/60 (30%), Positives = 34/60 (56%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG LSP+ + ++E F FGE+ + + D +T K +G+ F++F ++ + +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Score = 30.7 bits (69), Expect = 0.18
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIESI 262
++ GG D EE + + F FG + +D + K +G+ F+ F +E +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 263 -HNTDINGHTVK 273
HN ++ +K
Sbjct: 62 YHNVGLSKCEIK 73
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 43.9 bits (104), Expect = 6e-06
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V +++ L+ F +G I + I D T + +G+A+V F +AE+A+ +
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 158 NGQWLGSRSIRTNWST--RKPP 177
+ R I ++ RK P
Sbjct: 63 DRTRFLGREIEIQFAQGDRKTP 84
Score = 32.3 bits (74), Expect = 0.068
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKV-----IREPGNDPYAFLEFVHHTVAATA 62
T+LYV N+ + + L LF + GP+ + R P +A+++F A A
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRG--FAYVQFEDVRDAEDA 58
Query: 63 LAAMNKRVFLEKEMKVNWA 81
L +++ FL +E+++ +A
Sbjct: 59 LYYLDRTRFLGREIEIQFA 77
Score = 30.0 bits (68), Expect = 0.36
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 227 FSPFGTIVDI------RVFKEKGYAFVKFTTKETATHAIESIHNTDING 269
F +G IVD+ + +G+A+V+F A A+ + T G
Sbjct: 21 FGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLG 69
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 43.8 bits (104), Expect = 7e-06
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+FV L + L++ F+ G+ + C++ P + +G+AFV + +AE A A
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNG-QPRGFAFVEYATAEDAEEAQQA 63
Query: 157 MNGQWLGSRSIR 168
+NG L IR
Sbjct: 64 LNGHSLQGSPIR 75
Score = 39.2 bits (92), Expect = 3e-04
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 6 QPTTLYVGNL-----DVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTV 58
L+V L DVS+ L LFSQ+G C++ P P +AF+E+
Sbjct: 1 HSRCLFVDRLPKTFRDVSI----LRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAED 56
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPG 85
A A A+N ++V++ +PG
Sbjct: 57 AEEAQQALNGHSLQGSPIRVSFG-NPG 82
Score = 33.8 bits (78), Expect = 0.021
Identities = 13/60 (21%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+ ++ K+FS G ++ +G+AFV++ T E A A ++++ + G ++
Sbjct: 16 DVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIR 75
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 43.0 bits (102), Expect = 7e-06
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETA 255
TVY GF KD + + + F FG + +IR+ ++ KG FV+F T+E A
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDA 53
Score = 30.6 bits (70), Expect = 0.20
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 105 PEIETQ-TLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
P+ T ++E F FG+++N R+ RD K KG FV F + +A+ +
Sbjct: 8 PKDATLDDIQEFFEKFGKVNNIRMRRDLDK-KFKGSVFVEFKTEEDAKKFLEK 59
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. hnRNP M functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 43.0 bits (102), Expect = 9e-06
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFV +L + Q LK+ F G + + D +SKG+ V F +A+ AI
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDG-RSKGFGTVLFESPEDAQRAIEMF 59
Query: 158 NGQWLGSRSI 167
NG L R +
Sbjct: 60 NGYDLEGREL 69
Score = 33.8 bits (78), Expect = 0.014
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 226 VFSPFGTIV--DIRV---FKEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+F G ++ D++ + KG+ V F + E A AIE + D+ G ++
Sbjct: 18 LFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELE 70
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 42.7 bits (100), Expect = 1e-05
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWG 277
+ EE++ K F FG + RV K K YAF+ F ++ A A+E ++ ++ G ++ +
Sbjct: 13 VTEEILEKAFGQFGKLE--RVKKLKDYAFIHFDERDGAVKAMEEMNGKELEGENIEIVFA 70
Query: 278 K 278
K
Sbjct: 71 K 71
Score = 39.6 bits (92), Expect = 2e-04
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 8/70 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L+ + + L++AF FG++ + ++D YAF+ F ++ A A+ M
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 55
Query: 158 NGQWLGSRSI 167
NG+ L +I
Sbjct: 56 NGKELEGENI 65
Score = 38.8 bits (90), Expect = 2e-04
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L+V NL +VTEE+L F Q G ++ K +++ YAF+ F A A+ MN +
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-----YAFIHFDERDGAVKAMEEMNGK 58
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 43.0 bits (102), Expect = 1e-05
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 18/90 (20%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRI---VRDPQTLKSKGY--------------A 140
+FVG+L + + LK+ F FG I + R + L K A
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTN 170
+V F ++ AE A+ +NG IR +
Sbjct: 63 YVVFKEEESAEKAL-KLNGTEFEGHHIRVD 91
Score = 34.5 bits (80), Expect = 0.012
Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 26/90 (28%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIR---------------------VFKEKGY- 244
TV+ G ++ + K+F FG I +R +K
Sbjct: 1 RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60
Query: 245 -AFVKFTTKETATHAIESIHN-TDINGHTV 272
A+V F +E+A A++ N T+ GH +
Sbjct: 61 NAYVVFKEEESAEKALK--LNGTEFEGHHI 88
Score = 31.1 bits (71), Expect = 0.24
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPV 34
T++VGNL ++ ++ L LF Q GP+
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPI 27
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 and RRM4 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
and is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 82
Score = 42.6 bits (100), Expect = 1e-05
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 209 VYCG-----GFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIH 263
VY G G ++L E+ + K +G I IR+ +EK AF+ F A A+++++
Sbjct: 5 VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILREKACAFINFMNIPNAIAALQTLN 64
Query: 264 NTDINGHTVKCFWGKES 280
V+ +GK+
Sbjct: 65 GKKPYDTIVRINYGKDR 81
Score = 36.4 bits (84), Expect = 0.002
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 98 IFVGDLSPEIETQTLKEA-----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
+++G++S + + L E +GEI + RI L+ K AF++F+ A
Sbjct: 5 VYIGNVSDVGDERNLPEKELRKECEKYGEIESIRI------LREKACAFINFMNIPNAIA 58
Query: 153 AITAMNGQWLGSRSIRTNW 171
A+ +NG+ +R N+
Sbjct: 59 ALQTLNGKKPYDTIVRINY 77
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 42.4 bits (100), Expect = 1e-05
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
IFVG LS +K+ F+ FG++ + ++ D QT + +G+ FV+F + +
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57
Score = 40.1 bits (94), Expect = 9e-05
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG + E+ V K FS FG + D + +K G+ FV F +++ E I
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE-I 60
Query: 263 HNTDINGHTVKC 274
H +IN V+C
Sbjct: 61 HFHEINNKMVEC 72
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 42.4 bits (100), Expect = 1e-05
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G+L L+EAF FGEI + I + + YAF+ + A A+ M
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGG---NPAYAFIQYADIASVVKAMRKM 61
Query: 158 NGQWLGSRSIR 168
+G++LG+ ++
Sbjct: 62 DGEYLGNNRVK 72
Score = 39.3 bits (92), Expect = 2e-04
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TL++GNL+ + T L F + G + + ++ GN YAF+++ A+ M+
Sbjct: 4 TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMD 62
Score = 33.5 bits (77), Expect = 0.021
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG---YAFVKFTTKETATHAIESIHN 264
T++ G K + + F FG I+DI + K+ G YAF+++ + A+ +
Sbjct: 4 TLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDG 63
Query: 265 TDINGHTVK 273
+ + VK
Sbjct: 64 EYLGNNRVK 72
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 42.3 bits (100), Expect = 2e-05
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+ FVG+L L F + + R+VRD +T K KG+ +V F + A+
Sbjct: 2 FTAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE 60
Query: 156 AMNGQWLGSRSIRTN 170
+G RS+R +
Sbjct: 61 -YDGALFDDRSLRVD 74
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM2 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 42.2 bits (99), Expect = 2e-05
Identities = 14/64 (21%), Positives = 29/64 (45%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I+V + + + L+E F ++ + +D + K Y F+ F + A A+ +
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60
Query: 158 NGQW 161
G+W
Sbjct: 61 TGEW 64
Score = 38.7 bits (90), Expect = 3e-04
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIESI 262
+Y GF K L EE + + F + D+ K Y F+KF ++AT A++ I
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 77
Score = 42.2 bits (99), Expect = 2e-05
Identities = 22/72 (30%), Positives = 33/72 (45%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
V +L + +E +G I C +V T SKGY FV ++KK A A + G
Sbjct: 4 VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63
Query: 160 QWLGSRSIRTNW 171
+ LG ++ W
Sbjct: 64 KQLGESTLFAQW 75
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 42.0 bits (99), Expect = 2e-05
Identities = 20/55 (36%), Positives = 26/55 (47%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESI 262
VY G L EE + FS +G I + +EK AFV FT A AI+ +
Sbjct: 5 NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDGV 59
Score = 35.5 bits (82), Expect = 0.005
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G++ + + L+ F+ +GEI + L+ K AFV+F + A AI +
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESV------NYLREKNCAFVNFTNISNAIKAIDGV 59
Score = 33.6 bits (77), Expect = 0.019
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
+Y+GN+D S+TEE L FSQ G ++ +RE FV+ T + A+ A++
Sbjct: 5 NVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKN------CAFVNFTNISNAIKAIDG 58
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 41.9 bits (98), Expect = 2e-05
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 10/71 (14%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGK 278
+E+ + K F F RV K + YAFV FT++E A HA+ +++ T++ G ++
Sbjct: 14 SEDTIKKTFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCIEV---- 69
Query: 279 ESENNSTLAQP 289
TLA+P
Sbjct: 70 ------TLAKP 74
Score = 34.2 bits (78), Expect = 0.013
Identities = 23/61 (37%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGP--VKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
LYV NL + +E+ + F Q P V+ K IR+ YA FVH T A+ AMN
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD-----YA---FVHFTSREDAVHAMN 55
Query: 68 K 68
Sbjct: 56 N 56
Score = 32.3 bits (73), Expect = 0.064
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 11/71 (15%)
Query: 98 IFVGDLSPEIETQTLKEAFAPF--GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
++V +L E T+K+ F F G + + +RD YAFV F + +A +A+
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRD--------YAFVHFTSREDAVHAMN 55
Query: 156 AMNGQWL-GSR 165
+NG L GS
Sbjct: 56 NLNGTELEGSC 66
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM, but
unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might share
similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 41.9 bits (99), Expect = 2e-05
Identities = 17/71 (23%), Positives = 35/71 (49%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V LS + LK+ F+ +G++ +IV + ++ ++ + FV+ EA I +
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 158 NGQWLGSRSIR 168
+ L R I
Sbjct: 62 HRTELHGRVIS 72
Score = 36.9 bits (86), Expect = 0.001
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI---REPGNDPYAFLEFVHHTVAATALAAM 66
L+V L + L LFS+ G V G K++ R PG + F+ AA + +
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 67 NKRVF 71
++
Sbjct: 62 HRTEL 66
Score = 33.9 bits (78), Expect = 0.018
Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 227 FSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHTV 272
FS +G +V ++ + + FV + E A I+ +H T+++G +
Sbjct: 20 FSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVI 71
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 41.8 bits (98), Expect = 2e-05
Identities = 17/65 (26%), Positives = 34/65 (52%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
++ G D+ EE + K+F +G +I + K+KG+ F++ T+ A A + N +
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMPLR 63
Query: 269 GHTVK 273
G ++
Sbjct: 64 GKQLR 68
Score = 34.1 bits (78), Expect = 0.011
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L+VGNL +TEE + LF + G + ++ G + F+ T+A A A ++
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKG---FGFIRLETRTLAEIAKAELDNM 60
Query: 70 VFLEKEMKVNW 80
K+++V +
Sbjct: 61 PLRGKQLRVRF 71
Score = 34.1 bits (78), Expect = 0.011
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L P+I + +++ F +G+ I +D KG+ F+ + AE A +
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAEL 57
Query: 158 NGQWLGSRSIR 168
+ L + +R
Sbjct: 58 DNMPLRGKQLR 68
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 42.0 bits (99), Expect = 2e-05
Identities = 17/63 (26%), Positives = 34/63 (53%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+ +L+ + L++ F+ +G +S + D T K KG+AFV+++ A A +
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64
Query: 158 NGQ 160
+G
Sbjct: 65 DGT 67
Score = 37.4 bits (87), Expect = 0.001
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 7/67 (10%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGC-----KVIREPGNDPYAFLEFVHHTVAATALA 64
L++ NL + TEE L LFS+ GP+ K+ ++P +AF+ ++ A A A
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKG--FAFVTYMIPEHAVKAFA 62
Query: 65 AMNKRVF 71
++ VF
Sbjct: 63 ELDGTVF 69
Score = 30.8 bits (70), Expect = 0.21
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 220 EELVSKVFSPFGTIVDIRV------FKEKGYAFVKFTTKETATHAIESIHNTDING 269
EE + K+FS +G + ++ + K KG+AFV + E A A + T G
Sbjct: 16 EEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAELDGTVFQG 71
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces
cerevisiae protein Nrd1, Schizosaccharomyces pombe
Rpb7-binding protein seb1 and similar proteins. This
subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1
is a novel heterogeneous nuclear ribonucleoprotein
(hnRNP)-like RNA-binding protein encoded by gene NRD1
(for nuclear pre-mRNA down-regulation) from yeast S.
cerevisiae. It is implicated in 3' end formation of
small nucleolar and small nuclear RNAs transcribed by
polymerase II, and plays a critical role in pre-mRNA
metabolism. Nrd1 contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a short arginine-, serine-,
and glutamate-rich segment similar to the regions rich
in RE and RS dipeptides (RE/RS domains) in many metazoan
splicing factors, and a proline- and glutamine-rich
C-terminal domain (P+Q domain) similar to domains found
in several yeast hnRNPs. Disruption of NRD1 gene is
lethal to yeast cells. Its N-terminal domain is
sufficient for viability, which may facilitate
interactions with RNA polymerase II where Nrd1 may
function as an auxiliary factor. By contrast, the RRM,
RE/RS domains, and P+Q domain are dispensable. Seb1 is
an RNA-binding protein encoded by gene seb1 (for seven
binding) from fission yeast S. pombe. It is essential
for cell viability and bound directly to Rpb7 subunit of
RNA polymerase II. Seb1 is involved in processing of
polymerase II transcripts. It also contains one RRM
motif and a region rich in arginine-serine dipeptides
(RS domain).
Length = 79
Score = 41.8 bits (98), Expect = 2e-05
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F G ++ + L+ F FGE+ +C I+ K +AFV + +AENA AM
Sbjct: 6 LFPGGVTFNMIEYDLRSGFGRFGEVQSC-ILN-----NDKRHAFVKMYNRRDAENAREAM 59
Query: 158 NGQWLGSRSIRTNW 171
G +RT W
Sbjct: 60 EQYKSGDMQLRTRW 73
Score = 32.5 bits (74), Expect = 0.044
Identities = 17/70 (24%), Positives = 32/70 (45%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
T++ GG ++ E + F FG + + +K +AFVK + A +A E++
Sbjct: 5 TLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENAREAMEQYKS 64
Query: 268 NGHTVKCFWG 277
++ WG
Sbjct: 65 GDMQLRTRWG 74
Score = 28.7 bits (64), Expect = 1.1
Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
TL+ G + ++ E L + F + G V+ C + + +AF++ + A A AM +
Sbjct: 5 TLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNN---DKRHAFVKMYNRRDAENAREAMEQ 61
Query: 69 RVFLEKEMKVNW 80
+ +++ W
Sbjct: 62 YKSGDMQLRTRW 73
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 41.6 bits (98), Expect = 3e-05
Identities = 23/69 (33%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG-YAFVKFTTKETATHAIESIHNTD 266
+V+ GF + +EE + FS FG ++++ + K+KG YA V+F +KE + +T
Sbjct: 4 SVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVLSEPQHT- 62
Query: 267 INGH--TVK 273
+NGH V+
Sbjct: 63 LNGHRLRVR 71
Score = 27.7 bits (62), Expect = 2.1
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEF 53
+++V +EE L FS GPV VI + YA +EF
Sbjct: 4 SVFVSGFKRGTSEEQLMDYFSAFGPVM--NVIMDKDKGVYAIVEF 46
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 41.6 bits (97), Expect = 3e-05
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 8/70 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L+ + + L+++F+ FG++ + ++D YAFV F ++ A A+ M
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMDEM 55
Query: 158 NGQWLGSRSI 167
NG+ + I
Sbjct: 56 NGKEIEGEEI 65
Score = 41.6 bits (97), Expect = 3e-05
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWG 277
+ EE++ K FS FG + RV K K YAFV F ++ A A++ ++ +I G ++
Sbjct: 13 VTEEILEKSFSEFGKLE--RVKKLKDYAFVHFEERDAAVRAMDEMNGKEIEGEEIEIVLA 70
Query: 278 K 278
K
Sbjct: 71 K 71
Score = 40.4 bits (94), Expect = 8e-05
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L+V NL +VTEE+L FS+ G ++ K +++ YAF+ F A A+ MN +
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-----YAFVHFEERDAAVRAMDEMNGK 58
Query: 70 VFLEKEMKV 78
+E+++
Sbjct: 59 EIEGEEIEI 67
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its median
region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated in
protein shuttling and protein-protein interactions. .
Length = 77
Score = 41.9 bits (98), Expect = 3e-05
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L L+ AF+ +G + I R+P G+AFV F +AE+A+ +
Sbjct: 2 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 56
Query: 158 NGQWLGSRSIRTNWSTRKP 176
+G+ + +R ST P
Sbjct: 57 DGKVICGSRVRVELSTGMP 75
Score = 30.0 bits (67), Expect = 0.36
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
+YVGNL + L FS GP++ + R P +AF+EF A A+ ++ +
Sbjct: 2 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG--FAFVEFEDPRDAEDAVRGLDGK 59
Query: 70 VFLEKEMKV 78
V ++V
Sbjct: 60 VICGSRVRV 68
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 41.6 bits (98), Expect = 3e-05
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I+VG+L +I + +++ F +G I + ++ + + +AFV F +AE+A+
Sbjct: 2 IYVGNLPGDIRERDIEDLFYKYGPIKAIDL-KNRR--RGPPFAFVEFEDPRDAEDAVRGR 58
Query: 158 NGQWLGSRSIR 168
+G +R
Sbjct: 59 DGYDFDGYRLR 69
Score = 38.9 bits (91), Expect = 3e-04
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEF 53
+YVGNL + E + LF + GP+K + P+AF+EF
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEF 45
Score = 37.0 bits (86), Expect = 0.001
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRV---FKEKGYAFVKFTTKETATHAIESIHN 264
+Y G D+ E + +F +G I I + + +AFV+F A A+
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60
Query: 265 TDINGHTVK 273
D +G+ ++
Sbjct: 61 YDFDGYRLR 69
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 41.3 bits (97), Expect = 3e-05
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I+VG+L P+I T+ +++ F +G I + D + + +AFV F +AE+A+
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAIRDI----DLKNRRGPPFAFVEFEDPRDAEDAVYGR 57
Query: 158 NG 159
+G
Sbjct: 58 DG 59
Score = 34.4 bits (79), Expect = 0.009
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG--YAFVKFTTKETATHAIESIHNTD 266
+Y G D+ + + +F +G I DI + +G +AFV+F A A+ D
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGYD 61
Query: 267 INGHTVK 273
+G+ ++
Sbjct: 62 YDGYRLR 68
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 83
Score = 41.8 bits (98), Expect = 3e-05
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRT 169
LK+ F +G++ I R + K G+AFV+ K+ AE A+ NG + R +
Sbjct: 16 VKLKKIFGRYGKVREATIPRK-RGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAV 74
Query: 170 NWSTRK 175
+W+ +K
Sbjct: 75 DWAVQK 80
Score = 37.5 bits (87), Expect = 0.001
Identities = 14/61 (22%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 221 ELVSKVFSPFGTIVDIRVFKEK-----GYAFVKFTTKETATHAIESIHNTDINGHTVKCF 275
+ K+F +G + + + +++ G+AFV ++ A A+E+ + +I+G V
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75
Query: 276 W 276
W
Sbjct: 76 W 76
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 41.4 bits (98), Expect = 4e-05
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 212 GGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHN 264
GG G ++ E + +VF +GT+ D+ + K Y FV +++ E A A ++++
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNG 61
Score = 33.4 bits (77), Expect = 0.025
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 97 HIFV--GDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
H+ V G L + + L F +G + + +V P K Y FVS+ +A A
Sbjct: 3 HLVVANGGLGNGVSREELLRVFEKYGTVED--LVMPPG----KPYCFVSYSSIEDAAAAY 56
Query: 155 TAMNGQ 160
A+NG+
Sbjct: 57 DALNGK 62
Score = 32.6 bits (75), Expect = 0.049
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 10 LYVGN--LDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
L V N L V+ E L +F + G V+ ++ PG PY F+ + AA A A+N
Sbjct: 4 LVVANGGLGNGVSREELLRVFEKYGTVE--DLVMPPGK-PYCFVSYSSIEDAAAAYDALN 60
Query: 68 KRVFLEKEMKV 78
+ +
Sbjct: 61 GKELELPQQNK 71
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, an abundant eukaryotic nuclear RNA-binding protein
that may modulate splice site selection in pre-mRNA
splicing. hnRNP A1 has been characterized as a splicing
silencer, often acting in opposition to an activating
hnRNP H. It silences exons when bound to exonic elements
in the alternatively spliced transcripts of c-src, HIV,
GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle
between the nucleus and the cytoplasm. Thus, it may be
involved in transport of cellular RNAs, including the
packaging of pre-mRNA into hnRNP particles and transport
of poly A+ mRNA from the nucleus to the cytoplasm. The
cytoplasmic hnRNP A1 has high affinity with AU-rich
elements, whereas the nuclear hnRNP A1 has high affinity
with a polypyrimidine stretch bordered by AG at the 3'
ends of introns. hnRNP A1 is also involved in the
replication of an RNA virus, such as mouse hepatitis
virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 41.5 bits (97), Expect = 4e-05
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
IFVG + + E L++ F +G+I I+ D + K +G+AFV+F
Sbjct: 3 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49
Score = 33.0 bits (75), Expect = 0.030
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI------VDIRVFKEKGYAFVKFTTKETATHAIESI 262
++ GG +D E + F +G I D K++G+AFV F ++ +
Sbjct: 3 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 62
Query: 263 HNTDINGH 270
++T +NGH
Sbjct: 63 YHT-VNGH 69
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
or Set1 complex component, is encoded by SET1 from the
fission yeast S. pombe. It is essential for the H3
lysine-4 methylation. in vivo, and plays an important
role in telomere maintenance and DNA repair in an ATM
kinase Rad3-dependent pathway. spSet1p is the homology
counterpart of Saccharomyces cerevisiae Set1p (scSet1p).
