RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy300
(451 letters)
>gnl|CDD|178309 PLN02707, PLN02707, Soluble inorganic pyrophosphatase.
Length = 267
Score = 239 bits (611), Expect = 2e-76
Identities = 100/180 (55%), Positives = 128/180 (71%), Gaps = 12/180 (6%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
+SP+HDIPL++ D FN VVEIP+ T+AKME+ +EP PIKQD KKG LR
Sbjct: 57 VSPWHDIPLHAG--DGTFNFVVEIPKETSAKMEVATDEPFTPIKQDTKKGKLRDY----- 109
Query: 224 HHGYIWNYGALPQTWENPDETDAHT---GQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
+ WNYG LPQTWE+P T A+ G GD DP+DV+EIGER AK GE+++VK LGV
Sbjct: 110 PYNINWNYGLLPQTWEDP--THANPEVEGAFGDNDPVDVVEIGERAAKIGEVLKVKPLGV 167
Query: 281 IGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENV 340
+ +IDEG+ DWK++AI+ +DP A+ +NDV D+E HFPG L A +WF+ YKIPDGKP N
Sbjct: 168 LAMIDEGELDWKVVAISADDPKASLVNDVDDVEKHFPGTLTAIRDWFRDYKIPDGKPANK 227
Score = 50.9 bits (122), Expect = 4e-07
Identities = 21/34 (61%), Positives = 27/34 (79%), Gaps = 2/34 (5%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
+SP+HDIPL++ D FN VVEIP+ T+AKMEV
Sbjct: 57 VSPWHDIPLHAG--DGTFNFVVEIPKETSAKMEV 88
>gnl|CDD|238239 cd00412, pyrophosphatase, Inorganic pyrophosphatase. These enzymes
hydrolyze inorganic pyrophosphate (PPi) to two molecules
of orthophosphates (Pi). The reaction requires bivalent
cations. The enzymes in general exist as homooligomers.
Length = 155
Score = 186 bits (476), Expect = 8e-58
Identities = 65/162 (40%), Positives = 94/162 (58%), Gaps = 26/162 (16%)
Query: 179 KIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTW 238
++ N+V+EIP+ +NAK EI+ PIK D R++ + GY WNYG +PQT
Sbjct: 1 EVVNVVIEIPKGSNAKYEIDKET--GPIKVD------RFLYS---SMGYPWNYGFIPQTL 49
Query: 239 ENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINV 298
E DGDP+DVL IGE G +I+V+ LGV+ +IDEG+TDWK+IA+ V
Sbjct: 50 E------------DDGDPLDVLVIGEEPLFPGSVIRVRPLGVLKMIDEGETDWKVIAVPV 97
Query: 299 NDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENV 340
+DP + +ND++D+ P L +F+ YK +GK E
Sbjct: 98 DDPRYSHINDISDVP---PHLLDEIKHFFEHYKDLEGKKEVK 136
Score = 40.2 bits (95), Expect = 4e-04
Identities = 9/19 (47%), Positives = 16/19 (84%)
Query: 400 KIFNMVVEIPRWTNAKMEV 418
++ N+V+EIP+ +NAK E+
Sbjct: 1 EVVNVVIEIPKGSNAKYEI 19
>gnl|CDD|189686 pfam00719, Pyrophosphatase, Inorganic pyrophosphatase.
Length = 156
Score = 170 bits (434), Expect = 2e-51
Identities = 56/153 (36%), Positives = 84/153 (54%), Gaps = 26/153 (16%)
Query: 182 NMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENP 241
N+V+EIP+ + K EI+ L P+ + + Y + GY +NYG +PQT E
Sbjct: 1 NVVIEIPKGSRVKYEIDKESGLLPVDR------VLYTS-----MGYPFNYGFIPQTLE-- 47
Query: 242 DETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDP 301
GDGDP+DVL +G G +++V+ +GV+ +IDEG+TD KIIA+ V+DP
Sbjct: 48 ----------GDGDPLDVLVLGPEPLFPGSVVRVRPIGVLAMIDEGETDDKIIAVPVDDP 97
Query: 302 NAAKLNDVADIETHFPGYLKATNEWFKIYKIPD 334
+D+ DIE PG L +F+ YK +
Sbjct: 98 RY---DDIKDIEDLPPGLLDEIEHFFEHYKDLE 127
Score = 37.8 bits (89), Expect = 0.003
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 403 NMVVEIPRWTNAKMEV 418
N+V+EIP+ + K E+
Sbjct: 1 NVVIEIPKGSRVKYEI 16
>gnl|CDD|223299 COG0221, Ppa, Inorganic pyrophosphatase [Energy production and
conversion].