However, it is more closely related to Set1 found in
mammalian. Moreover, unlike scSet1p, spSet1p is not
required for heterochromatin assembly in fission yeast.
spSet1p contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 86
Score = 41.6 bits (98), Expect = 4e-05
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKK--------AE 149
I + LSP + ++ F PFGEI + DP+T +S G V+F
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60
Query: 150 AENAITAMNGQWLGSRSIRT 169
A+ A+ +NG+ +G + +R
Sbjct: 61 AKAAVDGLNGRRIGGKRVRV 80
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor and component of
the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RBM15 belongs to the Spen (split
end) protein family, which contain three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralog and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 41.5 bits (97), Expect = 4e-05
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN---DPYAFLEFVHHTVA 59
D+ TL++GNLD++VTE L F + G + I+ PG Y FL+F + +A
Sbjct: 3 DQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVD-IKRPGRGQTSTYGFLKFENLDMA 61
Query: 60 ATALAAMNKRVFLEKEMKVNW 80
A AM+ +V +K+ +
Sbjct: 62 HRAKLAMSGKVLRRNPIKIGY 82
Score = 37.6 bits (87), Expect = 0.001
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G+L + L+ AF FG I+ I R P ++ Y F+ F A A AM
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIKR-PGRGQTSTYGFLKFENLDMAHRAKLAM 68
Query: 158 NGQWLGSRSIRTNWSTRKP 176
+G+ L I+ + P
Sbjct: 69 SGKVLRRNPIKIGYGKATP 87
Score = 28.0 bits (62), Expect = 2.7
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG------YAFVKFTTKETATHAI 259
N T++ G + E + + F FG I ++ + K G Y F+KF + A A
Sbjct: 7 NRTLFLGNLDITVTETDLRRAFDRFGVITEVDI-KRPGRGQTSTYGFLKFENLDMAHRAK 65
Query: 260 ESIHNTDINGHTVKCFWGK 278
++ + + +K +GK
Sbjct: 66 LAMSGKVLRRNPIKIGYGK 84
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 41.1 bits (96), Expect = 4e-05
Identities = 17/47 (36%), Positives = 29/47 (61%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
IFVG + + E L++ F +G+I ++ D Q+ K +G+AFV+F
Sbjct: 3 IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49
Score = 34.2 bits (78), Expect = 0.012
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
++ GG +D E + F +G I I V K++G+AFV F +T +
Sbjct: 3 IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQK 62
Query: 263 HNTDINGH 270
++T INGH
Sbjct: 63 YHT-INGH 69
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family
including yeast cell wall integrity protein scw1, yeast
Whi3 protein, yeast Whi4 protein and similar proteins.
The strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates
septation and cell-wall structure in fission yeast. It
may function as an inhibitor of septum formation, such
that its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3),
a G1 cyclin that promotes transcription of many genes
to trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict
Cln3 synthesis to modulate cell cycle progression.
Moreover, Whi3 plays a key role in cell fate
determination in budding yeast. The RRM domain is
essential for Whi3 function. Whi4 is a partially
redundant homolog of Whi3, also containing one RRM.
Some uncharacterized family members of this subfamily
contain two RRMs; their RRM1 shows high sequence
homology to the RRM of RNA-binding protein with
multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 41.0 bits (97), Expect = 4e-05
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TL+V NL + TEE L LFS+ + K+ + G P F+EF + A A+N
Sbjct: 3 NTLFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGG-PVCFVEFED---VSFATQALN 58
Query: 68 K 68
Sbjct: 59 S 59
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 41.1 bits (97), Expect = 5e-05
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
S PTNC V+ G + + E+ +++ FS +G +V + + +++G A V F E A A+
Sbjct: 4 SMPTNC-VWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQAAVNE 62
Query: 262 IHNTDINGHTVK 273
+ + G ++
Sbjct: 63 MKGRKLGGRKLQ 74
Score = 33.4 bits (77), Expect = 0.025
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 5 SQPTT-LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL 63
S PT +++ LD SVTE+ L FS+ GPV + R+ G A + F A A+
Sbjct: 4 SMPTNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQ---ALVFFDKVEAAQAAV 60
Query: 64 AAMNKRVFLEKEMKV 78
M R ++++V
Sbjct: 61 NEMKGRKLGGRKLQV 75
Score = 28.0 bits (63), Expect = 1.7
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQW 161
L + Q L F+ +G + + I R +G A V F K A+ A+ M G+
Sbjct: 14 GLDESVTEQYLTRHFSRYGPVVHVVIDR------QRGQALVFFDKVEAAQAAVNEMKGRK 67
Query: 162 LGSRSIR 168
LG R ++
Sbjct: 68 LGGRKLQ 74
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 41.1 bits (96), Expect = 5e-05
Identities = 22/61 (36%), Positives = 33/61 (54%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG + ++ L F G I + R++ DP T ++GYAFV+F K A+ A+
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63
Query: 158 N 158
N
Sbjct: 64 N 64
Score = 40.4 bits (94), Expect = 1e-04
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ G +DL E+ + +F G I D+R+ + +GYAFV F TKE A A++
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63
Query: 263 HNTDI 267
+N +I
Sbjct: 64 NNHEI 68
Score = 30.7 bits (69), Expect = 0.20
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP---GNDPYAFLEFVHHTVAATALA 64
T ++VG + + E+ L LF + GP+ +++ +P N YAF+ F A A+
Sbjct: 2 TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK 61
Query: 65 AMN 67
N
Sbjct: 62 LYN 64
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 41.2 bits (97), Expect = 5e-05
Identities = 17/66 (25%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ +L ++ Q L+ P+G++ + RI+RD + +S+G F + + E+ I+
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKG-QSRGVGFARMESREKCEDIISKF 61
Query: 158 NGQWLG 163
NG++L
Sbjct: 62 NGKYLK 67
Score = 39.3 bits (92), Expect = 2e-04
Identities = 12/74 (16%), Positives = 30/74 (40%), Gaps = 7/74 (9%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAI 259
TN +Y ++E+ + + P+G ++ R+ ++ +G F + ++E I
Sbjct: 1 TN--LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDII 58
Query: 260 ESIHNTDINGHTVK 273
+ + G
Sbjct: 59 SKFNGKYLKGEGEP 72
Score = 28.9 bits (65), Expect = 1.1
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN 45
T LY+ NL + + E+ L + G V +++R+
Sbjct: 1 TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKG 38
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in the
system using SV40 DNA. MSSP-2 is identical with Scr3, a
human protein which complements the defect of cdc2
kinase in Schizosaccharomyces pombe. MSSP-2 has been
implied in regulating DNA replication, transcription,
apoptosis induction, and cell-cycle movement, via the
interaction with C-MYC, the product of protooncogene
c-myc. MSSP-2 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 75
Score = 40.9 bits (95), Expect = 5e-05
Identities = 20/60 (33%), Positives = 33/60 (55%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ L P Q L + P+G+I + + + D T K KGY FV F + A+ A+TA+
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63
Score = 28.2 bits (62), Expect = 2.0
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
+Y G ++ + K+ P+G IV + K KGY FV F + A A+ ++
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63
Query: 263 HNTDINGHTVK 273
+ + K
Sbjct: 64 KASGVQAQMAK 74
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52
motif-containing protein 1 (RDM1) and similar proteins.
This subfamily corresponds to the RRM of RDM1, also
termed RAD52 homolog B, a novel factor involved in the
cellular response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 40.9 bits (96), Expect = 5e-05
Identities = 26/79 (32%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 9 TLYVGNLDVSVTEEL----LCALFSQIGPVKGCKVIR-EPGNDP--YAFLEFVHHTVAAT 61
TLYV + +TEE LC+ FSQ G + KV P YAF++F A+
Sbjct: 2 TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61
Query: 62 ALAAMNKRVFLEKE-MKVN 79
A A N + + +KV
Sbjct: 62 AQKACNGKWLFQGSPLKVR 80
Score = 35.5 bits (82), Expect = 0.005
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 98 IFVGDLSPEIETQ----TLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
++V +SP++ + +L AF+ FG + + ++ + YAFV F A A
Sbjct: 3 LYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASRA 62
Query: 154 ITAMNGQWL 162
A NG+WL
Sbjct: 63 QKACNGKWL 71
Score = 31.6 bits (72), Expect = 0.12
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 220 EELVSKVFSPFGTIVDIRVFKEKG------YAFVKFTTKETATHA 258
E + FS FG + ++VF YAFVKF + A+ A
Sbjct: 18 YESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASRA 62
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. The family
also includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 40.8 bits (96), Expect = 6e-05
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN- 158
V +LSP + + L++AF+ FGE+ ++ D + +S G V F +K A+ AI +
Sbjct: 4 VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRG-RSTGEGIVEFSRKPGAQAAIKRCSE 62
Query: 159 GQWLGSRSIR 168
G +L + S R
Sbjct: 63 GCFLLTASPR 72
Score = 36.9 bits (86), Expect = 0.001
Identities = 23/69 (33%), Positives = 29/69 (42%), Gaps = 8/69 (11%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVI-----REPGNDPYAFLEFVHHTVAATAL 63
L V NL V+ ELL FSQ G V+ VI R G +EF A A+
Sbjct: 1 ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGE---GIVEFSRKPGAQAAI 57
Query: 64 AAMNKRVFL 72
++ FL
Sbjct: 58 KRCSEGCFL 66
Score = 30.0 bits (68), Expect = 0.39
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 221 ELVSKVFSPFG------TIVDIRVFKEKGYAFVKFTTKETATHAIESI 262
EL+ + FS FG IVD R + G V+F+ K A AI+
Sbjct: 14 ELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEFSRKPGAQAAIKRC 60
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 40.8 bits (95), Expect = 6e-05
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L ++ + LKE F+ G + I+ D KS+G V+F + EA AI+
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDG-KSRGIGTVTFEQPIEAVQAISMF 61
Query: 158 NGQWLGSR 165
NGQ L R
Sbjct: 62 NGQLLFDR 69
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 40.8 bits (95), Expect = 6e-05
Identities = 21/82 (25%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +++ + L+ F +G I + + D T + +G+A++ F +AE+A+ +
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 158 NGQWLGSRSIRTNWST--RKPP 177
N +W+ R I ++ RK P
Sbjct: 63 NRKWVCGRQIEIQFAQGDRKTP 84
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM1 of FCA, a gene controlling
flowering time in Arabidopsis, encoding a flowering time
control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains), and
a WW protein interaction domain. .
Length = 80
Score = 40.7 bits (95), Expect = 7e-05
Identities = 19/63 (30%), Positives = 33/63 (52%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG + I Q ++ F G + I++D +T +G FV + + EA+ AI A+
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61
Query: 158 NGQ 160
+ Q
Sbjct: 62 HNQ 64
Score = 36.1 bits (83), Expect = 0.003
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ G + + E+ V +F G ++++ + K+K G FVK++T++ A AI ++
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61
Query: 263 HN 264
HN
Sbjct: 62 HN 63
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 40.6 bits (96), Expect = 7e-05
Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIR-----VFKEKGYAFVKFTTKETATHAIES 261
T++ F ++ + +F +G I+ IR K + + +V+FT+ E+A A+
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60
Query: 262 IHNTDINGHT 271
++ G+
Sbjct: 61 LNGKLGEGYK 70
Score = 36.0 bits (84), Expect = 0.003
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDP--QTLKSKGYAFVSFVKKAEAENAIT 155
++V + P + +++ F +GEI + +R P + K++ + +V F A A+
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAAVA 59
Query: 156 AMNGQWLGSRSI 167
+NG+ +
Sbjct: 60 LLNGKLGEGYKL 71
Score = 27.9 bits (63), Expect = 2.3
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG-----NDPYAFLEFVHHTVAATA 62
+TL+V N S + + LF Q G + IR P + +++F AA A
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILS---IRFPSLRFNKTRRFCYVQFTSPESAAAA 57
Query: 63 LAAMNKR 69
+A +N +
Sbjct: 58 VALLNGK 64
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 40.8 bits (95), Expect = 7e-05
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F L+ I + L+E F+ G++ + R++ D + +SKG A+V FV + AI +
Sbjct: 4 VFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI-GL 62
Query: 158 NGQWL 162
GQ +
Sbjct: 63 TGQRV 67
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 40.4 bits (94), Expect = 7e-05
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFV +L ++ + LKE F+ G + I D KS+G V+F + EA AI+
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDG-KSRGMGTVTFEQPIEAVQAISMF 61
Query: 158 NGQWLGSRSI 167
NGQ+L R +
Sbjct: 62 NGQFLFDRPM 71
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 40.5 bits (95), Expect = 7e-05
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRV---FKEKGYAFVKFTTKETATHAIESIHN 264
TVY G D+ E V +F +G IVDI + + GYAF++F A AI
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60
Query: 265 TDINGHTVK 273
D +G ++
Sbjct: 61 YDFDGQRLR 69
Score = 36.3 bits (84), Expect = 0.002
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 6/48 (12%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKV---IREPGNDPYAFLEF 53
T+YVGNL + E + LF + GP+ + R PG YAF+EF
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPG---YAFIEF 45
Score = 35.5 bits (82), Expect = 0.004
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L +I + +++ F +G I + + P + GYAF+ F +AE+AI
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPP---RPPGYAFIEFEDARDAEDAIRGR 58
Query: 158 NG 159
+G
Sbjct: 59 DG 60
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 40.6 bits (96), Expect = 8e-05
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 135 KSKGYAFVSFVKKAEAENAITAMNG 159
K+KGYAFV F EA+ A+ A+NG
Sbjct: 48 KTKGYAFVEFATPEEAKEAVKALNG 72
Score = 39.5 bits (93), Expect = 2e-04
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 7/49 (14%)
Query: 223 VSKVFSPFGTIVDIRVF-------KEKGYAFVKFTTKETATHAIESIHN 264
+ K+FS FG + ++ K KGYAFV+F T E A A+++++
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNG 72
>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM1 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two of which are followed by a glutamine-rich
stretch that may be involved in transcriptional
activity. In addition, NGR1 has an asparagine-rich
region near the carboxyl terminus which also harbors a
methionine-rich region. The subgroup also includes
NAM8, a putative RNA-binding protein that acts as a
suppressor of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 81
Score = 40.5 bits (95), Expect = 8e-05
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIG--PVKGCKVIRE---PGNDPYAFLEFVHHTVAATAL 63
TL++G+L+ + E + +++ +G PV KVIR N Y F+EF A AL
Sbjct: 1 TLWMGDLEPWMDENFIKQVWASLGLEPVN-VKVIRSRNSGLNAGYCFVEFPSPHAAQNAL 59
Query: 64 AAMNKRV-FLEKEMKVNWASS 83
+ + + K+NWAS
Sbjct: 60 SLNGTPIPNSNRTFKLNWASG 80
Score = 38.6 bits (90), Expect = 4e-04
Identities = 22/80 (27%), Positives = 45/80 (56%), Gaps = 4/80 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEIS-NCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++GDL P ++ +K+ +A G N +++R + + GY FV F A+NA+ +
Sbjct: 2 LWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNAL-S 60
Query: 157 MNGQWL--GSRSIRTNWSTR 174
+NG + +R+ + NW++
Sbjct: 61 LNGTPIPNSNRTFKLNWASG 80
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 40.4 bits (95), Expect = 8e-05
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
IFVG L P + L++ F+ FG ++ ++ D + + +G+ F++F E+E++
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF----ESEDS 56
Query: 154 I 154
+
Sbjct: 57 V 57
Score = 38.9 bits (91), Expect = 3e-04
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
++ GG ++ E + K FS FGT+ ++ V + +G+ F+ F ++++ + +
Sbjct: 5 IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV-NE 63
Query: 263 HNTDINGHTVKC 274
H DING V+
Sbjct: 64 HFHDINGKKVEV 75
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for growth.
Srp1p is closely related to the SR protein family found
in metazoa. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine hinge and a RS
domain in the middle, and a C-terminal domain. Some
family members also contain another RRM domain.
Length = 78
Score = 40.2 bits (94), Expect = 8e-05
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIV--DI---RVFKEKGYAFVKFTTKETATHAIESI 262
T+Y GFG + ++ F +G +V DI R F+ + +AFV++ + A A E +
Sbjct: 1 TLYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEM 60
Query: 263 HN 264
H
Sbjct: 61 HG 62
Score = 33.6 bits (77), Expect = 0.021
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 10/59 (16%)
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
DL+ E F +G + C I P+T +S+ +AFV + +AE+A M+G+
Sbjct: 15 DLAYE---------FERYGRLVRCDI-PPPRTFQSRPFAFVEYESHRDAEDAYEEMHGR 63
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 40.7 bits (96), Expect = 9e-05
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 18/70 (25%)
Query: 103 LSPEIETQTLKEAFAPFGE---------ISNCRIVRDPQTL------KSKGYAFVSFVKK 147
L ++ + LKE F I +I+RD + + KSKGY FV F
Sbjct: 8 LPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFT-- 65
Query: 148 AEAENAITAM 157
E+A+ A+
Sbjct: 66 -NHEHALKAL 74
Score = 40.3 bits (95), Expect = 1e-04
Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 18/79 (22%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQI---------GPVKGCKVIRE-----PGNDP----YA 49
T L + NL SV E+ L LF + +K K++R+ P Y
Sbjct: 1 TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60
Query: 50 FLEFVHHTVAATALAAMNK 68
F+EF +H A AL A+N
Sbjct: 61 FVEFTNHEHALKALRALNN 79
Score = 30.3 bits (69), Expect = 0.50
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 240 KEKGYAFVKFTTKETATHAIESIHN 264
K KGY FV+FT E A A+ +++N
Sbjct: 55 KSKGYGFVEFTNHEHALKALRALNN 79
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 40.6 bits (94), Expect = 1e-04
Identities = 21/67 (31%), Positives = 36/67 (53%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
D + ++++ L P Q L + P+G+I + + + D T K KGY FV F A A
Sbjct: 3 DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAA 62
Query: 151 ENAITAM 157
+ A++A+
Sbjct: 63 QKAVSAL 69
Score = 29.8 bits (66), Expect = 0.50
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 8/81 (9%)
Query: 199 YNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTK 252
++Q S TN +Y G + ++ + K+ P+G IV + K KGY FV F +
Sbjct: 2 WDQLSKTN--LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 59
Query: 253 ETATHAIESIHNTDINGHTVK 273
A A+ ++ + + K
Sbjct: 60 AAAQKAVSALKASGVQAQMAK 80
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 75
Score = 40.1 bits (94), Expect = 1e-04
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
H++VG+L + + + E F +G + + +I+ + AFV FV A+ A A
Sbjct: 1 HLWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA-AFVDFVDIKSAQKAHNA 59
Query: 157 MNGQWLGSRSIRTNWSTR 174
+N +G R +RT+++
Sbjct: 60 VNK--MGDRDLRTDYNEP 75
Score = 33.2 bits (76), Expect = 0.025
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND--PYAFLEFVHHTVAATALAAMN 67
L+VGNL +V EE + F + G V+ K++ + G+D AF++FV A A A+N
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKAHNAVN 61
Query: 68 K 68
K
Sbjct: 62 K 62
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 39.8 bits (93), Expect = 1e-04
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 11/78 (14%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG----YAFVSFVKKAEAENA 153
I+VG+L ++ + L++ F +G I RD + LK++ +AFV F +AE+A
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRI------RDIE-LKNRRGLVPFAFVRFEDPRDAEDA 54
Query: 154 ITAMNGQWLGSRSIRTNW 171
+ NG G +R +
Sbjct: 55 VFGRNGYDFGQCRLRVEF 72
Score = 32.5 bits (74), Expect = 0.046
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEF 53
+YVGNL V E+ L LF + G ++ ++ G P+AF+ F
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRF 45
Score = 29.4 bits (66), Expect = 0.64
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG---YAFVKFTTKETATHAI 259
+Y G D+ E+ + +F +G I DI + +G +AFV+F A A+
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAV 55
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), an RNA-binding protein associated with the U1
snRNP, a small RNA-protein complex involved in pre-mRNA
splicing. U1A binds with high affinity and specificity
to stem-loop II (SLII) of U1 snRNA. It is predominantly
a nuclear protein and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large number
of non-snRNP proteins, including polypyrimidine tract
binding protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an important
role in virus replication. U1A contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and may
be free to bind other proteins. U1A also contains a
proline-rich region, and a nuclear localization signal
(NLS) in the central domain that is responsible for its
nuclear import. .
Length = 89
Score = 40.4 bits (94), Expect = 1e-04
Identities = 23/79 (29%), Positives = 45/79 (56%), Gaps = 7/79 (8%)
Query: 98 IFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
I++ +L+ +I+ LK++ F+ FG+I + + R +LK +G AFV F + + A NA
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 62
Query: 154 ITAMNGQWLGSRSIRTNWS 172
+ +M G + +R ++
Sbjct: 63 LRSMQGFPFYDKPMRIQYA 81
Score = 37.3 bits (86), Expect = 0.001
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + + ++ + K +FS FG I+DI R K +G AFV F +AT+A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62
Query: 259 IESIH 263
+ S+
Sbjct: 63 LRSMQ 67
Score = 33.1 bits (75), Expect = 0.037
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 9 TLYVGNLDVSVT-EEL---LCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA 64
T+Y+ NL+ + +EL L A+FS+ G + V R AF+ F + A AL
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64
Query: 65 AMNKRVFLEKEMKVNWASS 83
+M F +K M++ +A +
Sbjct: 65 SMQGFPFYDKPMRIQYAKT 83
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 39.9 bits (94), Expect = 1e-04
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 216 KDLNEELVSKVFSPFGTIVD-IRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKC 274
+NEE + F G V I +F + A V+F + A A S++ + G T+K
Sbjct: 10 DTVNEEQIKAFFEKIGPDVRKIELFPDHEGALVEFESPSDAGKASLSLNGSQFGGKTIKI 69
Score = 32.2 bits (74), Expect = 0.057
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGP-VKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
T+ + N+ +V EE + A F +IGP V+ ++ + A +EF + A A ++
Sbjct: 1 RTIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG---ALVEFESPSDAGKASLSL 57
Query: 67 NKRVFLEKEMKV 78
N F K +K+
Sbjct: 58 NGSQFGGKTIKI 69
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM2 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 39.6 bits (92), Expect = 1e-04
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
T L+VGN+ S T + L A F + GPV C ++++ YAF+ A A+ ++
Sbjct: 1 TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD-----YAFVHMERAEDAVEAIRGLD 55
Query: 68 KRVFLEKEMKV 78
F K M V
Sbjct: 56 NTEFQGKRMHV 66
Score = 38.9 bits (90), Expect = 2e-04
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 9/67 (13%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM-N 158
VG++S Q L+ F +G + C IV+D YAFV + +A AI + N
Sbjct: 5 VGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDN 56
Query: 159 GQWLGSR 165
++ G R
Sbjct: 57 TEFQGKR 63
Score = 33.8 bits (77), Expect = 0.012
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDING 269
N+EL +K F +G +++ + K+ YAFV E A AI + NT+ G
Sbjct: 14 NQELRAK-FEEYGPVIECDIVKD--YAFVHMERAEDAVEAIRGLDNTEFQG 61
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 39.5 bits (92), Expect = 1e-04
Identities = 15/34 (44%), Positives = 24/34 (70%)
Query: 240 KEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+ KGYAFV+F + E A A+ S +NT+I G +++
Sbjct: 36 RPKGYAFVEFESAEDAKEALNSCNNTEIEGRSIR 69
Score = 34.1 bits (78), Expect = 0.013
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTL-KSKGYAFVSFVKKAEAENAITA 156
+ V +LS +L+E F I R PQ + KGYAFV F +A+ A+ +
Sbjct: 4 LVVNNLSYSASEDSLQEVFEKATSI------RIPQNNGRPKGYAFVEFESAEDAKEALNS 57
Query: 157 MNGQWLGSRSIR 168
N + RSIR
Sbjct: 58 CNNTEIEGRSIR 69
Score = 30.3 bits (68), Expect = 0.27
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 10/65 (15%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND----PYAFLEFVHHTVAATALA 64
L V NL S +E+ L +F + IR P N+ YAF+EF A AL
Sbjct: 3 VLVVNNLSYSASEDSLQEVF------EKATSIRIPQNNGRPKGYAFVEFESAEDAKEALN 56
Query: 65 AMNKR 69
+ N
Sbjct: 57 SCNNT 61
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 39.6 bits (93), Expect = 1e-04
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G L + ++ F +G I LK+ G+ FV F +A++A+ +
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREI-------NLKN-GFGFVEFEDPRDADDAVYEL 53
Query: 158 NGQWLGSRSI 167
NG+ L +
Sbjct: 54 NGKELCGERV 63
Score = 33.8 bits (78), Expect = 0.014
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
VY G E V + F +G I +I + + G+ FV+F A A+ ++ ++
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREINL--KNGFGFVEFEDPRDADDAVYELNGKELC 59
Query: 269 GHTV 272
G V
Sbjct: 60 GERV 63
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with wild
type of survival motor neuron (SMN) proteins directly,
further providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, and in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; it binds RNA
through its RRM domains. .
Length = 79
Score = 39.6 bits (92), Expect = 1e-04
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+FVG + ++ L F G I + R++ DP + +++GYAF++F K A+ A+
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60
Score = 38.4 bits (89), Expect = 5e-04
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESI 262
V+ G +DL E+ + +F G I D+R+ + +GYAF+ F KE A A++
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63
Query: 263 HNTDI 267
N +I
Sbjct: 64 DNYEI 68
Score = 32.2 bits (73), Expect = 0.071
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP---GNDPYAFLEFVHHTVAATAL 63
T ++VG + + E+ L LF + GP+ +++ +P N YAF+ F A A+
Sbjct: 2 TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 39.7 bits (93), Expect = 2e-04
Identities = 19/78 (24%), Positives = 27/78 (34%), Gaps = 12/78 (15%)
Query: 213 GFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD------ 266
G DL E + F FG + V FV+F T+E A +I
Sbjct: 9 GVEDDLPEYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKFAAAISENGLNAGLS 68
Query: 267 ------INGHTVKCFWGK 278
+ G ++ WGK
Sbjct: 69 RGGLLVLEGCPLRVAWGK 86
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subgroup corresponds
to the RRM2 in a family that represents a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), at
their N-terminus, and an RS domain at their C-terminus.
Length = 70
Score = 39.1 bits (91), Expect = 2e-04
Identities = 15/41 (36%), Positives = 29/41 (70%), Gaps = 2/41 (4%)
Query: 227 FSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
F P+G +V++R+ + +AFV++ T+E AT A+ES + + +
Sbjct: 21 FEPYGKLVNVRI--RRNFAFVQYETQEDATKALESTNMSKV 59
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 43.1 bits (101), Expect = 2e-04
Identities = 37/138 (26%), Positives = 63/138 (45%), Gaps = 16/138 (11%)
Query: 45 NDPYAFLEFVHHTVAATALAA-MNKRVFL-EKEMKVNWASSPGNQPKQDTSNHYHI-FVG 101
N +AF+E+ H AA A M R+ L + V+WA P + +D I +V
Sbjct: 181 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAE-PEEEVDEDVMAKVKILYVR 239
Query: 102 DLSPEIETQTLKEAFAPF--GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
+L + ++++F+ F G++ + +RD YAFV F + +A A+ +NG
Sbjct: 240 NLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------YAFVHFEDREDAVKAMDELNG 291
Query: 160 QWLGSRSIRTNWSTRKPP 177
+ L I + KP
Sbjct: 292 KELEGSEIEVTLA--KPV 307
Score = 42.7 bits (100), Expect = 3e-04
Identities = 76/395 (19%), Positives = 136/395 (34%), Gaps = 68/395 (17%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE--PGNDPYAFLEFVHHTVAATALAA 65
++VG + + E+ L LF + GP+ +++ + N YAF+ F A A+
Sbjct: 59 CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKL 118
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTS-NHYHIFVGDLSPEIETQTLKEAFAPFGE-IS 123
+N N+ PG S ++ +FVG + + + + E F+ E +
Sbjct: 119 LN-----------NYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVV 167
Query: 124 NCRIVRDP-QTLKSKGYAFVSFVK-KAEAENAITAMNGQ-WLGSRSIRTNWSTRKPPAMT 180
+ + K++G+AFV + +A A M G+ L I +W+ +P
Sbjct: 168 DVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWA--EPEEEV 225
Query: 181 NERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK 240
+E + V N + T EE++ K FS F RV K
Sbjct: 226 DEDVMA-----KVKILYVRNLMTTTT-------------EEIIEKSFSEFKPGKVERVKK 267
Query: 241 EKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWG----KESENNSTLAQPSAPTTPQ 296
+ YAFV F +E A A++ ++ ++ G ++ K+S T Q
Sbjct: 268 IRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQ 327
Query: 297 PNSTAPQFPYI----YNQQMGYWYPQAAA----YTATAAQL--------------PQQFY 334
+ Y Y+Y A + + + +
Sbjct: 328 AARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIRGRGRGGAPSRAAGGRGYP 387
Query: 335 QYGQLGYPQGY----VGMVGRQVPGWQGIPGAQPT 365
YG Y Y + + PG + T
Sbjct: 388 PYGYEAYYGDYYGYHDYRGKYEDKYYGYDPGMELT 422
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding
Raly-like protein (RALYL). This subgroup corresponds to
the RRM of RALYL, also termed heterogeneous nuclear
ribonucleoprotein C-like 3, or hnRNP core protein C-like
3, a putative RNA-binding protein that shows high
sequence homology with Raly, an RNA-binding protein
playing a critical role in embryonic development. The
biological role of RALYL remains unclear. Like Raly,
RALYL contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain. .
Length = 69
Score = 38.8 bits (90), Expect = 2e-04
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 98 IFVGDLSPEIETQTLKEA-FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G+L+ I + EA FA +G+I C + KGYAFV ++ + A A+
Sbjct: 4 VFIGNLNTAIVKKADIEAIFAKYGKIVGCSV--------HKGYAFVQYISERHARAAVAG 55
Query: 157 MNGQWLGSRSIRTN 170
N + + + + N
Sbjct: 56 ENARIIAGQPLDIN 69
Score = 36.9 bits (85), Expect = 0.001
Identities = 18/73 (24%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 8 TTLYVGNLDVSVTEEL-LCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
+ +++GNL+ ++ ++ + A+F++ G + GC V + YAF++++ A A+A
Sbjct: 2 SRVFIGNLNTAIVKKADIEAIFAKYGKIVGCSV-----HKGYAFVQYISERHARAAVAGE 56
Query: 67 NKRVFLEKEMKVN 79
N R+ + + +N
Sbjct: 57 NARIIAGQPLDIN 69
Score = 30.8 bits (69), Expect = 0.18
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 11/59 (18%)
Query: 206 NCTVYCGGFGKDLNEELVSK-----VFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
N V+ G +LN +V K +F+ +G IV V KGYAFV++ ++ A A+
Sbjct: 1 NSRVFIG----NLNTAIVKKADIEAIFAKYGKIVGCSV--HKGYAFVQYISERHARAAV 53
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 39.0 bits (91), Expect = 2e-04
Identities = 17/52 (32%), Positives = 33/52 (63%), Gaps = 5/52 (9%)
Query: 223 VSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIHNTDING 269
V +FS +G + +RV K+ +G+AFV+F+T + A +A+ ++ +T + G
Sbjct: 17 VRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKDTHLLG 68
Score = 38.3 bits (89), Expect = 5e-04
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTL--KSKGYAFVSFVKKAEAENAIT 155
I V +L E + ++ F+ +G++ + VR P+ ++G+AFV F EA NA+
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQL---KSVRVPKKFDQSARGFAFVEFSTAKEALNAMN 59
Query: 156 AMNGQWLGSRSIRTNWS 172
A+ L R + ++
Sbjct: 60 ALKDTHLLGRRLVLQYA 76
Score = 28.2 bits (63), Expect = 1.4
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAA 65
T + V NL T++ + LFS G +K +V ++ +AF+EF A A+ A
Sbjct: 1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60
Query: 66 MNKRVFLEKEMKVNWA 81
+ L + + + +A
Sbjct: 61 LKDTHLLGRRLVLQYA 76
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 38.9 bits (90), Expect = 2e-04
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGP--VKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
LYV NL +S TEE + A F++ P V+ K +R+ YAF+ F + A A++ MN
Sbjct: 4 LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD-----YAFVHFFNREDAVAAMSVMN 58
Query: 68 KRVFLEKEMKVNWA 81
+ ++V A
Sbjct: 59 GKCIDGASIEVTLA 72
Score = 31.6 bits (71), Expect = 0.099
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 98 IFVGDLSPEIETQTLKEAFAPF--GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
++V +L +T+K F F G + + +RD YAFV F + +A A++
Sbjct: 4 LYVRNLMISTTEETIKAEFNKFKPGVVERVKKLRD--------YAFVHFFNREDAVAAMS 55
Query: 156 AMNGQWLGSRSI 167
MNG+ + SI
Sbjct: 56 VMNGKCIDGASI 67
Score = 30.8 bits (69), Expect = 0.21
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 220 EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKE 279
EE + F+ F V RV K + YAFV F +E A A+ ++ I+G +++
Sbjct: 15 EETIKAEFNKFKPGVVERVKKLRDYAFVHFFNREDAVAAMSVMNGKCIDGASIEV----- 69
Query: 280 SENNSTLAQP 289
TLA+P
Sbjct: 70 -----TLAKP 74
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 38.9 bits (91), Expect = 2e-04
Identities = 22/74 (29%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF-----VKKA 148
+H +FVG+L +I LKE F FG + RI + + FV F V+K
Sbjct: 3 SH-QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61
Query: 149 EAENAITAMNGQWL 162
A I L
Sbjct: 62 LANKPIYFRGDHRL 75
Score = 33.1 bits (76), Expect = 0.030
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
D Q L+VGNL +TE+ L F + G V ++ + G + F+ F
Sbjct: 2 DSHQ---LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAV 58
Query: 60 ATALAAM 66
LA
Sbjct: 59 QKILANK 65
Score = 32.4 bits (74), Expect = 0.059
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG------YAFVKFTTKETATH 257
P + ++ G D+ E+ + + F FG ++++R+ + G + FV F E
Sbjct: 1 PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60
Query: 258 AIESIHNTDINGHTV 272
+ + H +
Sbjct: 61 ILANKPIYFRGDHRL 75
>gnl|CDD|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM1 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa,which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 74
Score = 39.0 bits (91), Expect = 3e-04
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 208 TVYCGGFGKDLN-EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETAT--HAIESIHN 264
TVY G + +EL+S V G I ++R+ EK AF+ F AT H+ +
Sbjct: 3 TVYLGNLPPNTTVKELLSHV--RSGPIENVRILPEKNCAFISFLDPSAATAFHSDAILKR 60
Query: 265 TDINGHTVKCFWGK 278
I G +K WGK
Sbjct: 61 LSIKGVELKIGWGK 74
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 39.1 bits (92), Expect = 3e-04
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG++ + +++ G++ + + V+DP T K K + F F + E A+ A+
Sbjct: 3 VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEF---EDPEGALRAL 59
Score = 37.6 bits (88), Expect = 9e-04
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVAATALA 64
TT++VGN+ V+++ + L + G V K +++P + F EF A AL
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60
Query: 65 AMNKRVFLEKEMKVN 79
+N K++ V
Sbjct: 61 LLNGLELGGKKLLVK 75
Score = 29.1 bits (66), Expect = 0.91
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIV------DIRVFKEKGYAFVKFTTKETATHAIE 260
TV+ G + ++++ + K+ G ++ D K K + F +F E A A+
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60
Query: 261 SIHNTDINGH--TVKC 274
++ ++ G VK
Sbjct: 61 LLNGLELGGKKLLVKV 76
>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and
CTD-associated factor 4 (SCAF4) and similar proteins.
The CD corresponds to the RRM of SCAF4 (also termed
splicing factor, arginine/serine-rich 15 or SFR15, or
CTD-binding SR-like protein RA4) that belongs to a new
class of SCAFs (SR-like CTD-associated factors).
Although its biological function remains unclear, SCAF4
shows high sequence similarity to SCAF8 that interacts
specifically with a highly serine-phosphorylated form
of the carboxy-terminal domain (CTD) of the largest
subunit of RNA polymerase II (pol II) and may play a
direct role in coupling with both, transcription and
pre-mRNA processing, processes. SCAF4 and SCAF8 both
contain a conserved N-terminal CTD-interacting domain
(CID), an atypical RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and serine/arginine-rich
motifs.
Length = 81
Score = 38.9 bits (90), Expect = 3e-04
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TTL+VG LD T++ + +L + GP++ +I G A++ VH A AL ++
Sbjct: 5 TTLWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPRG---CAYIVMVHRQDAYRALQKLS 61
Query: 68 KRVFL--EKEMKVNWASSPG 85
+ +K +K+ WA + G
Sbjct: 62 RGNVKVNQKSIKIAWALNKG 81
Score = 30.0 bits (67), Expect = 0.39
Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD- 266
T++ G K ++ V+ + FG I I + +G A++ ++ A A++ + +
Sbjct: 6 TLWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPRGCAYIVMVHRQDAYRALQKLSRGNV 65
Query: 267 -INGHTVKCFWG 277
+N ++K W
Sbjct: 66 KVNQKSIKIAWA 77
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs) connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 38.7 bits (91), Expect = 3e-04
Identities = 18/58 (31%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN-GHTVK 273
+ +E++ +F+ F ++R+ +G AFV+F T+E AT A++++ I GH +K
Sbjct: 13 ETTKEMLEMLFNQFPGFKEVRLVPRRGIAFVEFETEEQATVALQALQGFKITPGHAMK 70
Score = 32.2 bits (74), Expect = 0.065
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN- 67
L++ NL T+E+L LF+Q G K +R AF+EF A AL A+
Sbjct: 4 ILFLQNLPEETTKEMLEMLFNQF---PGFKEVRLVPRRGIAFVEFETEEQATVALQALQG 60
Query: 68 KRVFLEKEMKV 78
++ MK+
Sbjct: 61 FKITPGHAMKI 71
Score = 31.0 bits (71), Expect = 0.13
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+ +L E + L+ F F R+V +G AFV F + +A A+ A+
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVALQAL 58
Query: 158 NG 159
G
Sbjct: 59 QG 60
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 39.1 bits (92), Expect = 3e-04
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 8/70 (11%)
Query: 101 GDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGY--AFVSFVKKAEAENAITAMN 158
DL EIE E +G++ N + ++ FV F EA A+ A+N
Sbjct: 17 EDLKDEIE-----EECEKYGKVLNVIVHEVAS-SEADDAVRIFVEFSDADEAIKAVRALN 70
Query: 159 GQWLGSRSIR 168
G++ G R +
Sbjct: 71 GRFFGGRKVT 80
Score = 33.7 bits (78), Expect = 0.022
Identities = 12/65 (18%), Positives = 28/65 (43%), Gaps = 8/65 (12%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEKGY-------AFVKFTTKETATHAIESIHNTDING 269
DL +E + + +G ++++ V + FV+F+ + A A+ +++ G
Sbjct: 18 DLKDE-IEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFGG 76
Query: 270 HTVKC 274
V
Sbjct: 77 RKVTA 81
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 38.6 bits (90), Expect = 3e-04
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
V+CG F D + + ++F +G VD RV + G+AFV + A AI + N +
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGR-VD-RVDMKSGFAFVYMEDERDAEDAIRGLDNFE 58
Score = 32.1 bits (73), Expect = 0.067
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 10/77 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F G+ + ++ F +G + D +KS G+AFV + +AE+AI +
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRV-------DRVDMKS-GFAFVYMEDERDAEDAIRGL 54
Query: 158 NGQWLG--SRSIRTNWS 172
+ G R +R W+
Sbjct: 55 DNFEFGRQRRRLRVEWA 71
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 38.7 bits (91), Expect = 4e-04
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKE--KGYAFVKFTTKETATHAIESIHN 264
+D+ EE S FG + I+V K +G +VKF T E A I++++
Sbjct: 26 EDVLEEC-----SKFGPVEHIKVDKNSPEGVVYVKFKTVEAAQKCIQALNG 71
Score = 34.1 bits (79), Expect = 0.015
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 106 EIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSR 165
EI+ L+E + FG + + ++ D +G +V F A+ I A+NG+W R
Sbjct: 23 EIKEDVLEEC-SKFGPVEHIKV--DK--NSPEGVVYVKFKTVEAAQKCIQALNGRWFDGR 77
Query: 166 SI 167
I
Sbjct: 78 QI 79
Score = 29.0 bits (66), Expect = 1.0
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 10/69 (14%)
Query: 7 PTTLYVGNLDVSVTEELL--CALFSQIGPVKGCKVIREP--GNDPYAFLEFVHHTVAATA 62
P D + E++L C S+ GPV+ KV + G +++F A
Sbjct: 12 PAEETEDEWDDEIKEDVLEEC---SKFGPVEHIKVDKNSPEGV---VYVKFKTVEAAQKC 65
Query: 63 LAAMNKRVF 71
+ A+N R F
Sbjct: 66 IQALNGRWF 74
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 38.4 bits (90), Expect = 4e-04
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 211 CGGFGKDLNEELVSKVFSPFGTIVDIRVF-KEKGYAFVKFTTKETATHAIES 261
D +E+ + K+FS +G + D+ V K+KG A V+F +K+ A A+E+
Sbjct: 9 RKKGNGDYSEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVEN 60
Score = 34.6 bits (80), Expect = 0.008
Identities = 24/86 (27%), Positives = 35/86 (40%), Gaps = 23/86 (26%)
Query: 76 MKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLK 135
+KV W GN GD S + L++ F+ +G++S+ +V K
Sbjct: 3 LKVKWKRKKGN--------------GDYSED----ELRKIFSKYGDVSDV-VVSS----K 39
Query: 136 SKGYAFVSFVKKAEAENAITAMNGQW 161
KG A V F K AE A+ G
Sbjct: 40 KKGSAIVEFASKKAAEAAVENECGLP 65
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 38.1 bits (89), Expect = 5e-04
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 10 LYVGNLDVSVTEELLCALFS-QIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
LY+GNL V E L LF PV V + YAF++ + A A+ +N
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK----GGYAFVDCPDQSWADKAIEKLNG 56
Query: 69 RVFLEKEMKVNWASS 83
++ K ++V +
Sbjct: 57 KILQGKVIEVEHSVP 71
Score = 34.3 bits (79), Expect = 0.009
Identities = 18/60 (30%), Positives = 28/60 (46%)
Query: 210 YCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDING 269
Y G D+NE + ++F V + K+ GYAFV + A AIE ++ + G
Sbjct: 2 YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKILQG 61
Score = 32.3 bits (74), Expect = 0.051
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G+LS ++ L++ F I +K GYAFV ++ A+ AI +
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHK------IPVSSVLVKKGGYAFVDCPDQSWADKAIEKL 54
Query: 158 NGQWLGSRSIRTNWSTRK 175
NG+ L + I S K
Sbjct: 55 NGKILQGKVIEVEHSVPK 72
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1) and has been implicated in the maintenance of
the stem-cell state, differentiation, and tumorigenesis.
It translationally regulates the expression of a
mammalian numb gene by binding to the 3'-untranslated
region of mRNA of Numb, encoding a membrane-associated
inhibitor of Notch signaling, and further influences
neural development. It represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 74
Score = 38.1 bits (88), Expect = 5e-04
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
IFVG LS + +K+ F FG++ + ++ D T + +G+ FV+F
Sbjct: 2 IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM2 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 86
Score = 38.4 bits (89), Expect = 6e-04
Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGE--ISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
I + +++P ++ A AP+ ++N R+++D QT +++G+AFV EA +
Sbjct: 5 IILRNIAPHTVVDSILTALAPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64
Query: 156 AMNG 159
+
Sbjct: 65 ILQS 68
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 37.9 bits (88), Expect = 6e-04
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +L I LKE F +I R+ + SKG A++ F +AEAE A+
Sbjct: 6 LFVKNLPYNITVDELKEVFEDAVDI---RLPSG-KDGSSKGIAYIEFKTEAEAEKALEEK 61
Query: 158 NGQWLGSRSI 167
G + RSI
Sbjct: 62 QGAEVDGRSI 71
Score = 30.6 bits (69), Expect = 0.26
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 230 FGTIVDIRV-----FKEKGYAFVKFTTKETATHAIESIHNTDINGHTV 272
F VDIR+ KG A+++F T+ A A+E +++G ++
Sbjct: 24 FEDAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQGAEVDGRSI 71
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface
Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX)
proteins. This subgroup corresponds to the conserved
RNA recognition motif (RRM) in ECTO-NOX proteins (also
termed ENOX), comprising a family of plant and animal
NAD(P)H oxidases exhibiting both, oxidative and protein
disulfide isomerase-like, activities. They are
growth-related and drive cell enlargement, and may play
roles in aging and neurodegenerative diseases. ENOX
proteins function as terminal oxidases of plasma
membrane electron transport (PMET) through catalyzing
electron transport from plasma membrane quinones to
extracellular oxygen, forming water as a product. They
are also hydroquinone oxidases that oxidize externally
supplied NADH, hence NOX. ENOX proteins harbor a
di-copper center that lack flavin. ENOX proteins display
protein disulfide interchange activity that is also
possessed by protein disulfide isomerase. In contrast to
the classic protein disulfide isomerases, ENOX proteins
lack the double CXXC motif. This family includes two
ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed
candidate growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous and
refractory to drugs. ENOX2, also termed APK1 antigen, or
cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role in
cell proliferation and tumor progression. In contrast to
ENOX1, ENOX2 is drug-responsive and harbors a drug
binding site to which the cancer-specific S-peptide
tagged pan-ENOX2 recombinant (scFv) is directed.
Moreover, ENOX2 is specifically inhibited by a variety
of quinone site inhibitors that have anticancer activity
and is unique to the surface of cancer cells. ENOX
proteins contain many functional motifs.