Length = 171
Score = 147 bits (374), Expect = 2e-42
Identities = 50/169 (29%), Positives = 79/169 (46%), Gaps = 25/169 (14%)
Query: 165 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPH 224
H IP + D+ N+V+EIP+ +N K E++ + + +K
Sbjct: 1 MDLHKIPAGPD--DEDINVVIEIPKGSNIKYEVDKETGRLLVDRPLKTP----------- 47
Query: 225 HGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLI 284
GY NYG +P T DGDP+DVL IGE G +IQ + +GV+ +I
Sbjct: 48 MGYPVNYGFIPNTLS------------DDGDPLDVLVIGEEPLAPGCVIQARPIGVLKMI 95
Query: 285 DEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIP 333
DEG+ D K+IA+ DP + D++D+ H ++ E +K +
Sbjct: 96 DEGEKDDKVIAVPKLDPRYEHIKDISDLPEHLLDEIQHFFETYKDLEKG 144
Score = 41.1 bits (97), Expect = 3e-04
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 386 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
H IP + D+ N+V+EIP+ +N K EV
Sbjct: 1 MDLHKIPAGPD--DEDINVVIEIPKGSNIKYEV 31
>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 = 78.5 bits (194), Expect = 3e-18
Identities = 24/67 (35%), Positives = 40/67 (59%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
LF+ NLP TEE+ +E F ++G+I +++++ DGK KG F+ + + A KA+ N
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 95 KKPYKGK 101
K G+
Sbjct: 61 GKELDGR 67
Score = 62.7 bits (153), Expect = 1e-12
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEE+ +E F ++G+I +++++ DGK KG F+ + + A KA+ N K G
Sbjct: 9 DTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDG 66
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 78.4 bits (194), Expect = 4e-18
Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
LF+ NLP TEEE +E F ++G + +L+++ + GK KG F+ + ++ A KA+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 93 SNKKPYKGK 101
N K G+
Sbjct: 61 LNGKELDGR 69
Score = 61.1 bits (149), Expect = 5e-12
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
TEEE +E F ++G + +L+++ + GK KG F+ + ++ A KA+ N K G
Sbjct: 10 DTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGR 69
Query: 160 E 160
Sbjct: 70 P 70
>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 = 74.2 bits (183), Expect = 1e-16
Identities = 22/67 (32%), Positives = 39/67 (58%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
LF+ NLP TEE+ K+ F ++G I +++++ G+ KG F+ + ++ A KA+ N
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 95 KKPYKGK 101
K G+
Sbjct: 61 GKELGGR 67
Score = 60.7 bits (148), Expect = 6e-12
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
TEE+ K+ F ++G I +++++ G+ KG F+ + ++ A KA+ N K G E
Sbjct: 10 TTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRE 68
>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 = 79.9 bits (197), Expect = 5e-16
Identities = 43/193 (22%), Positives = 85/193 (44%), Gaps = 49/193 (25%)
Query: 11 KKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG 70
K+ + + KK ER+ K L++KNL + E++ +E F ++G+I A ++K+ G
Sbjct: 157 KEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSG 216
Query: 71 KLKGCGFINYANKISAVKAILKSN----------KKPYKGK------------------- 101
+ +G F+N+ A KA+ + N KK Y G+
Sbjct: 217 RSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQ 276
Query: 102 --------------------ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 141
+T+E+ +E F + G+I A+++ + G +G GF+ ++N
Sbjct: 277 QERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNP 336
Query: 142 ISAVKAILKSNKK 154
A +A+ + + +
Sbjct: 337 EEANRAVTEMHGR 349
Score = 78.7 bits (194), Expect = 1e-15
Identities = 39/164 (23%), Positives = 77/164 (46%), Gaps = 32/164 (19%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
G +F+KNL + + + F ++G+I+ ++ + +GK +G GF+++ + SA AI K
Sbjct: 89 GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148
Query: 93 SN------KKPYKGK--------------------------ITEEEFKEHFGQYGDIIDA 120
N K+ Y G+ + E++ +E F ++G+I A
Sbjct: 149 VNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSA 208
Query: 121 QLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLI 164
++K+ G+ +G F+N+ A KA+ + N K ++ G
Sbjct: 209 AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKK 252
Score = 58.7 bits (142), Expect = 3e-09