Length = 84
Score = 38.2 bits (89), Expect = 6e-04
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 204 PTNC-TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
P C TV+ GG ++ EE++ +VF G I+ IR+ K K + ++F + AI
Sbjct: 3 PPGCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMSK-KNFCHIRFAEEFAVDKAI 58
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 37.6 bits (87), Expect = 6e-04
Identities = 16/67 (23%), Positives = 35/67 (52%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
C ++ G D+ E+ K+F+ +G ++ + K KG+ F+K ++ A A + +T
Sbjct: 2 CRLFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTP 61
Query: 267 INGHTVK 273
+ G ++
Sbjct: 62 MRGRQLR 68
Score = 34.5 bits (79), Expect = 0.009
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG+L +I K+ FA +GE I K KG+ F+ +A AE A +
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYGEPGEVFIN------KGKGFGFIKLESRALAEIAKAEL 57
Query: 158 NGQWLGSRSIR 168
+ + R +R
Sbjct: 58 DDTPMRGRQLR 68
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1,
or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3,
or CUG-BP2, or NAPOR) belong to the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family
of RNA-binding proteins that have been implicated in
regulation of pre-mRNA splicing, and control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. The
human CELF-1 is a nuclear and cytoplasmic RNA-binding
protein that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for onset
of type 1 myotonic dystrophy (DM1), a neuromuscular
disease associated with an unstable CUG triplet
expansion in the 3'-UTR (3'-untranslated region) of the
DMPK (myotonic dystrophy protein kinase) gene; it
preferentially targets UGU-rich mRNA elements. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contain three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains): two consecutive RRMs (RRM1
and RRM2) situated in the N-terminal region followed by
a linker region and the third RRM (RRM3) close to the
C-terminus of the protein. The two N-terminal RRMs of
EDEN-BP are necessary for the interaction with EDEN as
well as a part of the linker region (between RRM2 and
RRM3). Oligomerization of EDEN-BP is required for
specific mRNA deadenylation and binding. CELF-2 is
expressed in all tissues at some level, but highest in
brain, heart, and thymus. It has been implicated in the
regulation of nuclear and cytoplasmic RNA processing
events, including alternative splicing, RNA editing,
stability and translation. CELF-2 shares high sequence
identity with CELF-1, but shows different binding
specificity; it binds preferentially to sequences with
UG repeats and UGUU motifs. It has been shown to bind to
a Bruno response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to the
3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2
of CELF-2, can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. This subgroup also
includes Drosophila melanogaster Bruno protein, which
plays a central role in regulation of Oskar (Osk)
expression in flies. It mediates repression by binding
to regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 84
Score = 37.9 bits (88), Expect = 7e-04
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQT--LKSKGYAFVSFVKKAEAENAIT 155
+FVG + + L+E F +G + ++RD +SKG FV+F + A A
Sbjct: 4 MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63
Query: 156 AM 157
A+
Sbjct: 64 AL 65
Score = 33.6 bits (77), Expect = 0.026
Identities = 16/64 (25%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE--------KGYAFVKFTTKETATHAIE 260
++ G + +E+ + ++F +G + I V ++ KG FV F T++ A A
Sbjct: 4 MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63
Query: 261 SIHN 264
++HN
Sbjct: 64 ALHN 67
Score = 26.3 bits (58), Expect = 7.8
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYA-----FLEFVHHTVAATALA 64
++VG + S +E+ L LF Q G V V+R+ +P F+ F A A
Sbjct: 4 MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63
Query: 65 AM 66
A+
Sbjct: 64 AL 65
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of nuclear
proteins consisting of Matrin 3 (MATR3), nuclear protein
220 (NP220) and similar proteins. MATR3 is a highly
conserved inner nuclear matrix protein that has been
implicated in various biological processes. NP220 is a
large nucleoplasmic DNA-binding protein that binds to
cytidine-rich sequences, such as CCCCC (G/C), in
double-stranded DNA (dsDNA). Both, Matrin 3 and NP220,
contain two RNA recognition motif (RRM), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a Cys2-His2 zinc finger-like motif at the
C-terminal region. .
Length = 76
Score = 37.6 bits (88), Expect = 8e-04
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 7/73 (9%)
Query: 207 CTVYCGGF--GKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHN 264
V G EL+ K+ PFG + + AF++ + E A A+ S +
Sbjct: 1 RVVRLSNLPEGGYTEAELL-KLAEPFGKVDHYIFLPNRNKAFIEMESPEDAQ-ALVSFYK 58
Query: 265 TD---INGHTVKC 274
T I G ++K
Sbjct: 59 TYPLTIGGKSIKV 71
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 37.5 bits (87), Expect = 0.001
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
IFVG + + L++ F+ +G + +IV D + SKGY FV+F + +A+
Sbjct: 5 IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGV-SKGYGFVTFETQEDAQK 58
Score = 35.2 bits (81), Expect = 0.007
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDPYAFLEFVHHTVAATALA 64
P ++VG +D E L FSQ G VK K++ R + Y F+ F A L
Sbjct: 2 PNRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQ 61
Query: 65 AMNKRVFLEKEMKVNWA 81
N+ F +K++ + A
Sbjct: 62 EANRLCFRDKKLNIGQA 78
Score = 34.8 bits (80), Expect = 0.007
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETA 255
++ GG NE + K FS +GT+ ++++ + KGY FV F T+E A
Sbjct: 5 IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDA 56
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable
RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 37.3 bits (86), Expect = 0.001
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F L+ I + L++ F+ G++ + RI+ D + +SKG A+V F + AI +
Sbjct: 4 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 62
Query: 158 NGQWL 162
GQ L
Sbjct: 63 TGQRL 67
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 37.2 bits (87), Expect = 0.001
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 3/54 (5%)
Query: 116 FAPFGEISNC-RIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIR 168
F+ + IV D + G A+V F +A A+ + +G R I
Sbjct: 20 FSGLDIPPDGIHIVYDDDG-RPTGEAYVEFASPEDARRAL-RKHNNKMGGRYIE 71
Score = 29.4 bits (67), Expect = 0.53
Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 7/71 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFG-TIVDIRVF-----KEKGYAFVKFTTKETATHAIES 261
V G EE + FS I + + G A+V+F + E A A+
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60
Query: 262 IHNTDINGHTV 272
HN + G +
Sbjct: 61 -HNNKMGGRYI 70
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding
protein Raly. This subgroup corresponds to the RRM of
Raly, also termed autoantigen p542, or heterogeneous
nuclear ribonucleoprotein C-like 2, or hnRNP core
protein C-like 2, or hnRNP associated with lethal yellow
protein homolog, an RNA-binding protein that may play a
critical role in embryonic development. It is encoded by
Raly, a ubiquitously expressed gene of unknown function.
Raly shows a high degree of identity with the 5'
sequences of p542 gene encoding autoantigen, which can
cross-react with EBNA-1 of the Epstein Barr virus. Raly
contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes a unique
glycine/serine-rich stretch. .
Length = 76
Score = 37.0 bits (85), Expect = 0.001
Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 98 IFVGDLSPEIETQT-LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G+L+ + ++ ++ F+ +G + C + KGYAFV + + A A+
Sbjct: 4 VFIGNLNTAVVKKSDVETIFSKYGRVVGCSV--------HKGYAFVQYSNERHARGAVIG 55
Query: 157 MNGQWLGSRSIRTNWSTRKPP 177
NG+ L +++ N + P
Sbjct: 56 ENGRVLAGQTLDINMAGEPKP 76
Score = 37.0 bits (85), Expect = 0.001
Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 8 TTLYVGNLDVSVTEEL-LCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
+ +++GNL+ +V ++ + +FS+ G V GC V + YAF+++ + A A+
Sbjct: 2 SRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSV-----HKGYAFVQYSNERHARGAVIGE 56
Query: 67 NKRVFLEKEMKVNWASSP 84
N RV + + +N A P
Sbjct: 57 NGRVLAGQTLDINMAGEP 74
Score = 28.5 bits (63), Expect = 1.5
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 11/72 (15%)
Query: 206 NCTVYCGGFGKDLNEELVSK-----VFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
N V+ G +LN +V K +FS +G +V V KGYAFV+++ + A A+
Sbjct: 1 NSRVFIG----NLNTAVVKKSDVETIFSKYGRVVGCSV--HKGYAFVQYSNERHARGAVI 54
Query: 261 SIHNTDINGHTV 272
+ + G T+
Sbjct: 55 GENGRVLAGQTL 66
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 36.9 bits (86), Expect = 0.001
Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
+FVG L+ ++ + L++ F+ FGE+++ I + + +AFV+F A++
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQS 52
Score = 31.5 bits (72), Expect = 0.10
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-KGYAFVKFTTKETATHAIESIHNT 265
V+ G +D+ EE + + FS FG + D+ + K + +AFV F E A H
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQSLCGEDH-- 58
Query: 266 DINGHTV 272
I G +V
Sbjct: 59 IIKGVSV 65
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM3 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 83
Score = 37.3 bits (86), Expect = 0.001
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGP--VKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
LYV NL +S TEE + F+ I P V+ K IR+ YAF+ F + A A+ A+N
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD-----YAFVHFSNREDAVDAMNALN 65
Query: 68 KRVFLEKEMKVNWA 81
+V ++V A
Sbjct: 66 GKVIDGSPIEVTLA 79
Score = 34.6 bits (79), Expect = 0.010
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 220 EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKE 279
EE + K F+ RV K + YAFV F+ +E A A+ +++ I+G ++
Sbjct: 22 EETIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVDAMNALNGKVIDGSPIEV----- 76
Query: 280 SENNSTLAQP 289
TLA+P
Sbjct: 77 -----TLAKP 81
Score = 31.2 bits (70), Expect = 0.16
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 98 IFVGDLSPEIETQTLKEAFAPF--GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
++V +L +T+++ F G + + +RD YAFV F + +A +A+
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRD--------YAFVHFSNREDAVDAMN 62
Query: 156 AMNGQWLGSRSI 167
A+NG+ + I
Sbjct: 63 ALNGKVIDGSPI 74
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 37.6 bits (88), Expect = 0.001
Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 14/78 (17%)
Query: 90 QDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVR--DPQTLKSKGYAFVSFVKK 147
+D + + F D+ PE E FGE+ ++ +P +G +V + +
Sbjct: 32 EDLYSDFEEFYDDVLPEFEK---------FGEVVQFKVCCNYEPHL---RGNVYVQYQSE 79
Query: 148 AEAENAITAMNGQWLGSR 165
EA A NG+W +
Sbjct: 80 EEALAAFKMFNGRWYAGK 97
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins. The
research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 98
Score = 37.4 bits (87), Expect = 0.001
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIR 168
FV F +EAE AI A+NG+W G R ++
Sbjct: 56 FVEFSLPSEAEKAIQALNGRWFGGRKVK 83
Score = 32.0 bits (73), Expect = 0.13
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 13/72 (18%)
Query: 216 KDLNEELVSKVF---SPFGTIVDIRVFKEKGYA----------FVKFTTKETATHAIESI 262
+DL+++L +V FG + + +++EK FV+F+ A AI+++
Sbjct: 13 EDLDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSLPSEAEKAIQAL 72
Query: 263 HNTDINGHTVKC 274
+ G VK
Sbjct: 73 NGRWFGGRKVKA 84
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 36.5 bits (84), Expect = 0.001
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 9/74 (12%)
Query: 98 IFVGDLSPEIETQTLKEA-FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G+L+ + ++ EA F+ +G+I C + KG+AFV +V + A A+
Sbjct: 4 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAG 55
Query: 157 MNGQWLGSRSIRTN 170
+G+ + + + N
Sbjct: 56 EDGRMIAGQVLDIN 69
Score = 36.5 bits (84), Expect = 0.002
Identities = 20/75 (26%), Positives = 43/75 (57%), Gaps = 6/75 (8%)
Query: 8 TTLYVGNLD-VSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
+ +++GNL+ + V + + A+FS+ G + GC V + +AF+++V+ A A+A
Sbjct: 2 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-----HKGFAFVQYVNERNARAAVAGE 56
Query: 67 NKRVFLEKEMKVNWA 81
+ R+ + + +N A
Sbjct: 57 DGRMIAGQVLDINLA 71
Score = 33.8 bits (77), Expect = 0.014
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 11/59 (18%)
Query: 206 NCTVYCGGFGKDLNEELVSK-----VFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
N V+ G +LN +V K +FS +G IV V KG+AFV++ + A A+
Sbjct: 1 NSRVFIG----NLNTLVVKKSDVEAIFSKYGKIVGCSV--HKGFAFVQYVNERNARAAV 53
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 36.6 bits (85), Expect = 0.001
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 10/67 (14%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVF---------KEKGYAFVKFTTKETATHAIESIHNTDI 267
D EL + FG + I ++G ++ F E A AI ++
Sbjct: 4 DFERELKEEEEY-FGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYF 62
Query: 268 NGHTVKC 274
+G VK
Sbjct: 63 DGRLVKA 69
Score = 28.1 bits (63), Expect = 1.5
Identities = 8/33 (24%), Positives = 19/33 (57%)
Query: 136 SKGYAFVSFVKKAEAENAITAMNGQWLGSRSIR 168
+G +++F + +A AI +NG++ R ++
Sbjct: 36 KRGNVYITFERSEDAARAIVDLNGRYFDGRLVK 68
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is an integral part of the U2
small nuclear ribonucleoprotein (snRNP) and the U11/U12
di-snRNP. SF3B is essential for the accurate excision of
introns from pre-messenger RNA and has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 36.8 bits (86), Expect = 0.001
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V +L +I ++ L + F +G I RI +T +G AFV + +A+NA +
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHL 61
Query: 158 NG 159
+G
Sbjct: 62 SG 63
Score = 28.0 bits (63), Expect = 1.9
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP 47
LYV NL ++ E L LF + G ++ IR GN
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQ---IRI-GNTK 38
Score = 27.2 bits (61), Expect = 3.7
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 220 EELVSKVFSPFGTIVDIRVFKE---KGYAFVKFTTKETATHAIESIHNTDINGHTV 272
EEL +F +G I IR+ +G AFV + A +A + ++G V
Sbjct: 17 EELYD-LFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDH-----LSGFNV 66
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein (SXL).
SNF contains two RNA recognition motifs (RRMs); it can
self-associate through RRM1, and each RRM can recognize
poly(U) RNA binding independently. .
Length = 78
Score = 36.8 bits (85), Expect = 0.002
Identities = 21/66 (31%), Positives = 40/66 (60%), Gaps = 7/66 (10%)
Query: 98 IFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
I++ +L+ +++ + LK++ F+ FG+I + ++ TLK +G AFV F + A NA
Sbjct: 2 IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALK---TLKMRGQAFVVFKDISSATNA 58
Query: 154 ITAMNG 159
+ +M G
Sbjct: 59 LRSMQG 64
Score = 35.3 bits (81), Expect = 0.006
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 208 TVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHAIE 260
T+Y + + +E + K +FS FG I+DI + K +G AFV F +AT+A+
Sbjct: 1 TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60
Query: 261 SIH 263
S+
Sbjct: 61 SMQ 63
Score = 33.7 bits (77), Expect = 0.017
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 9 TLYVGNLDVSVT-EEL---LCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA 64
T+Y+ NL+ V EEL L A+FSQ G + ++ AF+ F + A AL
Sbjct: 1 TIYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALR 60
Query: 65 AMNKRVFLEKEMKVNWA 81
+M F +K M++ ++
Sbjct: 61 SMQGFPFYDKPMRIAYS 77
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 2 (Musashi-2) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 79
Score = 36.6 bits (84), Expect = 0.002
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
IFVG LS + +K+ F FG++ + ++ D T + +G+ FV+F
Sbjct: 6 IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog of
DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 36.7 bits (85), Expect = 0.002
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
+FVG + ++ ++ FA +G + +I+ D +T SKGY FVSF
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSF 53
Score = 35.6 bits (82), Expect = 0.005
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG--NDPYAFLEF 53
P T++VG +D+ + E + + F++ G VK K+I + + Y F+ F
Sbjct: 5 PNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSF 53
Score = 32.5 bits (74), Expect = 0.049
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKF 249
TV+ GG ++E + F+ +G++ ++++ + KGY FV F
Sbjct: 7 TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSF 53
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 36.5 bits (84), Expect = 0.002
Identities = 25/71 (35%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
IFV +L ++ Q LKE F+ G + I + KSKG V F AE A
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEI--KMENGKSKGCGTVRFDSPESAEKACRL 58
Query: 157 MNGQWLGSRSI 167
MNG + R I
Sbjct: 59 MNGIKINGREI 69
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 36.4 bits (84), Expect = 0.002
Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
VY G + E+ + + F +G +++I + + GY FV+F A A+ ++ D+
Sbjct: 2 VYIGRLSYHVREKDIQRFFGGYGKLLEIDL--KNGYGFVEFEDSRDADDAVYELNGKDLC 59
Query: 269 GHTV 272
G V
Sbjct: 60 GERV 63
Score = 34.1 bits (78), Expect = 0.012
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 9/71 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G LS + + ++ F +G++ + GY FV F +A++A+ +
Sbjct: 2 VYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYEL 53
Query: 158 NGQWL-GSRSI 167
NG+ L G R I
Sbjct: 54 NGKDLCGERVI 64
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 80
Score = 36.7 bits (84), Expect = 0.002
Identities = 18/61 (29%), Positives = 33/61 (54%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++++ L P Q L + P+G+I + + + D T + KGY FV F A A+ A+ +
Sbjct: 6 NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65
Query: 157 M 157
+
Sbjct: 66 L 66
Score = 28.3 bits (62), Expect = 1.5
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKET 254
Q S TN +Y G ++ + K+ P+G IV + +K GY FV F +
Sbjct: 1 QLSKTN--LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAA 58
Query: 255 ATHAIESIHNTDINGHTVK 273
A A+ S+ + K
Sbjct: 59 AQKAVASLKANGVQAQMAK 77
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 36.1 bits (84), Expect = 0.002
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIR 168
+KE FA FG + + D ++ +S G A V F ++A+A A+ NG L R ++
Sbjct: 17 IKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMKQYNGVPLDGRPMK 72
Score = 35.3 bits (82), Expect = 0.005
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKV 39
T L V NLD V+++ + LF++ G +K V
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAV 32
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 36.6 bits (84), Expect = 0.002
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-KGYAFVKFTTKETATHAIESI 262
P +C VY G G + N+ + + F +G + + V + G+AFV+F A A+ +
Sbjct: 2 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVREL 61
Query: 263 HNTDINGHTVK 273
+ G V+
Sbjct: 62 DGRTLCGCRVR 72
Score = 36.2 bits (83), Expect = 0.003
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L L+ AF +G + + + R+P G+AFV F +A +A+ +
Sbjct: 7 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 61
Query: 158 NGQWLGSRSIRTNWS 172
+G+ L +R S
Sbjct: 62 DGRTLCGCRVRVELS 76
Score = 30.0 bits (67), Expect = 0.48
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
+YVGNL + + L F GP++ V R P +AF+EF AA A+ ++ R
Sbjct: 7 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG--FAFVEFEDPRDAADAVRELDGR 64
Query: 70 VFLEKEMKV 78
++V
Sbjct: 65 TLCGCRVRV 73
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains).
The RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 36.1 bits (84), Expect = 0.002
Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 12 VGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPY-----AFLEFVHHTVAATALAAM 66
V N+ TEE + LF +G ++ ++ + F+++ AL
Sbjct: 4 VTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVALHLT 63
Query: 67 NKRVFLEKEMKV 78
N VF+++ + V
Sbjct: 64 NT-VFIDRALIV 74
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 36.4 bits (85), Expect = 0.002
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 14/68 (20%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK---------GYAFVKFTTKETATHAIESIHNTD 266
+D+ EE K +G ++ + + + + G FV+F E A A ++
Sbjct: 26 EDVKEE-CGK----YGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRK 80
Query: 267 INGHTVKC 274
+G TV
Sbjct: 81 FDGRTVVA 88
Score = 30.2 bits (69), Expect = 0.37
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSK---GYAFVSFVKKAEAENAITAMNGQWLGSRSIR 168
+KE +G++ + I R G FV F +A+ A A+ G+ R++
Sbjct: 28 VKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVV 87
Query: 169 T 169
Sbjct: 88 A 88
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 86
Score = 36.4 bits (84), Expect = 0.003
Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEI--SNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
I + +++P ++ A AP+ + SN R+++D QT +++G+AFV EA +
Sbjct: 5 IILRNIAPHTVVDSILSALAPYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQ 64
Query: 156 AMNG 159
+
Sbjct: 65 ILQA 68
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 35.7 bits (82), Expect = 0.003
Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G L+P + ++ F +G I + + R G+ FV F +A++A+ +
Sbjct: 2 VFIGRLNPAAREKDVERFFKGYGRIRDIDLKR--------GFGFVEFDDPRDADDAVYEL 53
Query: 158 NGQWLGSRSI 167
+G+ L + +
Sbjct: 54 DGKELCNERV 63
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 36.8 bits (85), Expect = 0.003
Identities = 15/57 (26%), Positives = 26/57 (45%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+FV +L + ++L F+ FG + V D T ++KG FV F + +
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60
Score = 34.5 bits (79), Expect = 0.020
Identities = 15/47 (31%), Positives = 20/47 (42%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFV 54
TL+V NL TEE L FS+ G V+ + + FV
Sbjct: 2 FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFV 48
>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM2 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contain two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 88
Score = 36.2 bits (83), Expect = 0.004
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++++ +L ++ Q L+ PFG + + RI+RD + S+G F + E I
Sbjct: 3 NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGV-SRGVGFARMESTEKCEVVIQH 61
Query: 157 MNGQWL 162
NG++L
Sbjct: 62 FNGKYL 67
Score = 27.8 bits (61), Expect = 2.9
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIRE 42
PT LY+ NL VS+ E+ L + G V +++R+
Sbjct: 1 PTNLYISNLPVSMDEQELENMLKPFGHVISTRILRD 36
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 36.1 bits (84), Expect = 0.004
Identities = 16/57 (28%), Positives = 26/57 (45%)
Query: 103 LSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
L+ I+ LK+ +GE+ +I P+T K G A V F A+ + +N
Sbjct: 10 LNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQ 66
Score = 29.2 bits (66), Expect = 0.89
Identities = 13/62 (20%), Positives = 31/62 (50%), Gaps = 10/62 (16%)
Query: 220 EELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+++ K +G + +++++ K G A V F + ++A +E ++ T + G +K
Sbjct: 20 KDMCKK----YGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIK 75
Query: 274 CF 275
F
Sbjct: 76 VF 77
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. Structurally related CFIm68 and
CFIm59, also termed cleavage and polyadenylation
specificity factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59), are functionally redundant. Both contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. Their N-terminal RRM mediates the interaction
with CFIm25, and also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 76
Score = 35.7 bits (83), Expect = 0.004
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 233 IVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDING 269
+ I+ F K KG+A+V+F ++ A E + + NG
Sbjct: 27 VKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNG 69
Score = 29.6 bits (67), Expect = 0.48
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFG--EISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
++VG+L+ + L+ A A G ++ + + KSKG+A+V F +A A
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 156 AMNGQWLGSRS 166
+ G+ +
Sbjct: 61 KLEGREFNGKK 71
Score = 28.8 bits (65), Expect = 0.95
Identities = 23/74 (31%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 10 LYVGNLDVSVTEELLCALFSQIG--PVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
LYVGNL T+E L ++ G VK K N +A++EF AA
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 65 AMNKRVFLEKEMKV 78
+ R F K+ V
Sbjct: 61 KLEGREFNGKKCVV 74
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 38.6 bits (90), Expect = 0.004
Identities = 28/118 (23%), Positives = 34/118 (28%), Gaps = 2/118 (1%)
Query: 275 FWGKESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQ--MGYWYPQAAAYTATAAQLPQQ 332
W + +AQ P P + A Q +QQ AA AT A
Sbjct: 48 PWDPSPQAPPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALPAGP 107
Query: 333 FYQYGQLGYPQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFPTQ 390
Q Q Y V V AQQ A+ Q Q A + Q Q
Sbjct: 108 AGPTIQTEPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQ 165
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an N-terminal
C4C4 type RING finger motif, followed by a RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The RING
fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 36.0 bits (84), Expect = 0.004
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 6/84 (7%)
Query: 98 IFVGDLSPEIET-QTLK--EAFAPFGEISNCRIVRD---PQTLKSKGYAFVSFVKKAEAE 151
++V L P + + LK E F +G+I I R+ + A+V++ +K +A
Sbjct: 8 VYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDAL 67
Query: 152 NAITAMNGQWLGSRSIRTNWSTRK 175
I A++G +L R ++ ++ T K
Sbjct: 68 RCIQAVDGFYLDGRLLKASFGTTK 91
Score = 34.8 bits (81), Expect = 0.011
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 11/73 (15%)
Query: 216 KDLNEELVSK--VFSPFGTIVDIRVFKEKGY---------AFVKFTTKETATHAIESIHN 264
+ +EE++ K F +G I I + + Y A+V ++ KE A I+++
Sbjct: 16 RLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDG 75
Query: 265 TDINGHTVKCFWG 277
++G +K +G
Sbjct: 76 FYLDGRLLKASFG 88
>gnl|CDD|240965 cd12521, RRM3_MRN1, RNA recognition motif 3 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM3 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 74
Score = 35.5 bits (82), Expect = 0.004
Identities = 25/76 (32%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 206 NCTVYCGGFGKDLN-EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETAT--HAIESI 262
N TVY G D EE+ + V G + IR EK FV F A +A+ SI
Sbjct: 1 NRTVYLGNIHPDTKIEEICNAVRG--GLLQSIRYIPEKHICFVTFIDPTAAAQFYAMSSI 58
Query: 263 HNTDINGHTVKCFWGK 278
++ +K WGK
Sbjct: 59 QGLTLHNRRLKVGWGK 74
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein
19 (RBM19) and similar proteins. This subfamily
corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 72
Score = 35.4 bits (82), Expect = 0.004
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
+ ++E F+P + RIV++ + G+AFV + + + A+ N ++G R I
Sbjct: 15 KHIREFFSPL-KPVAIRIVKNDHG-RKTGFAFVDLKSEEDLKKALK-RNKDYMGGRYI 69
>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM2 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2). MSSP-1 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence CT(A/T)(A/T)T, and stimulates
DNA replication in the system using SV40 DNA. MSSP-1 is
identical with Scr2, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-1 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with c-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 85
Score = 35.5 bits (81), Expect = 0.005
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++++ +L ++ Q L+ PFG++ + RI+RD + S+G F + E I+
Sbjct: 2 NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISH 60
Query: 157 MNGQWL 162
NG+++
Sbjct: 61 FNGKFI 66
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 38.3 bits (89), Expect = 0.005
Identities = 34/178 (19%), Positives = 69/178 (38%), Gaps = 31/178 (17%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L ++ L EA PFG +S + L K A V F + A+ +
Sbjct: 5 VHVRNLPQDVVEADLVEALIPFGPVSYVMM------LPGKRQALVEFEDEESAKACVNFA 58
Query: 158 --NGQWLGSRSIRTNWSTRK----PPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYC 211
++ + N+ST + + N + I + +Y +
Sbjct: 59 TSVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITL-------- 110
Query: 212 GGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGY--AFVKFTTKETATHAIESIHNTDI 267
+++ ++F+P+G ++ I F + A V+F + +A HA +++ DI
Sbjct: 111 ---------DVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADI 159
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM4 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 35.3 bits (82), Expect = 0.005
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQI-GPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM- 66
TL++ N+ SVTEE L LF+Q G VK K + + A ++ A AL A+
Sbjct: 1 TLHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPK--DRKMALIQMGSVEEAIEALIALH 58
Query: 67 NKRVFLEKEMKVNWASS 83
N ++ ++V+++ S
Sbjct: 59 NYQLSESSHLRVSFSKS 75
Score = 33.0 bits (76), Expect = 0.034
Identities = 13/53 (24%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 219 NEELVSKVFSP-FGTIVDIRVF-KEKGYAFVKFTTKETATHAIESIHNTDING 269
EE + ++F+ GT+ + F K++ A ++ + E A A+ ++HN ++
Sbjct: 12 TEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIEALIALHNYQLSE 64
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 35.2 bits (82), Expect = 0.006
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 10/68 (14%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPF-------GTIVDIRVFKE---KGYAFVKFTTKETA 255
+ +Y K + EE + +F F + DIR+ E KG AFV F ++E A
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIA 60
Query: 256 THAIESIH 263
T A+ ++
Sbjct: 61 TKALNLVN 68
Score = 27.5 bits (62), Expect = 3.1
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFA---PFGEISNCRI-VRDPQTLKSKGYAFVSFVKKAEAENA 153
++V +LS + + L F +R + KG AFV+F + A A
Sbjct: 4 LYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKA 63
Query: 154 ITAMNG 159
+ +NG
Sbjct: 64 LNLVNG 69
>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM2 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3). MSSP-2 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence T(C/A)TT, and stimulates DNA
replication in the system using SV40 DNA. MSSP-2 is
identical with Scr3, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-2 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-2 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 35.4 bits (81), Expect = 0.006
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++++ +L ++ Q L+ PFG++ + RI+RD S+G F + E IT
Sbjct: 2 NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASG-TSRGVGFARMESTEKCEAIITH 60
Query: 157 MNGQWL 162
NG+++
Sbjct: 61 FNGKYI 66
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 34.9 bits (80), Expect = 0.007
Identities = 24/70 (34%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFV +L + + LK+ F G + I + KSKG V F AE A M
Sbjct: 2 IFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRMM 59
Query: 158 NGQWLGSRSI 167
NG L R I
Sbjct: 60 NGYKLNGREI 69
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 34.5 bits (80), Expect = 0.008
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKGY----AFVKFTTKETATHAIESIHNTDINGHT 271
L+E+ + FG +RV +G AF F ++ A+ A+ +H I G
Sbjct: 11 LSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQLKILGKR 67
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 87
Score = 35.0 bits (80), Expect = 0.008
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEIS--NCRIVRDPQTLKSKGYAFVSFVKKAEA 150
I + +L+P ++ A AP+ +S N R+++D QT ++G+AF+ EA
Sbjct: 5 IILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEA 59
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its C-terminal
RRM motif. .
Length = 72
Score = 34.7 bits (80), Expect = 0.008
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
++ V + ++ T LKE F G++ V+ L SKG VSF
Sbjct: 3 YLKVTGVPKDVSTSNLKEIFEKMGDVKGI-FVK---KLLSKGIVIVSF 46
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 82
Score = 34.8 bits (81), Expect = 0.008
Identities = 25/67 (37%), Positives = 32/67 (47%), Gaps = 16/67 (23%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----------YAFLEF--VHH 56
LYVGNL +TEE L F+Q + + + PGN P +AF+EF V
Sbjct: 4 LYVGNLPPGITEEELVDFFNQA--MLAAGLNQAPGN-PVLSVQINPEKNFAFVEFRTVEE 60
Query: 57 TVAATAL 63
AA AL
Sbjct: 61 ATAALAL 67
Score = 29.4 bits (67), Expect = 0.58
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 209 VYCGGFGKDLNEELVSKVFS-----------PFGTIVDIRVFKEKGYAFVKFTTKETATH 257
+Y G + EE + F+ P ++ +++ EK +AFV+F T E AT
Sbjct: 4 LYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEATA 63
Query: 258 A 258
A
Sbjct: 64 A 64
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to the
RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein and
is localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 34.3 bits (79), Expect = 0.010
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG + ++ F+ GEI ++ P T + +G AF++F + A+ A+ A+
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL-AL 59
Query: 158 NGQWLGSRSIRT 169
+G+ +G R ++
Sbjct: 60 DGEDMGGRFLKV 71
Score = 33.5 bits (77), Expect = 0.022
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTI--VDIRVFKE----KGYAFVKFTTKETATHAIE 260
VY GG E+ + FS G I +D+ F + +G AF+ F T+E A A+
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA 58
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to
the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15)
family of RNA-binding proteins. This ubiquitously
expressed family of similarly structured proteins
predominantly localizing to the nuclear, includes FUS
(also known as TLS or Pigpen or hnRNP P2), EWS (also
known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N
or RPB56), and Drosophila Cabeza (also known as SARFH).
The corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a
degenerate hexapeptide repeat motif at the N-terminus.
The C-terminal region consists of a conserved nuclear
import and retention signal (C-NLS), a putative
zinc-finger domain, and a conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 34.6 bits (80), Expect = 0.010
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP 43
+Y+ L VTE+ L LF IG +K K P
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPP 34
Score = 29.2 bits (66), Expect = 0.80
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 9/78 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEIS--------NCRIVRDPQTLKSKGYAFVSFVKKAE 149
I++ L ++ +L E F G I +I D +T + KG A V++ +
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSA 59
Query: 150 AENAITAMNGQWLGSRSI 167
A+ AI NG I
Sbjct: 60 AQAAIEWFNGYEFRGNKI 77
Score = 28.4 bits (64), Expect = 1.5
Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 19/81 (23%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVK-FTTKET------------- 254
+Y G D+ E+ ++++F G I I+ K +K +T KET
Sbjct: 1 IYISGLPDDVTEDSLAELF---GGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDP 57
Query: 255 --ATHAIESIHNTDINGHTVK 273
A AIE + + G+ +K
Sbjct: 58 SAAQAAIEWFNGYEFRGNKIK 78
>gnl|CDD|240961 cd12517, RRM_RBM27, RNA recognition motif of vertebrate RNA-binding
protein 27 (RBM27). This subgroup corresponds to the
RRM of RBM27 which contains a single RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). Although the specific
function of the RRM in RBM27 remains unclear, it shows
high sequence similarity with RRM1of RBM26, which
functions as a cutaneous lymphoma (CL)-associated
antigen. .
Length = 76
Score = 34.3 bits (78), Expect = 0.011
Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 216 KDLNE-ELVSKVFSPFGTIVDIRV-FK-EKGYAFVKFTTKETATHAIESIHNTDINGHTV 272
+DLN +++ FS FGTIV+I+V F+ + A +++ T E A AI S +N +
Sbjct: 11 QDLNNITQLNEHFSKFGTIVNIQVAFQGDPEAALIQYLTNEEARRAISSTEAV-LNNRFI 69
Query: 273 KCFWGKE 279
+ W +E
Sbjct: 70 RVLWHRE 76
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 34.4 bits (79), Expect = 0.012
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 9/73 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG--YAFVSFVKKAEAENAIT 155
I++ +LS + + LK+ F FGEI C+++ +KS+G Y F+++ A ++
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVL-----IKSRGEKYGFITYRHSEHAALSLG 59
Query: 156 AMNGQWLGSRSIR 168
G L R+
Sbjct: 60 --KGASLRKRNEP 70
Score = 31.7 bits (72), Expect = 0.093
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL---AAM 66
+Y+ NL S++ L F G ++ CKV+ + + Y F+ + H AA +L A++
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGEKYGFITYRHSEHAALSLGKGASL 64
Query: 67 NKR 69
KR
Sbjct: 65 RKR 67
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La) family.
It is expressed predominantly in neurons and muscle in
vertebrates. LARP6 functions as a key regulatory protein
that may play a role in mediating a variety of
developmental and homeostatic processes in animals,
including myogenesis, neurogenesis and possibly
metastasis. LARP6 binds to Ca2+/calmodulin-dependent
serine protein kinase (CASK), and forms a complex with
inhibitor of differentiation transcription factors. It
is structurally related to the La autoantigen and
contains a La motif (LAM), nuclear localization and
export (NLS and NES) signals, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 34.6 bits (80), Expect = 0.013
Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 20/60 (33%)
Query: 221 ELVSKVFSPFGTIVDIRVFKEKG--------------------YAFVKFTTKETATHAIE 260
E V ++FS G I IR+ + A V+F E A A+E
Sbjct: 16 ESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECAVVEFEKLEAARKAVE 75
Score = 30.7 bits (70), Expect = 0.26
Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 15/86 (17%)
Query: 98 IFVGDLSPEIET-QTLKEAFAPFGEISNCRIVRDPQTLKS--------------KGYAFV 142
+ +L E T +++ E F+ G I+ RI+R +T+ K A V
Sbjct: 3 VVAVNLPEEESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECAVV 62
Query: 143 SFVKKAEAENAITAMNGQWLGSRSIR 168
F K A A+ ++ + I+
Sbjct: 63 EFEKLEAARKAVEELSARDDWRDGIK 88
Score = 30.3 bits (69), Expect = 0.44
Identities = 19/88 (21%), Positives = 31/88 (35%), Gaps = 18/88 (20%)
Query: 9 TLYVGNLDV-SVTEELLCALFSQIGPVKGCKVIR-----------------EPGNDPYAF 50
T+ NL T E + LFS G + +++R + G A
Sbjct: 2 TVVAVNLPEEESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECAV 61
Query: 51 LEFVHHTVAATALAAMNKRVFLEKEMKV 78
+EF A A+ ++ R +KV
Sbjct: 62 VEFEKLEAARKAVEELSARDDWRDGIKV 89
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4, an
RNA-binding protein that is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. DND1 interacts specifically
with apolipoprotein B editing complex 3 (APOBEC3), a
multi-functional protein inhibiting retroviral
replication. The DND1-APOBEC3 interaction may play a
role in maintaining viability of germ cells and for
preventing germ cell tumor development. DND1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 33.6 bits (77), Expect = 0.018
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-----KEKGYAFVKFTTKETATHAIES 261
V+ G +D+ E+ + +F GT+ + R+ +G+A+ K++ + A+ AI +
Sbjct: 2 SEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIAT 61
Query: 262 IHNTDI 267
+HN ++
Sbjct: 62 LHNYEL 67
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. The additional
cytoplasmic localization of SAFB2 implies that it could
play additional roles in the cytoplasmic compartment
which are distinct from the nuclear functions shared
with SAFB1.
Length = 76
Score = 33.9 bits (77), Expect = 0.018
Identities = 17/71 (23%), Positives = 34/71 (47%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+++V LS LK F+ +G++ ++V + ++ ++ Y FV+ EA I
Sbjct: 3 NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62
Query: 157 MNGQWLGSRSI 167
++ L R I
Sbjct: 63 LHRTELHGRMI 73
Score = 31.2 bits (70), Expect = 0.13
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 6/53 (11%)
Query: 226 VFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHTV 272
+FS +G +V +V + Y FV +T E AT I +H T+++G +
Sbjct: 21 LFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHLHRTELHGRMI 73
Score = 28.2 bits (62), Expect = 1.9
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI---REPGNDPYAFLEFVHHTVAATALAAM 66
L+V L + L LFS+ G V G KV+ R PG Y F+ A + +
Sbjct: 4 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63
Query: 67 NK 68
++
Sbjct: 64 HR 65
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response element
(IGFRE). Moreover, PSF functions as a transcriptional
repressor interacting with Sin3A and mediating silencing
through the recruitment of histone deacetylases (HDACs)
to the DNA binding domain (DBD) of nuclear hormone
receptors. PSF is an essential pre-mRNA splicing factor
and is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. PSF
forms a heterodimer with the nuclear protein p54nrb,
also known as non-POU domain-containing octamer-binding
protein (NonO). The PSF/p54nrb complex displays a
variety of functions, such as DNA recombination and RNA
synthesis, processing, and transport. PSF contains two
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which are responsible for interactions with
RNA and for the localization of the protein in speckles.
It also contains an N-terminal region rich in proline,
glycine, and glutamine residues, which may play a role
in interactions recruiting other molecules. .
Length = 80
Score = 33.9 bits (77), Expect = 0.018
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
V +LSP + + L+EAF+ FG + ++ D + +S G V F K A A
Sbjct: 4 VRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRG-RSTGKGIVEFASKPAARKAF 57
Score = 29.7 bits (66), Expect = 0.58
Identities = 25/68 (36%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVI-----REPGNDPYAFLEFVHHTVAATALA 64
L V NL V+ ELL FSQ GPV+ VI R G +EF A A
Sbjct: 2 LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGK---GIVEFASKPAARKAFE 58
Query: 65 AMNKRVFL 72
+ VFL
Sbjct: 59 RCTEGVFL 66
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 34.6 bits (80), Expect = 0.019
Identities = 14/47 (29%), Positives = 19/47 (40%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
I V P +K F+ FGEI+ R DP T G + +
Sbjct: 5 IVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKY 51
Score = 29.6 bits (67), Expect = 0.88
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 14/75 (18%)
Query: 213 GFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKET--------ATHA 258
GF +E+++ FS FG I +IR F + G +K+ A A
Sbjct: 9 GFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAKAALKA 68
Query: 259 IESIHNTDINGHTVK 273
+ + I G K
Sbjct: 69 VRKAQDCRIGGAEFK 83
>gnl|CDD|240879 cd12433, RRM_Yme2p_like, RNA recognition motif in yeast
mitochondrial escape protein 2 (Yme2p) and similar
proteins. This subfamily corresponds to the RRM of
Yme2p, also termed protein RNA12, an inner mitochondrial
membrane protein that plays a critical role in
mitochondrial DNA transactions. It may serve as a
mediator of nucleoid structure and number in
mitochondria of the yeast Saccharomyces cerevisiae.
Yme2p contains an exonuclease domain, an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal domain. .
Length = 86
Score = 33.8 bits (78), Expect = 0.023
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 215 GKDLNEELVSKVFSPFGTIVDIRVFKEKG---YAFVKFTTKETATHAIESIHNTDING 269
G +L++E + +F P+G I DI YA V F A A +H ++N
Sbjct: 13 GPELSQEELYSLFRPYGKIKDITPPPPDSLPRYATVTFRRIRGAISAKNCLHGFELNE 70
>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome
proliferator-activated receptor gamma
coactivator-related protein 1 (PRC) and similar
proteins. This subgroup corresponds to the RRM of PRC,
also termed PGC-1-related coactivator, one of the
members of PGC-1 transcriptional coactivators family,
including peroxisome proliferator-activated receptor
gamma coactivators PGC-1alpha and PGC-1beta. Unlike
PGC-1alpha and PGC-1beta, PRC is ubiquitous and more
abundantly expressed in proliferating cells than in
growth-arrested cells. PRC has been implicated in the
regulation of several metabolic pathways, mitochondrial
biogenesis, and cell growth. It functions as a
growth-regulated transcriptional cofactor activating
many nuclear genes specifying mitochondrial respiratory
function. PRC directly interacts with nuclear
transcriptional factors implicated in respiratory chain
expression including nuclear respiratory factors 1 and 2
(NRF-1 and NRF-2), CREB (cAMP-response element-binding
protein), and estrogen-related receptor alpha
(ERRalpha). It interacts indirectly with the NRF-2beta
subunit through host cell factor (HCF), a cellular
protein involved in herpes simplex virus (HSV) infection
and cell cycle regulation. Furthermore, like PGC-1alpha
and PGC-1beta, PRC can transactivate a number of
NRF-dependent nuclear genes required for mitochondrial
respiratory function, including those encoding
cytochrome c, 5-aminolevulinate synthase, Tfam, and
TFB1M, and TFB2M. Further research indicates that PRC
may also act as a sensor of metabolic stress that
orchestrates a redox-sensitive program of inflammatory
gene expression. PRC is a multi-domain protein
containing an N-terminal activation domain, an LXXLL
coactivator signature, a central proline-rich region, a
tetrapeptide motif (DHDY) responsible for HCF binding, a
C-terminal arginine/serine-rich (SR) domain, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 91
Score = 33.7 bits (77), Expect = 0.026
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG--YAFVSFVKKAEAENAI 154
+++G + + LK+ F+ FGEI C I +S+G Y FV++ EA AI
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTI-----HFRSEGDNYGFVTYRYTEEAFAAI 58
Score = 31.8 bits (72), Expect = 0.12
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRV-FKEKG--YAFVKFTTKETATHAIESIH 263
VY G + + FS FG I + + F+ +G Y FV + E A AIE+ H
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDNYGFVTYRYTEEAFAAIENGH 62
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 33.0 bits (76), Expect = 0.027
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 242 KGYAFVKFTTKETATHAIESIHNTDINGHTVKCF 275
+G V+FT++E A+ + T+ G V+
Sbjct: 37 EGEGVVEFTSQEDMERALRKLDGTEFRGRRVRVE 70
Score = 31.1 bits (71), Expect = 0.14
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+ + V L Q LK+ G+++ + RD +G V F + + E A+
Sbjct: 1 FRVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRD-----QEGEGVVEFTSQEDMERALR 55
Query: 156 AMNGQWLGSRSIR 168
++G R +R
Sbjct: 56 KLDGTEFRGRRVR 68
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 33.5 bits (77), Expect = 0.027
Identities = 21/76 (27%), Positives = 31/76 (40%), Gaps = 9/76 (11%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEI--------SNCRIVRDPQTLKSKGYAFVSFVKKAE 149
+FV +L P Q L E F G I + +D T + KG A V++
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 150 AENAITAMNG-QWLGS 164
A AI N ++G+
Sbjct: 61 ASAAIEWFNNKDFMGN 76
Score = 30.1 bits (68), Expect = 0.37
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP 43
++V NL + TE+ L F IG +K K +P
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKP 34
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 33.4 bits (76), Expect = 0.029
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTI--------------VDIRVFKEKGYAFVKFTT 251
N T++ G G+D+ E V+ F G I D K KG A V F
Sbjct: 2 NNTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 61
Query: 252 KETATHAIESIHNTDINGHTVK 273
+A AI+ + +G+ +K
Sbjct: 62 PPSAKAAIDWFDGKEFSGNPIK 83
Score = 28.4 bits (63), Expect = 1.9
Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 8/82 (9%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCR--------IVRDPQTLKSKGYAFVSFVKKAE 149
IFV L ++ +++ + F G I + + D +T K KG A VSF
Sbjct: 5 IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64
Query: 150 AENAITAMNGQWLGSRSIRTNW 171
A+ AI +G+ I+ ++
Sbjct: 65 AKAAIDWFDGKEFSGNPIKVSF 86
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 33.8 bits (78), Expect = 0.030
Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 12/102 (11%)
Query: 68 KRVFLEKEMKVNWASSPGNQPKQD--TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC 125
K ++ + + G + H+ F D+ E+ FGEI +
Sbjct: 5 KNMYPNPDNAIASLDGQGVLTLSEEEIQEHFDEFYEDVFLELSR---------FGEIEDL 55
Query: 126 RIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
+ D G +V F + +AE A+ A+NG++ R +
Sbjct: 56 VVC-DNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPL 96
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically bind mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone and play a key role in
cell growth and differentiation. DND1 is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two
RRMs. .
Length = 82
Score = 33.0 bits (76), Expect = 0.032
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 10 LYVGNLDVSVT-EELLCALFSQIGPVKGCKVIREPGNDP----YAFLEFVHHTVAATALA 64
L+VG + + T EE+L V V R P + +AF+E+ H AA A
Sbjct: 4 LFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARR 63
Query: 65 AM--NKRVFLEKEMKVNWA 81
+ + + E+ V+WA
Sbjct: 64 KLVPGRILLWGHEVAVDWA 82
Score = 33.0 bits (76), Expect = 0.037
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 10/81 (12%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGT-IVDIRVF-------KEKGYAFVKFTTKETATH 257
NC ++ GG K +E + + FS +VD+ V+ K +G+AFV++ + A
Sbjct: 1 NCRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAM 60
Query: 258 AIESI--HNTDINGHTVKCFW 276
A + + GH V W
Sbjct: 61 ARRKLVPGRILLWGHEVAVDW 81
>gnl|CDD|241154 cd12710, RRM_RCAN3, RNA recognition motif in vertebrate regulator
of calcineurin 3 (RCAN3). This subgroup corresponds to
the RRM of RCAN3, also termed calcipressin-3, or Down
syndrome candidate region 1-like protein 2 (DSCR1L2), or
myocyte-enriched calcineurin-interacting protein 3
(MCIP3), encoded by a ubiquitously expressed DSCR1L2
gene. Overexpressed RCAN3 binds and inhibits the
Ca2+/calmodulin-dependent phosphatase calcineurin (also
termed PP2B or PP3C), and further down-regulates nuclear
factor of activated T cells (NFAT)-dependent cytokine
gene expression in activated human Jurkat T cells.
Moreover, RCAN3 interacts with cardiac troponin I
(TNNI3), a heart-specific inhibitory subunit of the
troponin complex, and may play a role in cardiac
contraction. RCAN3 consists of an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a highly
conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT motif
responsible for docking many substrates to calcineurin,
and an unrecognized C-terminal TxxP motif of unknown
function. .