Identities = 25/96 (26%), Positives = 56/96 (58%), Gaps = 1/96 (1%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
K+ + + E ++K ++ + +K K + L++KNL +T+E+ +E F + G+I A+++
Sbjct: 260 KRAEREAELRRKFEELQQERK-MKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVM 318
Query: 66 KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+ G +G GF+ ++N A +A+ + + + GK
Sbjct: 319 LDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK 354
Score = 53.3 bits (128), Expect = 1e-07
Identities = 30/148 (20%), Positives = 66/148 (44%), Gaps = 30/148 (20%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS 93
L++ +L +TE + + F +G ++ ++ +++ + G G++N+ N A +A+
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 94 NKKPYKGK-----------------------------ITEEEFKEHFGQYGDIIDAQLLK 124
N K GK + + + F ++G+I+ ++
Sbjct: 63 NFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT 122
Query: 125 NADGKLKGCGFINYANKISAVKAILKSN 152
+ +GK +G GF+++ + SA AI K N
Sbjct: 123 DENGKSRGYGFVHFEKEESAKAAIQKVN 150
Score = 31.7 bits (72), Expect = 0.79
Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+TE + + F +G ++ ++ +++ + G G++N+ N A +A+ N K G
Sbjct: 11 DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGG 69
>gnl|CDD|178001 PLN02373, PLN02373, soluble inorganic pyrophosphatase.
Length = 188
Score = 74.8 bits (184), Expect = 1e-15
Identities = 52/174 (29%), Positives = 83/174 (47%), Gaps = 31/174 (17%)
Query: 166 PFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHH 225
P+HD+ + IFN VVEI + + K E++ L IK + Y + V+PH
Sbjct: 11 PWHDLEIGPGAP-AIFNCVVEITKGSKVKYELDKKTGL------IKVDRVLYSSVVYPH- 62
Query: 226 GYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLID 285
NYG +P+T D DP+DVL + + G ++ +A+G++ +ID
Sbjct: 63 ----NYGFIPRTLCE------------DNDPLDVLVLMQEPVLPGCFLRARAIGLMPMID 106
Query: 286 EGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
+G+ D KIIA+ +DP D+ ++ H L +F+ YK K EN
Sbjct: 107 QGEKDDKIIAVCADDPEYRHYTDIKELPPH---RLAEIRRFFEDYK----KNEN 153
>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 = 69.6 bits (171), Expect = 5e-15
Identities = 27/68 (39%), Positives = 40/68 (58%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
RL ++NLPFK TE + K+ F +G + + + + DGK KG F+ + +K A KAI
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60
Query: 94 NKKPYKGK 101
N K KG+
Sbjct: 61 NGKKIKGR 68
Score = 53.4 bits (129), Expect = 2e-09
Identities = 21/58 (36%), Positives = 31/58 (53%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
K TE + K+ F +G + + + + DGK KG F+ + +K A KAI N K KG
Sbjct: 10 KCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKG 67
>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 = 66.8 bits (164), Expect = 4e-14
Identities = 28/67 (41%), Positives = 45/67 (67%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+++KNL + +E+ KE FG+YG I A+++K+ +GK KG GF+N+ N +A KA+ + N
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63
Query: 95 KKPYKGK 101
K GK
Sbjct: 64 GKEVNGK 70
Score = 54.5 bits (132), Expect = 9e-10
Identities = 24/57 (42%), Positives = 38/57 (66%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ +E+ KE FG+YG I A+++K+ +GK KG GF+N+ N +A KA+ + N K G
Sbjct: 13 MDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVNG 69
>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 = 63.0 bits (154), Expect = 1e-12
Identities = 21/62 (33%), Positives = 39/62 (62%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+ +KNLP +TE+ +EHF G++ D ++++ DGK + GF+ + ++ A +A+
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYF 61
Query: 94 NK 95
NK
Sbjct: 62 NK 63
Score = 48.8 bits (117), Expect = 1e-07
Identities = 16/52 (30%), Positives = 32/52 (61%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
+TE+ +EHF G++ D ++++ DGK + GF+ + ++ A +A+ NK
Sbjct: 12 VTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNK 63
>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 = 62.3 bits (152), Expect = 1e-12
Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
RLF++NLPF TEEE +E F +G+I + L L + KG F+++ AVKA +
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 93 SNKKPYKGKI 102
+ ++G++
Sbjct: 61 LDGSIFQGRL 70
Score = 41.1 bits (97), Expect = 4e-05