Length = 77
Score = 33.0 bits (75), Expect = 0.032
Identities = 18/72 (25%), Positives = 33/72 (45%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
C+V+ F D +E +F + V ++FK + F+ E A A +H +D
Sbjct: 6 CSVHEAVFEVDEQKERFEALFRIYDDQVSFQMFKSFRRVRINFSNPEAAARARIELHESD 65
Query: 267 INGHTVKCFWGK 278
NG +K ++ +
Sbjct: 66 FNGKKLKLYFAQ 77
>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subgroup corresponds to the RRM of SCAF8 (also
termed CDC5L complex-associated protein 7, or
RNA-binding motif protein 16, or CTD-binding SR-like
protein RA8), a nuclear matrix protein that interacts
specifically with a highly serine-phosphorylated form
of the carboxy-terminal domain (CTD) of the largest
subunit of RNA polymerase II (pol II). The pol II CTD
plays a role in coupling transcription and pre-mRNA
processing. SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8, together with SCAF4,
represents a new class of SCAFs (SR-like CTD-associated
factors). They contain a conserved N-terminal
CTD-interacting domain (CID), an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and
serine/arginine-rich motifs.
Length = 79
Score = 33.1 bits (75), Expect = 0.033
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TTL+VG +D T++ L LF + G ++ +I G A++ VH A AL ++
Sbjct: 3 TTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRG---CAYVCMVHRQDAYRALQKLS 59
Query: 68 KRVFL--EKEMKVNWASSPG 85
+ K +K+ WA + G
Sbjct: 60 SGSYKIGSKVIKIAWALNKG 79
Score = 28.5 bits (63), Expect = 1.3
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG + + Q L F FG+I + ++ +G A+V V + +A A+ +
Sbjct: 5 LWVGQVDKKATQQDLTNLFEEFGQIESINMI------PPRGCAYVCMVHRQDAYRALQKL 58
Query: 158 NGQW--LGSRSIRTNWSTRK 175
+ +GS+ I+ W+ K
Sbjct: 59 SSGSYKIGSKVIKIAWALNK 78
Score = 28.1 bits (62), Expect = 1.9
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD- 266
T++ G K ++ ++ +F FG I I + +G A+V ++ A A++ + +
Sbjct: 4 TLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSSGSY 63
Query: 267 -INGHTVKCFWG 277
I +K W
Sbjct: 64 KIGSKVIKIAWA 75
>gnl|CDD|240707 cd12261, RRM1_3_MRN1, RNA recognition motif 1 and 3 in RNA-binding
protein MRN1 and similar proteins. This subfamily
corresponds to the RRM1 and RRM3 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
which is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 73
Score = 33.0 bits (76), Expect = 0.035
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 208 TVYCGGFGKDLN-EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
TVY G +D +++S + G + I++ K A V F + A N
Sbjct: 2 TVYLGNLPEDTTIRDILSAIRG--GPLESIKLLPTKNSATVSFLDEAAAEAFYAYARNNG 59
Query: 267 --INGHTVKCFWGK 278
ING +K WGK
Sbjct: 60 FYINGKRIKVGWGK 73
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 33.0 bits (75), Expect = 0.036
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G+LSP + + L++ F + ++ Q L GYAFV + + A AI +
Sbjct: 4 LYIGNLSPAVTAEDLRQLFG------DRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIETL 57
Query: 158 NGQW-LGSRSIRTNWSTRK 175
+G+ L + + ++S K
Sbjct: 58 SGKVELHGKVMEVDYSVPK 76
Score = 31.9 bits (72), Expect = 0.079
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 6/76 (7%)
Query: 10 LYVGNLDVSVTEELLCALFSQIG-PVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
LY+GNL +VT E L LF P+ G +V+ + G YAF+++ A A+ ++
Sbjct: 4 LYIGNLSPAVTAEDLRQLFGDRKLPLTG-QVLLKSG---YAFVDYPDQNWAIRAIETLSG 59
Query: 69 RVFLE-KEMKVNWASS 83
+V L K M+V+++
Sbjct: 60 KVELHGKVMEVDYSVP 75
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 33.1 bits (75), Expect = 0.037
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
V +LSP + + L++AF+ FG + ++ D + + G FV F K A A+
Sbjct: 4 VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRG-RPTGKGFVEFAAKPAARKAL 57
Score = 30.8 bits (69), Expect = 0.21
Identities = 25/65 (38%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPY--AFLEFVHHTVAATALAAMN 67
L V NL V+ ELL FSQ GPV+ VI + P F+EF A AL
Sbjct: 2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALERCA 61
Query: 68 KRVFL 72
FL
Sbjct: 62 DGAFL 66
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding
protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or modifier
of damage tolerance Mdt1, a novel phosphothreonine
(pThr)-containing protein that specifically interacts
with the pThr-binding site of the Rad53 FHA1 domain. It
is encoded by gene MDT1 (YBL051C) from yeast
Saccharomyces cerevisiae. PIN4 is involved in normal
G2/M cell cycle progression in the absence of DNA damage
and functions as a novel target of checkpoint-dependent
cell cycle arrest pathways. It contains an N-terminal
RRM, a nuclear localization signal, a coiled coil, and a
total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein
1) and cip2 (Csx1-interacting protein 2) are novel
cytoplasmic RRM-containing proteins that counteract Csx1
function during oxidative stress. They are not essential
for viability in fission yeast Schizosaccharomyces
pombe. Both cip1 and cip2 contain one RRM. Like PIN4,
Cip2 also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 32.8 bits (75), Expect = 0.037
Identities = 9/37 (24%), Positives = 21/37 (56%)
Query: 242 KGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGK 278
+G AF F + E A +E+++ +I+G ++ + +
Sbjct: 43 RGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79
Score = 29.0 bits (65), Expect = 0.91
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 137 KGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
+G AF +F EA+ + A+NG + R +R +
Sbjct: 43 RGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEY 77
>gnl|CDD|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins
related to the La autoantigen. This subfamily
corresponds to the RRM of plant La-like proteins related
to the La autoantigen. A variety of La-related proteins
(LARPs or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding proteins
in eukaryotic cellular processes. Members in this family
contain an LAM domain followed by an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 33.3 bits (76), Expect = 0.041
Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 19/82 (23%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKS----------------KGYAF 141
+ +L + + L+E F G + N RI DP + S K +A
Sbjct: 3 VVAENLPEDHSIENLEEIFGTVGSVKNVRI-CDPGRVGSGSTASKAKKPDTLVSNKLHAL 61
Query: 142 VSFVKKAEAENAITAMN--GQW 161
V + AE A+T ++ G W
Sbjct: 62 VEYETVEAAEKAVTELSDEGNW 83
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. Moreover, hnRNP M is able to
interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. hnRNP M
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 32.8 bits (75), Expect = 0.043
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 240 KEKGYAFVKFTTKETATHAIESIHNTDING 269
K +G V+F KE+ A+E+++ ++ G
Sbjct: 39 KSRGCGVVEFKDKESVQKALETMNRYELKG 68
Score = 31.6 bits (72), Expect = 0.095
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 98 IFVGDLSPEIETQTLKEAF-APFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+ ++ +++ Q LK+ F GE++ + +D + KS+G V F K + A+
Sbjct: 2 VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEG-KSRGCGVVEFKDKESVQKALET 60
Query: 157 MNGQWLGSRSI 167
MN L R +
Sbjct: 61 MNRYELKGRKL 71
>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM4 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 72
Score = 32.3 bits (74), Expect = 0.049
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
I V +L T L+E F+ FG + R++ P + A V F++ +EA+ A
Sbjct: 3 ILVKNLPAGTLTAELRELFSKFGSLG--RVLLPPAGIT----AIVEFLEPSEAKLAFR 54
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 32.3 bits (74), Expect = 0.050
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 242 KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
V+F T AIE + T++NG +K
Sbjct: 37 PNEGVVEFATYSDMKRAIEKLDGTELNGRKIK 68
Score = 29.6 bits (67), Expect = 0.41
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
Y + V +LS + Q LK+ GE++ + + V F ++ + AI
Sbjct: 1 YRLIVENLSSRVSWQDLKDFMRKAGEVTYADAHK-----QRPNEGVVEFATYSDMKRAIE 55
Query: 156 AMNGQWLGSRSIR 168
++G L R I+
Sbjct: 56 KLDGTELNGRKIK 68
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM1 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding protein
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 32.1 bits (73), Expect = 0.051
Identities = 14/70 (20%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV ++ ++ TL+ F +G++ + R S+G V F +A+ A+ +
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGDVRGVQTER-----ISEGIVTVHFYDIRDAKRAVREL 58
Query: 158 NGQWLGSRSI 167
G+ + +++
Sbjct: 59 CGRHMQQQAL 68
Score = 29.1 bits (65), Expect = 0.76
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKG 36
+L+V N+ VTE L LF G V+G
Sbjct: 3 SLFVINVPRDVTESTLRRLFEVYGDVRG 30
>gnl|CDD|220950 pfam11029, DAZAP2, DAZ associated protein 2 (DAZAP2). DAZ
associated protein 2 has a highly conserved sequence
throughout evolution including a conserved polyproline
region and several SH2/SH3 binding sites. It occurs as a
single copy gene with a four-exon organisation and is
located on chromosome 12. It encodes a ubiquitously
expressed protein and binds to DAZ and DAZL1 through DAZ
repeats.
Length = 136
Score = 33.7 bits (77), Expect = 0.059
Identities = 29/111 (26%), Positives = 36/111 (32%), Gaps = 15/111 (13%)
Query: 284 STLAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQL--GY 341
S L QPS PQ PY M Q A ++ P +Y G Y
Sbjct: 9 SELYQPSYVVPPQAQMPQASAPYP-GPSMYLPMAQVMAVGPQSSHPPMAYYPIGAPPPVY 67
Query: 342 PQGYVGMV------GRQVPGWQGI------PGAQPTAQQMAVAQAQPSMMA 380
P G +V G + G PG P A Q+A Q +M
Sbjct: 68 PPGSTVLVQGGFDAGARFGPGTGSSIPPPPPGCAPNAAQLAAMQGANVVMT 118
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 32.1 bits (73), Expect = 0.062
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP-GNDP--YAFLEFVHHTVAATALAA 65
++YVGN+D T E L A FS GP+ ++ + P YA++EF + A A
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRD-SVEAAVA 59
Query: 66 MNKRVFLEKEMKV 78
+++ F + +KV
Sbjct: 60 LDESSFRGRVIKV 72
Score = 31.8 bits (72), Expect = 0.10
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG++ + L+ F+ G I+ I+ D + KGYA++ F + E A+ A+
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV-AL 60
Query: 158 NGQWLGSRSIR 168
+ R I+
Sbjct: 61 DESSFRGRVIK 71
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 35.1 bits (81), Expect = 0.073
Identities = 24/119 (20%), Positives = 27/119 (22%), Gaps = 14/119 (11%)
Query: 285 TLAQPSAPTTP-----QPNSTAPQFPYIYNQQMGYWYP--------QAAAYTATAAQLPQ 331
L Q P P P +P P QA A QLPQ
Sbjct: 179 VLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQ 238
Query: 332 QFYQYGQLGYPQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFPTQ 390
Q Q +P M P Q Q QP+ Q
Sbjct: 239 QPPPLQQPQFPGLSQQMPPPPPQP-PQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPL 296
Score = 34.0 bits (78), Expect = 0.16
Identities = 28/129 (21%), Positives = 29/129 (22%), Gaps = 17/129 (13%)
Query: 276 WGKES--ENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQ--LPQ 331
WG E A S P P + Q Q A Q LPQ
Sbjct: 126 WGTAPKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQ---RQQAPQLPQPPQQVLPQ 182
Query: 332 Q-------FYQYGQLGYPQGYVGMVGRQVPGW--QGIPGAQPTAQQMAVAQAQ-PSMMAA 381
F Q G P GY Q A A Q P
Sbjct: 183 GMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPP 242
Query: 382 YAMQQFPTQ 390
QFP
Sbjct: 243 LQQPQFPGL 251
Score = 33.2 bits (76), Expect = 0.25
Identities = 23/110 (20%), Positives = 25/110 (22%), Gaps = 11/110 (10%)
Query: 287 AQPSAPTTPQPNSTAPQFP--YIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQG 344
Q P P Q G Q Y Q PQ + Q
Sbjct: 167 QQAPQLPQPPQQVLPQGMPPRQAAFPQQGP-PEQPPGYP----QPPQGHPEQVQPQQFLP 221
Query: 345 YVGMVGRQVPGWQGIPGAQPTAQQMAV----AQAQPSMMAAYAMQQFPTQ 390
Q P +P P QQ Q P QQ P Q
Sbjct: 222 APSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQ 271
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM1 of the majority of family members that include
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), heterogeneous
nuclear ribonucleoprotein L (hnRNP-L), heterogeneous
nuclear ribonucleoprotein L-like (hnRNP-LL),
polypyrimidine tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTBP2
is highly homologous to PTB and is perhaps specific to
the vertebrates. Unlike PTB, PTBP2 is enriched in the
brain and in some neural cell lines. It binds more
stably to the downstream control sequence (DCS) RNA than
PTB does but is a weaker repressor of splicing in vitro.
PTBP2 also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. In
addition, this family also includes RNA-binding motif
protein 20 (RBM20) that is an alternative splicing
regulator associated with dilated cardiomyopathy (DCM)
and contains only one RRM. .
Length = 74
Score = 31.8 bits (73), Expect = 0.074
Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES-------IHNTDI 267
D+ E + + SPFG + ++ + + K A V+ + E+A ++ I +
Sbjct: 10 DVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESAKSMVDYYLTVPALIRGRRV 67
Score = 27.5 bits (62), Expect = 2.6
Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 8/79 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ + +L P++ L +PFG+++N + L+ K A V A++ +
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLL------LRGKNQALVEMDSVESAKSMVDYY 55
Query: 158 --NGQWLGSRSIRTNWSTR 174
+ R + +S
Sbjct: 56 LTVPALIRGRRVYIQYSNH 74
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 32.2 bits (74), Expect = 0.079
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 101 GDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA--FVSFVKKAEAENAITAMN 158
DL PE+ KE + +G+++ I P FV F + A A+ +N
Sbjct: 18 EDLEPEV-----KEECSKYGKVTKVLIFEIPGASPDDEAVRIFVEFERVESAIKAVVDLN 72
Query: 159 GQWLGSRSIR 168
G++ G R+++
Sbjct: 73 GRFFGGRTVK 82
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 34.8 bits (79), Expect = 0.086
Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
++ GG G+ + + + K+FSP GT+ + + KG +F ++T+++ + +T N
Sbjct: 13 LHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFST-YN 71
Query: 269 GHTVKCFW 276
G C W
Sbjct: 72 G----CVW 75
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 31.5 bits (71), Expect = 0.098
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDIN 268
VY G E V + F +G I+++ + + GY FV+F A A+ ++ D+
Sbjct: 2 VYIGRLSYQARERDVERFFKGYGKILEVDL--KNGYGFVEFDDLRDADDAVYELNGKDLC 59
Query: 269 GHTV 272
G V
Sbjct: 60 GERV 63
Score = 30.7 bits (69), Expect = 0.21
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 9/71 (12%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G LS + + ++ F +G+I + GY FV F +A++A+ +
Sbjct: 2 VYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYEL 53
Query: 158 NGQWL-GSRSI 167
NG+ L G R I
Sbjct: 54 NGKDLCGERVI 64
>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast
sporulation-specific protein 2 (Ssp2) and similar
protein. This subfamily corresponds to the RRM of the
lineage specific yeast sporulation-specific protein 2
(Ssp2) and similar proteins. Ssp2 is encoded by a
sporulation-specific gene necessary for outer spore wall
assembly in the yeast Saccharomyces cerevisiae. It
localizes to the spore wall and may play an important
role after meiosis II and during spore wall formation.
Ssp2 contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 31.6 bits (72), Expect = 0.10
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 213 GFGKDLNEELVSKVFSPFGTIVDI-RVFKEKGYAFVKFTTKETATHAIESIHN 264
D + E + F+ FG IVDI + K + F +A A E++ +
Sbjct: 1 VLPSDFDVEELKDDFTVFGEIVDISPIISRKLCVSIFFADIRSAIRAKETLED 53
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 31.5 bits (72), Expect = 0.10
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG--YAFVKFTTKETATHAI----E 260
TV KD E + + F G I ++++ + +G A ++F T++ A A+ +
Sbjct: 1 LTVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEALAALTKDHK 60
Query: 261 SIHNTDIN 268
+ +I+
Sbjct: 61 RLGGNEIS 68
Score = 29.9 bits (68), Expect = 0.34
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM- 66
T+ V NL TE + F G ++ K I E A +EF ALAA+
Sbjct: 1 LTVKVKNLPKDTTENKIRQFFKDCGEIREVK-IVESEGGLVAVIEFETED---EALAALT 56
Query: 67 -NKRVFLEKEMKVN 79
+ + E+ V+
Sbjct: 57 KDHKRLGGNEISVS 70
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B") a unique protein that comprises the U2 snRNP.
It was initially identified as binding to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA. In addition, the
nuclear transport of U2B" is independent of U2 snRNA
binding. U2B" contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also contains a nuclear
localization signal (NLS) in the central domain.
However, nuclear import of U2B'' does not depend on this
NLS. The N-terminal RRM is sufficient to direct U2B" to
the nucleus. .
Length = 91
Score = 31.9 bits (72), Expect = 0.10
Identities = 22/83 (26%), Positives = 45/83 (54%), Gaps = 8/83 (9%)
Query: 94 NHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAE 149
NH I++ +L+ +I+ + LK + F+ FG + + ++ T+K +G AFV F + +
Sbjct: 1 NHT-IYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELSS 56
Query: 150 AENAITAMNGQWLGSRSIRTNWS 172
A NA+ + G + +R ++
Sbjct: 57 ATNALRQLQGFPFYGKPMRIQYA 79
Score = 31.5 bits (71), Expect = 0.15
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 206 NCTVYCGGFGKDLNEELVSK----VFSPFGTIVDI---RVFKEKGYAFVKFTTKETATHA 258
N T+Y + +E + + +FS FG +VDI + K +G AFV F +AT+A
Sbjct: 1 NHTIYINNLNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNA 60
Query: 259 IESIH 263
+ +
Sbjct: 61 LRQLQ 65
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic
translation initiation factor 4B (eIF-4B) and similar
proteins. This subfamily corresponds to the RRM of
eIF-4B, a multi-domain RNA-binding protein that has
been primarily implicated in promoting the binding of
40S ribosomal subunits to mRNA during translation
initiation. It contains two RNA-binding domains; the
N-terminal well-conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), binds the 18S rRNA of the
40S ribosomal subunit and the C-terminal basic domain
(BD), including two arginine-rich motifs (ARMs), binds
mRNA during initiation, and is primarily responsible
for the stimulation of the helicase activity of eIF-4A.
eIF-4B also contains a DRYG domain (a region rich in
Asp, Arg, Tyr, and Gly amino acids) in the middle,
which is responsible for both, self-association of
eIF-4B and binding to the p170 subunit of eIF3.
Additional research indicates that eIF-4B can interact
with the poly(A) binding protein (PABP) in mammalian
cells, which can stimulate both, the eIF-4B-mediated
activation of the helicase activity of eIF-4A and
binding of poly(A) by PABP. eIF-4B has also been shown
to interact specifically with the internal ribosome
entry sites (IRES) of several picornaviruses which
facilitate cap-independent translation initiation. .
Length = 77
Score = 31.6 bits (72), Expect = 0.11
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP----YAFLEF 53
P T Y+GNL VTEE + F + V ++ REPG+ + + EF
Sbjct: 1 PYTAYLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEF 50
>gnl|CDD|240960 cd12516, RRM1_RBM26, RNA recognition motif 1 of vertebrate
RNA-binding protein 26 (RBM26). This subgroup
corresponds to the RRM1 of RBM26, also known as
cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2,
which represents a cutaneous lymphoma (CL)-associated
antigen. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The RRMs may play some
functional roles in RNA-binding or protein-protein
interactions. .
Length = 76
Score = 31.5 bits (71), Expect = 0.11
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 227 FSPFGTIVDIRVF--KEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKE 279
FS FGT+V+++V + A ++F T E A AI S +N +K +W +E
Sbjct: 23 FSKFGTLVNLQVAYKGDPEGALIQFATHEEAKKAISSTEAV-LNNRFIKVYWHRE 76
>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM3 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence show that the
RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 93
Score = 31.9 bits (72), Expect = 0.12
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 6/95 (6%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ V +L+PE + Q L F +G++ +I+ K A V +A+ A++
Sbjct: 2 LLVSNLNPERVTPQCLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAMSH 56
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTK 191
+NGQ L + +R S + + E + TK
Sbjct: 57 LNGQKLHGKPLRITLSKHQTVQLPREGQEDQGLTK 91
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 31.1 bits (71), Expect = 0.13
Identities = 16/35 (45%), Positives = 22/35 (62%)
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
C + RDP T KSKG+A+V++ A A A +NG
Sbjct: 29 CDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNG 63
Score = 28.8 bits (65), Expect = 1.1
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
L+V + SVT+E L LF I ++ C + R+P +V ++ A+A+ A K
Sbjct: 3 LFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEK 60
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 91
Score = 31.4 bits (72), Expect = 0.14
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 112 LKEAFAPFGEISNCRIV-RDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI 167
L+E FG++ + R P G A V F + EA+ I A+NG+W R +
Sbjct: 29 LREECEKFGQVKKVVVFDRHPD-----GVASVKFKEPEEADRCIEALNGRWFAGRQL 80
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM3 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 86
Score = 31.4 bits (72), Expect = 0.15
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 130 DPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
D + + GYAF++FV AE A NG+
Sbjct: 36 DFKNKCNVGYAFINFVNPEYAEKFYKAFNGK 66
>gnl|CDD|241158 cd12714, RRM1_MATR3, RNA recognition motif 1 in vertebrate
matrin-3. This subgroup corresponds to the RRM1 of
Matrin 3 (MATR3 or P130), a highly conserved inner
nuclear matrix protein with a bipartite nuclear
localization signal (NLS), two zinc finger domains
predicted to bind DNA, and two RNA recognition motifs
(RRM), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that are known to interact
with RNA. MATR3 has been implicated in various
biological processes. It is involved in RNA processing
by interacting with other nuclear proteins to anchor
hyperedited RNAs to the nuclear matrix. It plays a role
in mRNA stabilization through maintaining the stability
of certain mRNA species. Besides, it modulates the
activity of proximal promoters by binding to highly
repetitive sequences of matrix/scaffold attachment
region (MAR/SAR). The phosphorylation of MATR3 is
assumed to cause neuronal death. It is phosphorylated by
the protein kinase ATM, which activates the cellular
response to double strand breaks in the DNA. Its
phosphorylation by protein kinase A (PKA) is responsible
for the activation of the N-methyl-d-aspartic acid
(NMDA) receptor. Furthermore, MATR3 has been identified
as both a Ca2+-dependent CaM-binding protein and a
downstream substrate of caspases. Additional research
indicates that matrin 3 also binds Rev/Rev responsive
element (RRE)-containing viral RNA and functions as a
cofactor that mediates the post-transcriptional
regulation of HIV-1. .
Length = 76
Score = 31.3 bits (71), Expect = 0.15
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 215 GKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
G +L E+L+ PFGTIV+ + + AF++ +T E A +
Sbjct: 11 GPNLREQLLQLA-KPFGTIVNHLILNKINEAFLEMSTHEEAVAMVN 55
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 31.5 bits (71), Expect = 0.15
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
+ + +FVG+L +I+ LKE F FG + RI K + FV F
Sbjct: 4 DSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVF 54
>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM2 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 82
Score = 31.3 bits (71), Expect = 0.15
Identities = 25/60 (41%), Positives = 30/60 (50%), Gaps = 9/60 (15%)
Query: 120 GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN--GQWLGSRSIRTNWSTRKPP 177
GE+S R++ D S AFV F AE+AI A+N G LGS IR S K P
Sbjct: 30 GEVSRLRLLGDYH--HSTRIAFVEFAM---AESAIAALNCSGAVLGSLPIRV--SPSKTP 82
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 30.9 bits (70), Expect = 0.16
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDING 269
K +++E + ++FS +G + I V K Y FV+F + E+ +AI I G
Sbjct: 10 KRVSKEDLFRIFSTYGELAQI-VLKN-AYGFVQFDSPESCANAINCEQGKMIRG 61
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both, nuclear and
cytoplasmic, roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RRMs.
Length = 71
Score = 30.6 bits (70), Expect = 0.18
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEK-GYAFVKFTTKETATHAIESIHNTDINGHT 271
+N + + +F +G ++ I+ K K G A V+ + A AIE ++ + G
Sbjct: 12 MNCDKLFNLFCLYGNVLRIKFLKSKPGTAMVQMGDPQAAERAIEYLNGVVLFGQK 66
>gnl|CDD|218290 pfam04847, Calcipressin, Calcipressin. Calcipressin is also known
as calcineurin-binding protein, since it inhibits
calcineurin-mediated transcriptional modulation by
binding to calcineurin's catalytic domain.
Length = 177
Score = 32.4 bits (74), Expect = 0.19
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 6/80 (7%)
Query: 219 NEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHA-IESIHNTDINGHTVKCFWG 277
N++ + ++F + IV + K V F++ E A A I+ ++ G +K ++
Sbjct: 9 NKDKLRELFRQYNPIVTFQPLKSFRRVRVNFSSPEAAAAARIKLHEGSEFLGKELKLYFA 68
Query: 278 K-----ESENNSTLAQPSAP 292
+ S LA P
Sbjct: 69 QPQHPERSAAKQHLAPPPPE 88
>gnl|CDD|240732 cd12286, RRM_Man1, RNA recognition motif in inner nuclear membrane
protein Man1 (Man1) and similar proteins. This
subfamily corresponds to the RRM of Man1, also termed
LEM domain-containing protein 3 (LEMD3), an integral
protein of the inner nuclear membrane that binds to
nuclear lamins and emerin, thus playing a role in
nuclear organization. It is part of a protein complex
essential for chromatin organization and cell division.
It also functions as an important negative regulator for
the transforming growth factor (TGF) beta/activin/Nodal
signaling pathway by directly interacting with
chromatin-associated proteins and transcriptional
regulators, including the R-Smads, Smad1, Smad2, and
Smad3. Moreover, Man1 is a unique type of left-right
(LR) signaling regulator that acts on the inner nuclear
membrane. Man1 plays a crucial role in angiogenesis. The
vascular remodeling can be regulated at the inner
nuclear membrane through the interaction between Man1
and Smads. Man1 contains an N-terminal LEM domain, two
putative transmembrane domains, a MAN1-Src1p C-terminal
(MSC) domain, and a C-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The LEM domain interacts
with the DNA and chromatin-binding protein
Barrier-to-Autointegration Factor, and is also necessary
for efficient localization of MAN1 in the inner nuclear
membrane. Research has indicated that C-terminal
nucleoplasmic region of Man1 exhibits a DNA binding
winged helix domain and is responsible for both DNA- and
Smad-binding. .
Length = 92
Score = 31.1 bits (71), Expect = 0.20
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 215 GKDLNEELVSKVFSPFGTIVDIRVFKE--KGYAFVKFTTKETATHAIESIHNTDINGH-- 270
+ + ++ K IV I+V K +G ++K ++ E A A +++H +G
Sbjct: 19 HVRIQDAILEKC-GDNNGIVHIQVDKASREGCVYIKCSSPEDAGKAFKALHGWWFDGRLV 77
Query: 271 TVK 273
TVK
Sbjct: 78 TVK 80
>gnl|CDD|241157 cd12713, RRM_TNRC6C, RNA recognition motif in vertebrate
trinucleotide repeat-containing gene 6C protein
(TNRC6C). This subgroup corresponds to the RRM of
TNRC6C, one of three GW182 paralogs in mammalian
genomes. It is enriched in P-bodies and important for
efficient miRNA-mediated repression. TNRC6C is composed
of an N-terminal glycine/tryptophan (G/W)-rich region
containing an Ago hook responsible for Ago
protein-binding; a ubiquitin-associated (UBA) domain and
a glutamine (Q)-rich region in the middle region; a
middle G/W-rich region, a RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal G/W-rich
region, at the C-terminus. A bipartite C-terminal region
including the middle and C-terminal G/W-rich regions is
referred as silencing domain that triggers silencing of
bound transcripts by inhibiting protein expression and
promoting mRNA decay via deadenylation. The C-terminal
half containing the RRM domain functions as a key
effector domain mediating protein synthesis repression
by TNRC6C. .
Length = 83
Score = 30.8 bits (69), Expect = 0.22
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 231 GTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESENNSTLAQ 288
G ++ + +G A V++++KE A A +S+H + T+ + E E N LAQ
Sbjct: 26 GPLITFHLNLTQGNAVVRYSSKEEAAKAQKSLHMCVLGNTTILAEFAGEEEVNRFLAQ 83
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both, nuclear and
cytoplasmic, roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 30.8 bits (70), Expect = 0.23
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 103 LSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT--AMNGQ 160
L + L EA + FG IS + P+ K A V F ++A+ + N
Sbjct: 10 LPDGVTEADLVEALSEFGPISY--VTMMPK----KRQALVEFEDISDAKACVNHAQQNPV 63
Query: 161 WLGSRSIRTNWSTRK 175
++ R N+ST +
Sbjct: 64 YIAGRQAYFNYSTSQ 78
Score = 28.9 bits (65), Expect = 0.89
Identities = 10/42 (23%), Positives = 17/42 (40%)
Query: 220 EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
E + + S FG I + + +K A V+F A +
Sbjct: 16 EADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVNH 57
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 3 in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologues exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 72
Score = 30.3 bits (69), Expect = 0.24
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
T + V NL TEE L LF + G + +++ P A +EF+ + A A ++
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLG--RLLLPPSRT-IALVEFLEPSDARKAFKSLA 57
Query: 68 KRVFLEKEMKVNWA 81
+ F + + WA
Sbjct: 58 YKRFKHVPLYLEWA 71
Score = 28.7 bits (65), Expect = 1.1
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I V +L + L+E F FG + R++ P S+ A V F++ ++A A ++
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSLG--RLLLPP----SRTIALVEFLEPSDARKAFKSL 56
Query: 158 N 158
Sbjct: 57 A 57
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 30.7 bits (70), Expect = 0.24
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTI--VDI-RVFKEKGYAFVKFTTKETATHAIESI 262
C ++ G G+ + E + + F FG + VD R E +V+F + A A+E +
Sbjct: 1 GCVLHFSGVGEQTSREDLKEAFEEFGEVAWVDFARGQTE---GYVRFKEENAAKEALEKL 57
Query: 263 ---HNTDINGHTVKC 274
N I G V
Sbjct: 58 KEAKNLKIKGSEVTV 72
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 84
Score = 30.8 bits (70), Expect = 0.26
Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 8/78 (10%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVK---GCKVIREPGNDPY-----AFLEFVHHTVAA 60
+Y+ NL S +EE L PV + +R + A+ EF A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 61 TALAAMNKRVFLEKEMKV 78
+ +N +VF +++ V
Sbjct: 61 KVVKDLNGKVFKNRKLFV 78
Score = 28.1 bits (63), Expect = 1.9
Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEIS---NCRIVR--DPQTLKSKGYAFVSFVKKAEAEN 152
+++ +LS + L+E F +S + VR + ++ G A+ F +AE
Sbjct: 2 VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61
Query: 153 AITAMNGQWLGSRSIR 168
+ +NG+ +R +
Sbjct: 62 VVKDLNGKVFKNRKLF 77
Score = 27.0 bits (60), Expect = 4.6
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 13/61 (21%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEK-----GYAFVKFTTKETATHAIESIHNTDINGHTV 272
L + V P T+ R F+ + G A+ +F++ E A ++ D+NG
Sbjct: 20 LKDFEPVSVLIPSQTV---RGFRSRRVRPLGIAYAEFSSPEQAEKVVK-----DLNGKVF 71
Query: 273 K 273
K
Sbjct: 72 K 72
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 30.1 bits (68), Expect = 0.26
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 218 LNEELVSKVFSPFGTIVDIRV--FKEKGYAFVKFTTKETAT 256
EE VS+ F FG ++D+R+ +++ + FV F ET
Sbjct: 11 FTEEDVSEYFGQFGPVLDVRIPYQQKRMFGFVTFENAETVK 51
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 30.5 bits (69), Expect = 0.26
Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG++ + L+ F G ++ I+ D + KG+A++ F K A+ A+
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-AL 60
Query: 158 NGQWLGSRSIRTN 170
+ R I+
Sbjct: 61 DESLFRGRQIKVM 73
Score = 30.2 bits (68), Expect = 0.35
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATALAA 65
++YVGN+D T E L A F G V ++ + G+ +A++EF TAL A
Sbjct: 1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-A 59
Query: 66 MNKRVFLEKEMKVN 79
+++ +F +++KV
Sbjct: 60 LDESLFRGRQIKVM 73
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 30.4 bits (68), Expect = 0.27
Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFS-PFGTIVDIRVFKEKGYAFVKFTTKETATHAIESI 262
P + T++ + + EE + +F+ GT+ + F++ A ++ +T E A A+ +
Sbjct: 1 PPSATLHLSNIPQSVTEEDLRTLFANTGGTVKAFKFFQDHKMALLQMSTVEEAIQALIDL 60
Query: 263 HNTDI-NGHTVKCFWGKES 280
HN ++ H ++ + K +
Sbjct: 61 HNYNLGENHHLRVSFSKST 79
>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar
proteins. This subgroup corresponds to the RRM of
PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect
modulator 6, a member of a family of transcription
coactivators that plays a central role in the regulation
of cellular energy metabolism. As an inducible
transcription coactivator, PGC-1alpha can interact with
a broad range of transcription factors involved in a
wide variety of biological responses, such as adaptive
thermogenesis, skeletal muscle fiber type switching,
glucose/fatty acid metabolism, and heart development.
PGC-1alpha stimulates mitochondrial biogenesis and
promotes oxidative metabolism. It participates in the
regulation of both carbohydrate and lipid metabolism and
plays a role in disorders such as obesity, diabetes, and
cardiomyopathy. PGC-1alpha is a multi-domain protein
containing an N-terminal activation domain region, a
central region involved in the interaction with at least
a nuclear receptor, and a C-terminal domain region. The
N-terminal domain region consists of three leucine-rich
motifs (L1, NR box 2 and 3), among which the two last
are required for interaction with nuclear receptors,
potential nuclear localization signals (NLS), and a
proline-rich region overlapping a putative repression
domain. The C-terminus of PGC-1alpha is composed of two
arginine/serine-rich regions (SR domains), a putative
dimerization domain, and an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). PGC-1alpha could interact
favorably with single-stranded RNA. .
Length = 91
Score = 30.7 bits (69), Expect = 0.28
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 11/64 (17%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG--YAFVSFVKKAEA----E 151
I+VG + P+ L++ F FGEI C + L+ G Y F+++ +A E
Sbjct: 5 IYVGKIRPDTTRTELRDRFEVFGEIEECTV-----NLRDDGDSYGFITYRYTCDAFAALE 59
Query: 152 NAIT 155
N T
Sbjct: 60 NGYT 63
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 30.3 bits (69), Expect = 0.30
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 213 GFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDING 269
GF K L + L ++F P I++ K + +AFV F ++E A+E + G
Sbjct: 18 GF-KQLKKFLKKQLFKP----HKIKLLKRQDFAFVTFRSEEERQKALEILDGFKWKG 69
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM1 domain in the Spen (split end) family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also known as one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong- to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 30.3 bits (69), Expect = 0.33
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 8 TTLYVGNLDVSVT----EELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL 63
TL V NL ++ E++L F + G V +V+ + ++ A++ F H A A
Sbjct: 2 KTLCVSNLPSKLSDEDIEDVLYHEFKKFGDVS-VRVLHDGEDERVAYVNFRHPEDAREAK 60
Query: 64 AAMNKRVFLEKEMKVNW 80
A + V ++ + V
Sbjct: 61 HAKGRLVLFDRPLNVEP 77
>gnl|CDD|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53
and similar proteins. This subfamily corresponds to the
RRM domain of nucleoporin Nup53, also termed mitotic
phosphoprotein 44 (MP-44), or nuclear pore complex
protein Nup53, required for normal cell growth and
nuclear morphology in vertebrate. It tightly associates
with the nuclear envelope membrane and the nuclear
lamina where it interacts with lamin B. It may also
interact with a group of nucleoporins including Nup93,
Nup155, and Nup205 and play a role in the association of
the mitotic checkpoint protein Mad1 with the nuclear
pore complex (NPC). The family also includes
Saccharomyces cerevisiae Nup53p, an ortholog of
vertebrate nucleoporin Nup53. A unique property of yeast
Nup53p is that it contains an additional Kap121p-binding
domain and interacts specifically with the karyopherin
Kap121p, which is involved in the assembly of Nup53p
into NPCs. Both, vertebrate Nup35 and yeast Nup53p,
contain an atypical RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a C-terminal amphipathic
alpha-helix and several FG repeats. This family
corresponds to the RRM domain which lacks the conserved
residues that typically bind RNA in canonical RRM
domains.
Length = 73
Score = 29.9 bits (68), Expect = 0.35
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
TV+ GF LV + FS GTI+++R + +K++++ A A+
Sbjct: 5 TVF--GFPPS-ALNLVLREFSSCGTILEVRYPPGANWIHLKYSSRLEAERALS 54
>gnl|CDD|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative
RNA-binding protein 15B (RBM15B) from vertebrate. This
subgroup corresponds to the RRM3 of RBM15B, also termed
one twenty-two 3 (OTT3), a paralog of RNA binding motif
protein 15 (RBM15), also known as One-twenty two protein
1 (OTT1). Like RBM15, RBM15B has post-transcriptional
regulatory activity. It is a nuclear protein sharing
with RBM15 the association with the splicing factor
compartment and the nuclear envelope as well as the
binding to mRNA export factors NXF1 and Aly/REF. RBM15B
belongs to the Spen (split end) protein family, which
shares a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 76
Score = 30.0 bits (67), Expect = 0.36
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 8/78 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L P L F FG I R +K +A++ + A+ A M
Sbjct: 5 LWVGGLGPNTSLAALAREFDRFGSI------RTIDYVKGDSFAYIQYESLDAAQAACAQM 58
Query: 158 NGQWLG--SRSIRTNWST 173
G LG R +R +++
Sbjct: 59 RGFPLGGPDRRLRVDFAK 76
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 30.8 bits (70), Expect = 0.36
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTI--VDIRVFKEKGYAFVKFTTKETATHAIES 261
+ G K + E + + FS G + VD ++GY V+F T E A A+E
Sbjct: 2 VILKFSGLNKPTSREDIKEAFSQHGEVKYVDFLEGDKEGY--VRFKTPEAAKKALEK 56
>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM2 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 89
Score = 30.4 bits (68), Expect = 0.36
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 10/83 (12%)
Query: 206 NCTVYCGGFGK-DLNEELVSKVFSPFGTIVDIRVF-------KEKGYAFVKFTTKETATH 257
NC ++ GG K EE++ ++ ++D+ V+ K +G+AFV++ + A
Sbjct: 1 NCRLFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60
Query: 258 AIESIHNTDIN--GHTVKCFWGK 278
A + I GH + W +
Sbjct: 61 ARRKLMPGRIQLWGHQIAVDWAE 83
>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin.
This subfamily corresponds to the RRM1 of ubiquitously
expressed protein nucleolin, also termed protein C23.
Nucleolin is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. RRM1,
together with RRM2, binds specifically to RNA stem-loops
containing the sequence (U/G)CCCG(A/G) in the loop. .
Length = 75
Score = 29.8 bits (67), Expect = 0.42
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
+ +FVG+L+P + LK A + F N + D + SK + +V F + E A+
Sbjct: 1 FSLFVGNLNPNKDFDELKTAISEFFSKKNLAVQ-DVRIGSSKKFGYVDFESAEDLEKAL 58
>gnl|CDD|240934 cd12490, RRM2_ACF, RNA recognition motif 2 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup corresponds
to the RRM2 of ACF, also termed APOBEC-1-stimulating
protein, an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. ACF shuttles between the cytoplasm
and nucleus. ACF contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high affinity
for an 11 nucleotide AU-rich mooring sequence 3' of the
edited cytidine in apoB mRNA. All three RRMs may be
required for complementation of editing activity in
living cells. RRM2/3 are implicated in ACF interaction
with APOBEC-1. .
Length = 85
Score = 30.0 bits (67), Expect = 0.44
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 206 NCTVYCGGFGK-DLNEELVSKVFSPFGTIVDIRVF-------KEKGYAFVKFTTKETATH 257
NC ++ GG K EE+++++ ++D+ V+ K +G+AFV++ + A
Sbjct: 2 NCRLFVGGIPKTKKREEILAEMKKVTDGVLDVIVYPSAADKAKNRGFAFVEYESHRAAAM 61
Query: 258 AIESIHNTDIN--GHTVKCFWGK 278
A + I GH + W +
Sbjct: 62 ARRKLLPGRIQLWGHPIAVDWAE 84
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44
(RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 29.5 bits (66), Expect = 0.50
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ VG LSP + L+ F + ++S + L + YA + F + ++A A+ M
Sbjct: 2 VHVGGLSPSVSEGDLRSHFQKY-QVSVISL----CKLSNYRYASLHFDRASDALLAVKKM 56
Query: 158 NGQWLGSRSIR 168
NG L SI+
Sbjct: 57 NGGVLSGLSIK 67
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both nuclear and
cytoplasmic roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 86
Score = 29.6 bits (67), Expect = 0.54
Identities = 12/51 (23%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKGY-AFVKFTTKETATHAIESIHNTDI 267
+ +++ + +P G ++ I +F++ G A V+F + ++A A +++ DI
Sbjct: 15 ITVDVIYTICNPHGKVLRIVIFRKNGVQAMVEFDSVDSAQRAKAALNGADI 65
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 81
Score = 29.7 bits (67), Expect = 0.55
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 126 RIVRDPQTLKSKGYAFVSFVKKAEAE 151
R++R T S+G+AFV F+ EA
Sbjct: 34 RLMRRKTTGASRGFAFVEFMSLEEAT 59
Score = 28.1 bits (63), Expect = 1.7
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 10/50 (20%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIE 260
D+ LVS P D+R+ + K G+AFV+F + E AT +E
Sbjct: 18 DIRNALVSHGVEP----KDVRLMRRKTTGASRGFAFVEFMSLEEATRWME 63
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 32.3 bits (73), Expect = 0.58
Identities = 24/107 (22%), Positives = 29/107 (27%), Gaps = 13/107 (12%)
Query: 280 SENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQL 339
+ + QP P Q QQ Q QQ Q Q
Sbjct: 190 QQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQN--------QQQQQMDQQ 241
Query: 340 GYPQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQ 386
P +G+Q G G+ QQM Q Q M QQ
Sbjct: 242 QGPADAQAQMGQQQQGQGGMQ-----PQQMQGGQMQVPMQQQPPQQQ 283
Score = 31.5 bits (71), Expect = 0.83
Identities = 20/111 (18%), Positives = 23/111 (20%), Gaps = 8/111 (7%)
Query: 288 QPSAPTTPQPNSTA--PQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGY 345
+ N P Q P Q Q Q
Sbjct: 171 GQAQGQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQL 230
Query: 346 VGMVGRQVPGWQGIPGAQPTAQQMAVAQAQP---SMMAAY---AMQQFPTQ 390
+Q+ QG AQ Q Q M MQQ P Q
Sbjct: 231 QNQQQQQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQ 281
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family may share similar expression
patterns and functions. CPEB-2 is an RNA-binding protein
that is abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation; it directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a Zn-finger motif.
In addition, they do have conserved nuclear export
signals that are not present in CPEB-1. .
Length = 92
Score = 29.7 bits (67), Expect = 0.58
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIV--------DIRVFKEKGYAFVKFTTKETATHAIE 260
V+ GG D++E+ ++ F FG +V F KGYAF+ F + + I+
Sbjct: 3 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 62
Query: 261 SIHNTD 266
+ D
Sbjct: 63 ACIEED 68
Score = 29.0 bits (65), Expect = 1.1
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 10/53 (18%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKS------KGYAFVSF 144
+FVG L P+I+ + +F FG + +V P +S KGYAF+ F
Sbjct: 3 VFVGGLPPDIDEDEITASFRRFGPL----VVDWPHKAESKSYFPPKGYAFLLF 51
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in yeast.
Yra2p belongs to the evolutionarily conserved REF (RNA
and export factor binding proteins) family of hnRNP-like
proteins. It is a major component of endogenous Yra1p
complexes. It interacts with Yra1p and functions as a
negative regulator of Yra1p. Yra2p consists of two
highly conserved N- and C-terminal boxes and a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 29.3 bits (66), Expect = 0.64
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 230 FGTIVDIRVF--KEKGYAFVKFTTKETATHAIESIHNTDINGHTV 272
FG V + + K+ A +F +E + ++NG +
Sbjct: 24 FGEPVYSKFYDHKDSRTAVFEFEDPSILEKVVEKYNGKELNGAKI 68
>gnl|CDD|241141 cd12697, RRM3_ROD1, RNA recognition motif 3 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM3 of ROD1 coding protein Rod1, a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. Rod1 contains
four repeats of RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain) and does have RNA binding activities. .
Length = 76
Score = 29.5 bits (66), Expect = 0.64
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ V +L+P+ I L F +G++ +I+ K A V +A+ A++
Sbjct: 3 LLVSNLNPDAITPHGLFILFGVYGDVHRVKIM-----FNKKENALVQMADATQAQLAMSH 57
Query: 157 MNGQWLGSRSIRTNWS 172
+NGQ L + IR S
Sbjct: 58 LNGQRLYGKVIRATLS 73
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and similar
proteins. This subfamily corresponds to the RRM of
Acinus, a caspase-3-activated nuclear factor that
induces apoptotic chromatin condensation after cleavage
by caspase-3 without inducing DNA fragmentation. It is
essential for apoptotic chromatin condensation and may
also participate in nuclear structural changes occurring
in normal cells. Acinus contains a P-loop motif and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), which
indicates Acinus might have ATPase and DNA/RNA-binding
activity. .
Length = 90
Score = 29.5 bits (67), Expect = 0.67
Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 5/74 (6%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF--KEKGYAFVKFTTKETATHAIESIH 263
++ + + ++ S GT V + K K + +V ++T E A E++H
Sbjct: 1 TRALHIDNLVRPFTLNQLKELLSETGTGVIEGFWMDKIKSHCYVTYSTVEEAVATREALH 60
Query: 264 NT---DINGHTVKC 274
N +K
Sbjct: 61 GLQWPSSNPKRLKV 74
Score = 28.0 bits (63), Expect = 2.8
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 137 KGYAFVSFVKKAEAENAITAMNG-QW 161
K + +V++ EA A++G QW
Sbjct: 39 KSHCYVTYSTVEEAVATREALHGLQW 64
>gnl|CDD|241221 cd12777, RRM1_PTBP1, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM1 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence shows that
the RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 81
Score = 29.2 bits (65), Expect = 0.74
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETA 255
D+ E V + PFG + ++ + K K AF++ T+E A
Sbjct: 11 DVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMNTEEAA 49
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2, Smad3
and Smad4, and stimulates Smad-mediated transactivation.