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEEE +E F +G+I + L L + KG F+++ AVKA + + ++G
Sbjct: 12 TEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQG 68
>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 = 61.9 bits (151), Expect = 2e-12
Identities = 24/62 (38%), Positives = 34/62 (54%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
RL +KNLP I E++ ++ F +G I D QL DGK + GF+ Y + A KA+
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHF 61
Query: 94 NK 95
N
Sbjct: 62 NN 63
Score = 48.8 bits (117), Expect = 1e-07
Identities = 18/53 (33%), Positives = 27/53 (50%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
I E++ ++ F +G I D QL DGK + GF+ Y + A KA+ N
Sbjct: 11 GIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNN 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 = 61.8 bits (151), Expect = 3e-12
Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 90
+FI+NLPF TEEE KE F Q+G++ A+++K+ KG F+ + K SA K +
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59
Score = 45.7 bits (109), Expect = 2e-06
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 148
TEEE KE F Q+G++ A+++K+ KG F+ + K SA K +
Sbjct: 13 TEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59
>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 = 61.3 bits (149), Expect = 5e-12
Identities = 25/69 (36%), Positives = 42/69 (60%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+LF+ LPF +T+EE ++ F ++G + +L+ N GK KG ++ Y N+ SA +A+LK
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63
Query: 94 NKKPYKGKI 102
+ K K
Sbjct: 64 DGTEIKEKT 72
Score = 43.9 bits (104), Expect = 6e-06
Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T+EE ++ F ++G + +L+ N GK KG ++ Y N+ SA +A+LK + K
Sbjct: 15 TKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKE 70
>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 = 59.7 bits (145), Expect = 1e-11
Identities = 28/72 (38%), Positives = 48/72 (66%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
++F+ LP +TEEEFKE+F Q+G ++DAQL+++ D G+ +G GF+ + ++ SAV+ +
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE-SAVERVFS 59
Query: 93 SNKKPYKGKITE 104
+ GK E
Sbjct: 60 AGMLELGGKQVE 71
Score = 52.8 bits (127), Expect = 4e-09
Identities = 22/49 (44%), Positives = 38/49 (77%), Gaps = 2/49 (4%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 149
+TEEEFKE+F Q+G ++DAQL+++ D G+ +G GF+ + ++ SAV+ +
Sbjct: 11 VTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE-SAVERVF 58
>gnl|CDD|179080 PRK00642, PRK00642, inorganic pyrophosphatase; Provisional.
Length = 205
Score = 63.1 bits (154), Expect = 1e-11
Identities = 33/118 (27%), Positives = 55/118 (46%), Gaps = 11/118 (9%)
Query: 231 YGALPQTWENP------DETDAHTGQKGDGDPIDVLEIGERIAKRGEII-QVKALGVIGL 283
YG +P+T+ E KGDGDP+D+ + E+ G I+ Q + +G + +
Sbjct: 64 YGFIPRTYCGDLSGKLSGEQSGREDIKGDGDPLDICVLTEKNITHGNILLQARPIGGLRM 123
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK-IPDGKPENV 340
ID G+ D KIIA+ +D ++ D+++ L +F YK P + V
Sbjct: 124 IDGGEADDKIIAVLEDDLVYGEIKDISECP---GTLLDRLQHYFLTYKATPGELIKGV 178
>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 = 59.6 bits (145), Expect = 2e-11
Identities = 27/58 (46%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
RL +KNLP +TE E KEHF + G+I D +LL+ DGK + FI Y + A KA
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAK 59
Score = 44.6 bits (106), Expect = 3e-06
Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 101 KITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
+TE E KEHF + G+I D +LL+ DGK + FI Y + A KA
Sbjct: 11 SLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAK 59
>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 = 65.3 bits (159), Expect = 2e-11
Identities = 40/187 (21%), Positives = 77/187 (41%), Gaps = 40/187 (21%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
+ +++ ++ G+ E + +F+ L K E + E F + G + D Q +
Sbjct: 63 GDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCI 122
Query: 66 KNAD-GKLKGCGFINYANKISAVKAI---------------------------------- 90
K+ + + KG ++ + + S +KA+
Sbjct: 123 KDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGD 182