Cpo may play an important role in regulating normal
function of the nervous system, whereas mutations in
Mec-8 affect mechanosensory and chemosensory neuronal
function. All members contain a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Some
uncharacterized family members contain two RRMs; this
subfamily includes their RRM1. Their RRM2 shows high
sequence homology to the RRM of yeast proteins scw1,
Whi3, and Whi4.
Length = 79
Score = 29.2 bits (66), Expect = 0.81
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIR-VFKEKG------YAFVKFTTKETATHAIE 260
T++ G D+ E ++ +F PF R VFKEK FV F++ + A A++
Sbjct: 2 TLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMD 61
Query: 261 SIHNTDINGHT 271
++ + T
Sbjct: 62 ALQGYRFDPDT 72
Score = 28.4 bits (64), Expect = 1.6
Identities = 21/71 (29%), Positives = 28/71 (39%), Gaps = 12/71 (16%)
Query: 9 TLYVGNLDVSVTEELLCALF--------SQIGPVKGCKVIREPGNDPYAFLEFVHHTVAA 60
TL+V L V E L LF S++ V K E P F++F AA
Sbjct: 2 TLFVSGLPSDVKERELAHLFRPFPGYEASRL--VFKEKKGGEKQ--PVGFVDFSSAQCAA 57
Query: 61 TALAAMNKRVF 71
A+ A+ F
Sbjct: 58 AAMDALQGYRF 68
>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of
uncharacterized plant proteins similar to fission yeast
Vip1. This subfamily corresponds to the Vip1-like,
uncharacterized proteins found in plants. Although their
biological roles remain unclear, these proteins show
high sequence similarity to the fission yeast Vip1. Like
Vip1 protein, members in this family contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 69
Score = 29.0 bits (65), Expect = 0.86
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
V +LSP+ + + + F+ G+I I R + ++ A+V+F E A+
Sbjct: 3 VTNLSPKATERDIYDFFSFSGDIEYVEIQRSGEQSQT---AYVTFKDPQAQETAL 54
>gnl|CDD|227871 COG5584, COG5584, Predicted small secreted protein [Function
unknown].
Length = 103
Score = 29.4 bits (66), Expect = 0.95
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG-YAFV 142
I ++S E + +KEAF F I IV +P+ Y V
Sbjct: 20 VTISLIKDKNISRENALKVVKEAFKQFMNIKGSWIVYEPEVYPKTDKYRLV 70
>gnl|CDD|197850 smart00738, NGN, In Spt5p, this domain may confer affinity for
Spt4p. It possesses a RNP-like fold. In Spt5p, this
domain may confer affinity for Spt4p.Spt4p.
Length = 106
Score = 29.6 bits (67), Expect = 0.97
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 220 EELVSKVFSPFGTIVDIRVFKEK--------GYAFVKFTTKETATHAIESI 262
E+ + + P + +IR K+K GY FV+ ++ AI
Sbjct: 29 EDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGT 79
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 31.2 bits (70), Expect = 1.2
Identities = 26/92 (28%), Positives = 28/92 (30%), Gaps = 9/92 (9%)
Query: 287 AQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYV 346
QP P PQ PQ P Q Y PQ Q+ Q Q PQ
Sbjct: 753 QQPQQPVAPQQQYQQPQQPVAPQPQ--YQQPQQPVAP------QPQYQQPQQPVAPQPQY 804
Query: 347 GMVGRQV-PGWQGIPGAQPTAQQMAVAQAQPS 377
+ V P Q QP A Q Q Q
Sbjct: 805 QQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQP 836
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding
protein with multiple splicing (RBP-MS). This subfamily
corresponds to the RRM of RBP-MS, also termed heart and
RRM expressed sequence (hermes), an RNA-binding proteins
found in various vertebrate species. It contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). RBP-MS
physically interacts with Smad2, Smad3 and Smad4 and
plays a role in regulation of Smad-mediated
transcriptional activity. In addition, RBP-MS may be
involved in regulation of mRNA translation and
localization during Xenopus laevis development. .
Length = 76
Score = 28.5 bits (63), Expect = 1.3
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV L +I+ + L F PF I + + FVSF ++EAE A A+
Sbjct: 4 LFVSGLPLDIKPRELYLLFRPFKGYEGSLI----KLTSKQPVGFVSFDSRSEAEAAKNAL 59
Query: 158 NG 159
NG
Sbjct: 60 NG 61
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 92
Score = 28.7 bits (64), Expect = 1.4
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 3/85 (3%)
Query: 95 HYHIFVGDLSPE--IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
H D P + L+EAF+ + C++ Q + KG+A + + AE
Sbjct: 1 HSKCLCVDQLPPSLCDVGDLREAFSKIHAPTFCQLACG-QDGQLKGFAVLEYESAEMAEM 59
Query: 153 AITAMNGQWLGSRSIRTNWSTRKPP 177
+G L IR ++ PP
Sbjct: 60 VQQQADGLSLAGSHIRVSFCAPGPP 84
>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein
Vip1 and similar proteins. This subfamily corresponds
to Vip1, an RNA-binding protein encoded by gene vip1
from fission yeast Schizosaccharomyces pombe. Its
biological role remains unclear. Vip1 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 68
Score = 28.3 bits (63), Expect = 1.5
Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++V ++SP+ + + + F+ G+ISN + D ++ A ++F K + A+ A+
Sbjct: 1 VYVSNISPKTTEKQISDFFSFCGKISNLDLTNDGESQT----ATITFEKPSAAKTALLLD 56
Query: 158 NGQWLGSR 165
N G
Sbjct: 57 NALLGGKV 64
>gnl|CDD|241072 cd12628, RRM2_IGF2BP1, RNA recognition motif 2 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM2 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. It promotes mRNA
stabilization and functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD. It stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus (HCV)
5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing
HCV internal ribosome entry site (IRES)-mediated
translation initiation via the 3'-UTR. IGF2BP1 contains
four hnRNP K-homology (KH) domains, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a RGG RNA-binding
domain. It also contains two putative nuclear export
signals (NESs) and a putative nuclear localization
signal (NLS). .
Length = 76
Score = 28.1 bits (62), Expect = 1.6
Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
+ ++ P++ + L A +G + NC V T V++ + + AI +NG
Sbjct: 5 IRNIPPQLRWEVLDGLLAQYGTVENCEQV---NTDSETAVVNVTYGNREQTRQAIMKLNG 61
Query: 160 QWLGSRSIRTNW 171
L + +++ ++
Sbjct: 62 HQLENHALKVSY 73
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 28.1 bits (63), Expect = 1.7
Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA-FVSFVKKAEAENAITA 156
I + ++ P + + L + +G + NC V KS+ V++ +A+ A+
Sbjct: 3 IQISNIPPHVRWEDLDSLLSTYGTVKNCEQV----PTKSETATVNVTYESPEQAQQAVNK 58
Query: 157 MNG-QWLGS 164
+NG ++ GS
Sbjct: 59 LNGHEYEGS 67
>gnl|CDD|240874 cd12428, RRM_PARN, RNA recognition motif in poly(A)-specific
ribonuclease PARN and similar proteins. The subfamily
corresponds to the RRM of PARN, also termed
deadenylating nuclease, or deadenylation nuclease, or
polyadenylate-specific ribonuclease, a processive
poly(A)-specific 3'-exoribonuclease involved in the
decay of eukaryotic mRNAs. It specifically binds both,
the poly(A) tail at the 3' end and the 7-methylguanosine
(m7G) cap located at the 5' end of eukaryotic mRNAs, and
catalyzes the 3'- to 5'-end deadenylation of
single-stranded mRNA with a free 3' hydroxyl group both
in the nucleus and in the cytoplasm. PARN belongs to the
DEDD superfamily of exonucleases. It contains a nuclease
domain, an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and an R3H domain. PARN exists as a homodimer. The
nuclease domain is involved in the dimerization. RRM and
R3H domains are essential for the RNA-binding. .
Length = 65
Score = 27.6 bits (62), Expect = 1.8
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 11/74 (14%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
H+F E +T L + F+PFG I + + D A V+ +
Sbjct: 2 DHVFHLTFPKEWKTNDLLQLFSPFGGIK-IKWIDDTS-------ALVAL---SSPSAVTI 50
Query: 156 AMNGQWLGSRSIRT 169
A+ + S IRT
Sbjct: 51 ALKMSYHPSYKIRT 64
>gnl|CDD|241121 cd12677, RRM4_Nop4p, RNA recognition motif 4 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM4 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 156
Score = 29.6 bits (66), Expect = 1.9
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 128 VRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSI--RTNWSTRKPPAMTNERKR 185
+S+GY F+ F+ A A+ +NG + + I R P N++ R
Sbjct: 80 KAGSTAGRSRGYGFMEFISHKYALMALRWLNGHAVTVKKIIDAEIEWARLPNIDYNDKPR 139
Query: 186 Q 186
+
Sbjct: 140 R 140
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 28.2 bits (63), Expect = 1.9
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 2/70 (2%)
Query: 98 IFVGDLSPEIETQTLKEAFAP-FGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ V +L ++ ++E F G I + + KS G A ++F + +A A
Sbjct: 2 VIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGG-KSTGIANITFKRAGDATKAYDK 60
Query: 157 MNGQWLGSRS 166
NG+
Sbjct: 61 FNGRIDDGNR 70
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both, Nop12p and Nop13p, are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 85
Score = 28.3 bits (63), Expect = 2.0
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 215 GKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
G + +E +++V P V + KG+A+V FT++E AI
Sbjct: 24 GDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTSQEATKAAIA 69
>gnl|CDD|240992 cd12548, RRM_Set1A, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1A (Set1A). This
subgroup corresponds to the RRM of Setd1A, also termed
SET domain-containing protein 1A (Set1A), or lysine
N-methyltransferase 2F, or Set1/Ash2 histone
methyltransferase complex subunit Set1, a ubiquitously
expressed vertebrates histone methyltransferase that
exhibits high homology to yeast Set1. Set1A is localized
to euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1A contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), an N- SET
domain, and a C-terminal catalytic SET domain followed
by a post-SET domain. In contrast to Set1B, Set1A
additionally contains an HCF-1 binding motif that
interacts with HCF-1 in vivo. .
Length = 95
Score = 28.4 bits (63), Expect = 2.1
Identities = 14/56 (25%), Positives = 25/56 (44%)
Query: 103 LSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
L+ + L + FGE+ I+ P+T K G A V F A++ + ++
Sbjct: 10 LNDNVREPFLADMCRKFGEVEEVEILLHPKTRKHLGLARVLFTSTRGAKDTVKHLH 65
>gnl|CDD|241134 cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM3 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 97
Score = 28.3 bits (63), Expect = 2.2
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 226 VFSPFGTIVDIRVFKEKG--YAFVKFTTKETATHAIESI 262
VFS FG + I +F++ G A +++ TA +A E++
Sbjct: 23 VFSAFGFVQKIAIFEKNGGFQALIQYPDVPTAVNAKEAL 61
>gnl|CDD|240704 cd12258, RRM2_RBM26_like, RNA recognition motif 2 of vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM2 of RBM26, also
known as cutaneous T-cell lymphoma (CTCL) tumor antigen
se70-2, which represents a cutaneous lymphoma
(CL)-associated antigen. RBM26 contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
The RRMs may play some functional roles in RNA-binding
or protein-protein interactions.
Length = 72
Score = 27.6 bits (62), Expect = 2.3
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 116 FAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
FA FGEI + + + L ++F + EAE A A+ G+ +S+ +W
Sbjct: 25 FAQFGEIEDVEVDEEGLHL------VITFKTRKEAEIA--AVRGRRFKGKSLILSW 72
>gnl|CDD|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP)
and similar proteins. This subfamily corresponds to
the RRM2 of LKAP, a novel peroxisomal autoantigen that
co-localizes with a subset of cytoplasmic microbodies
marked by ABCD3 (ATP-binding cassette subfamily D
member 3, known previously as PMP-70) and/or PXF
(peroxisomal farnesylated protein, known previously as
PEX19). It associates with LIM kinase 2 (LIMK2) and may
serve as a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. LKAP contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). However, whether
those RRMs are bona fide RNA binding sites remains
unclear. Moreover, there is no evidence of LAKP
localization in the nucleus. Therefore, if the RRMs are
functional, their interaction with RNA species would be
restricted to the cytoplasm and peroxisomes.
Length = 89
Score = 28.1 bits (63), Expect = 2.4
Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 8/90 (8%)
Query: 5 SQPTTLYVGNLDVSVTE----ELLCALFSQIGPVKGCKVIREPGND--PYAFLEFVHHTV 58
S L V NLD ++ + L F + G V V P D A + +
Sbjct: 2 STGVDLQVSNLDYRLSRKELQQTLTNQFKRHGKVL--SVSLRPQTDGSLVASVRVPNLQD 59
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPGNQP 88
A A++ +++R K + V++A N+
Sbjct: 60 AQYAISQLHRRKIGSKRILVSYAQGSSNKS 89
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 29.5 bits (66), Expect = 2.4
Identities = 22/74 (29%), Positives = 25/74 (33%), Gaps = 13/74 (17%)
Query: 304 FPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQY-------GQLGYPQGYVGMVGRQVPGW 356
+P N QMG Y A Q QQ Y G G P G G V G
Sbjct: 7 YPQAMNPQMGG-----GNYPA-PGQPAQQGYANQGMGGPVGGGGGPGAGGGAPGGPVGGG 60
Query: 357 QGIPGAQPTAQQMA 370
G G P ++A
Sbjct: 61 GGGSGGPPGGGEVA 74
>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa
MCM3-associated protein (Map80) and similar proteins.
This subfamily corresponds to the RRM of Map80, also
termed germinal center-associated nuclear protein
(GANP), involved in the nuclear localization pathway of
MCM3, a protein necessary for the initiation of DNA
replication and also involves in controls that ensure
DNA replication is initiated once per cell cycle. Map80
contains one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 73
Score = 27.3 bits (61), Expect = 2.7
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 3/74 (4%)
Query: 208 TVYCGGFGKDLNE-ELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD 266
T+ C +LN+ + + + F FG + + K A V F +A A +
Sbjct: 2 TIQCKNIPDELNDKDWLERHFGKFGKVARVYCNPRKKSAVVHFFDHASAALAKKK--GKL 59
Query: 267 INGHTVKCFWGKES 280
+ ++ FWG +
Sbjct: 60 LQHKPIQIFWGSKK 73
Score = 27.0 bits (60), Expect = 4.3
Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 8/66 (12%)
Query: 110 QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRT 169
L+ F FG+ V K A V F A A A G+ L + I+
Sbjct: 16 DWLERHFGKFGK------VARVYCNPRKKSAVVHFFDHASAALA--KKKGKLLQHKPIQI 67
Query: 170 NWSTRK 175
W ++K
Sbjct: 68 FWGSKK 73
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 27.6 bits (61), Expect = 2.8
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRI 127
+ + +FVG+L +++ LKE F +G + RI
Sbjct: 2 DSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI 35
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM2 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 27.7 bits (61), Expect = 2.9
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
V +L + + L+EAF+ FG++ ++ D + + G V F K A A+
Sbjct: 4 VKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRG-RPTGKGIVEFAGKPSARKAL 57
>gnl|CDD|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM2 of RBM46, also termed
cancer/testis antigen 68 (CT68). It is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP R)
and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 85
Score = 27.7 bits (61), Expect = 3.3
Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 206 NCTVYCGGFGKD-LNEELVSKVFSPFGTIVDIRVF-------KEKGYAFVKFTTKETATH 257
NC ++ G K+ EE++ ++ ++D+ V+ K +G+AFV++ + A
Sbjct: 2 NCRLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRAAAM 61
Query: 258 AIESI--HNTDINGHTVKCFW 276
A + + GHT++ W
Sbjct: 62 ARRKLIPGTFQLWGHTIQVDW 82
>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM1 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 70
Score = 27.1 bits (60), Expect = 3.4
Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 11/80 (13%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I + +L ++ Q + + + + ++ C + KSK A V+ + +A AI +
Sbjct: 2 IVIRNLPADVTKQEVHDLLSDY-QVKYCDVD------KSKRTAQVTLLNGDQASRAIAKL 54
Query: 158 NGQWLGSRSIRTNWSTRKPP 177
+ R I S + P
Sbjct: 55 HQSSYKERKI----SVQLQP 70
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM3 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 27.2 bits (61), Expect = 3.5
Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ V +L+ E + L F +G++ +I+ K A + +A+ A+T
Sbjct: 2 LLVSNLNEEMVTPDALFTLFGVYGDVVRVKIL-----FNKKDTALIQMADPQQAQTALTH 56
Query: 157 MNGQWLGSRSIRTNWS 172
+NG L + +R S
Sbjct: 57 LNGIRLHGKKLRVTLS 72
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B). This
subgroup corresponds to the RRM of Setd1B, also termed
SET domain-containing protein 1B (Set1B), or lysine
N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits high
homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone H3
at Lys4. Set1B contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), an N- SET domain, and a
C-terminal catalytic SET domain followed by a post-SET
domain. .
Length = 93
Score = 27.7 bits (61), Expect = 3.7
Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDINGH 270
++ E ++ + +G + ++ + K G A V F T + A A++ +HNT + G+
Sbjct: 13 NIRENFLTDMCKKYGEVEEVEILYNPKNKKHLGIAKVVFATVKGAKDAVQHLHNTSVMGN 72
Query: 271 TV 272
+
Sbjct: 73 II 74
>gnl|CDD|172049 PRK13427, PRK13427, F0F1 ATP synthase subunit gamma; Provisional.
Length = 289
Score = 29.1 bits (65), Expect = 3.7
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 211 CGGFGKDLNEELVSKV--FSPFGTIVDIRVFKEKGYAFVKFTTKETAT 256
CGGF +LN +++ G V++ + +KG +F KF ++
Sbjct: 89 CGGFNSNLNRMAKARIAELKKKGVNVELHIVGKKGISFFKFAGEKAEK 136
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM3 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 72
Score = 27.0 bits (60), Expect = 4.1
Identities = 22/73 (30%), Positives = 31/73 (42%), Gaps = 9/73 (12%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TT+ V N T E L LF G + +V+ P A +EF + A A A+
Sbjct: 1 TTILVKNFPYGTTAEELRDLFEPHGKLT--RVLMPPAG-TIAIVEFANPQQARLAFKALA 57
Query: 68 KR------VFLEK 74
R ++LEK
Sbjct: 58 YRRFKDSILYLEK 70
>gnl|CDD|183031 PRK11194, PRK11194, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 372
Score = 28.9 bits (65), Expect = 4.9
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 117 APFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
AP+G SN RI R + L Y F V+K ++ I A GQ G RT + +K
Sbjct: 305 APYGRSSNSRIDRFSKVLME--YGFTVIVRKTRGDD-IDAACGQLAGDVIDRTKRTLKK 360
>gnl|CDD|241222 cd12778, RRM1_PTBP2, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM1 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 82
Score = 27.0 bits (59), Expect = 4.9
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 229 PFGTIVDIRVFKEKGYAFVKFTTKETAT 256
PFG + +I + K K AF++ T+E A
Sbjct: 24 PFGKVTNILMLKGKNQAFLELATEEAAI 51
>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 617
Score = 29.0 bits (65), Expect = 5.3
Identities = 18/96 (18%), Positives = 30/96 (31%), Gaps = 13/96 (13%)
Query: 283 NSTLAQPSAPTTPQPNSTAPQFPYIYNQQM-GYWYPQAAAYTATAAQLPQQFYQYGQLGY 341
+ + +P+ P ++ P+ P + GY P+A + Q + Y
Sbjct: 89 DPSAGEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQL--PTARPAY 146
Query: 342 PQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQPS 377
P + PGA P A Q Q
Sbjct: 147 PAYQQ----------RPEPGAWPRAADDYGWQQQRL 172
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 27.3 bits (61), Expect = 5.3
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 138 GYAFVSFVKKAEAENAITAMNGQWLGSRSIR 168
G +V F ++ +AE A+ +N +W + I
Sbjct: 69 GNVYVKFRREEDAEKAVNDLNNRWFNGQPIY 99
>gnl|CDD|241132 cd12688, RRM1_PTBP1_like, RNA recognition motif 1 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM1 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
functions at several aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein and negatively regulates the
onset of differentiation. ROD1 is predominantly
expressed in hematopoietic cells or organs. It may play
a role controlling differentiation in mammals. All
members in this family contain four RNA recognition
motifs (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 81
Score = 27.0 bits (60), Expect = 5.4
Identities = 10/46 (21%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 229 PFGTIVDIRVFKEKGYAFVKFTTKETA-------THAIESIHNTDI 267
PFG + ++ + K K AF++ +E A T+ ++ +
Sbjct: 23 PFGKVTNVLMLKGKNQAFLEMADEEAAVTMVNYYTYVTPNLRGRPV 68
>gnl|CDD|215803 pfam00225, Kinesin, Kinesin motor domain.
Length = 326
Score = 28.3 bits (64), Expect = 6.5
Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 9/73 (12%)
Query: 164 SRSIRTNWSTRKPPAMTNERKRQNS--HTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEE 221
SR + + + E + KT TFD V++ + T VY ++ +
Sbjct: 11 SRGSSDIVNVDETDSEDKESVVITNKGREKTFTFDRVFDPEA-TQEFVY-----EETAKP 64
Query: 222 LVSKVFSPF-GTI 233
LV V + TI
Sbjct: 65 LVESVLEGYNVTI 77
>gnl|CDD|241167 cd12723, RRM1_CPEB1, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding
protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 100
Score = 27.0 bits (60), Expect = 6.9
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 14/66 (21%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEIS------NCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+F+G + +I L F PFG +S + + R P KGY ++ F E+E
Sbjct: 5 VFLGGVPWDITEAGLINTFKPFGSVSVEWPGKDGKHPRHPP----KGYVYLIF----ESE 56
Query: 152 NAITAM 157
++ A+
Sbjct: 57 KSVKAL 62
>gnl|CDD|205507 pfam13327, T3SS_LEE_assoc, Type III secretion system subunit. This
is a family of bacterial putative type III secretion
apparatus proteins associated with the locus of
enterocyte effacement (LEE).
Length = 163
Score = 27.6 bits (62), Expect = 8.5
Identities = 7/30 (23%), Positives = 9/30 (30%)
Query: 309 NQQMGYWYPQAAAYTATAAQLPQQFYQYGQ 338
Q +G W QLP + G
Sbjct: 112 QQLIGLWPGGQCPAELPPEQLPSVALRLGT 141
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins is
found in bacteria. Proteins in this family are typically
between 115 and 181 amino acids in length. There are two
completely conserved residues (F and G) that may be
functionally important.
Length = 110
Score = 26.6 bits (59), Expect = 9.9
Identities = 12/51 (23%), Positives = 14/51 (27%)
Query: 295 PQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGY 345
P +T P QQ P PQQ + PQ Y
Sbjct: 2 PYQQNTNQYPPQNQQQQPYQQQPYHQQMPPPPYSPPQQQQGHFMPPQPQPY 52
>gnl|CDD|182713 PRK10768, PRK10768, ribonucleoside hydrolase RihC; Provisional.
Length = 304
Score = 28.0 bits (63), Expect = 9.9
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 243 GYAFVKFTTKETATHAIESIHNT 265
GY F + T K + A+E++ +
Sbjct: 88 GYDFPEHTRKPLSIPAVEAMRDA 110
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.130 0.395
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,354,479
Number of extensions: 1787256
Number of successful extensions: 3225
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2796
Number of HSP's successfully gapped: 996
Length of query: 390
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 291
Effective length of database: 6,546,556
Effective search space: 1905047796
Effective search space used: 1905047796
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (27.0 bits)