Query: 91 LKSNKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAV 145
+ + K Y G ITE+E ++ F +GDI D QL ++ + G+ KG GFI + + A
Sbjct: 183 IPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAK 242
Query: 146 KAILKSN 152
+A+ N
Sbjct: 243 EALEVMN 249
>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 = 59.1 bits (144), Expect = 2e-11
Identities = 21/58 (36%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
+LF+ LP TEE+ + F +YG+I + ++++ D G+ KGC F+ ++++ A KAI
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAI 58
Score = 49.1 bits (118), Expect = 8e-08
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK-SNKKPYKG 158
TEE+ + F +YG+I + ++++ D G+ KGC F+ ++++ A KAI K G
Sbjct: 10 TATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPG 69
Query: 159 SENGLI 164
+ L
Sbjct: 70 ASRPLQ 75
>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 = 58.5 bits (142), Expect = 3e-11
Identities = 19/62 (30%), Positives = 39/62 (62%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
LF+ NL + +++ +E F + G+++D ++ ++ DG+ KG G + +A + A KA+ KS
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60
Query: 94 NK 95
+
Sbjct: 61 GE 62
Score = 43.1 bits (102), Expect = 1e-05
Identities = 15/53 (28%), Positives = 33/53 (62%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
+++ +E F + G+++D ++ ++ DG+ KG G + +A + A KA+ KS +
Sbjct: 10 SAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKSGE 62
>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 = 56.9 bits (138), Expect = 2e-10
Identities = 22/67 (32%), Positives = 39/67 (58%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L++KNL I +E +E F +G I A+++ + G+ KG GF+ +++ A KA+ + N
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63
Query: 95 KKPYKGK 101
+ GK
Sbjct: 64 GRIIGGK 70
Score = 44.9 bits (107), Expect = 2e-06
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
I +E +E F +G I A+++ + G+ KG GF+ +++ A KA+ + N +
Sbjct: 13 IDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNGR 65
>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 = 55.5 bits (134), Expect = 5e-10
Identities = 20/71 (28%), Positives = 44/71 (61%), Gaps = 1/71 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAIL 91
GRLF++NLP+ E++ ++ F ++G++ + + + GK KG ++ + + AVKA
Sbjct: 3 GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62
Query: 92 KSNKKPYKGKI 102
+ + K ++G++
Sbjct: 63 ELDGKVFQGRL 73
Score = 37.4 bits (87), Expect = 0.001
Identities = 13/57 (22%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
E++ ++ F ++G++ + + + GK KG ++ + + AVKA + + K ++G
Sbjct: 15 KEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQG 71
>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 = 60.3 bits (146), Expect = 5e-10
Identities = 45/175 (25%), Positives = 72/175 (41%), Gaps = 29/175 (16%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
+ L + LP +T+EE + F G+I +L+++ G+ G GF+NY A KA+
Sbjct: 3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAV 62
Query: 91 -----LKSNKKPYK----------------------GKITEEEFKEHFGQYGDIIDAQLL 123
L+ K K +T+ E + F +G II +++L
Sbjct: 63 NSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRIL 122
Query: 124 KNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVK 177
+ G KG GFI + + A +AI N G + F + P SN K
Sbjct: 123 SDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSK 177
Score = 47.2 bits (112), Expect = 1e-05
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 16 KKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKG 74
K K R D K L++ LP +T+ E + F +G II +++L + G KG
Sbjct: 73 KTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKG 132
Query: 75 CGFINYANKISAVKAILKSN 94
GFI + + A +AI N
Sbjct: 133 VGFIRFDKRDEADRAIKTLN 152
Score = 34.5 bits (79), Expect = 0.11
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
+F+ NL E + FG +G + + +++++ + KG GF++ N A AIL
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 94 NKKPYKGKITEEEFK 108
N ++ + FK
Sbjct: 332 NGYTLGNRVLQVSFK 346
Score = 28.4 bits (63), Expect = 8.5
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 111 FGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN 152
FG +G + + +++++ + KG GF++ N A AIL N
Sbjct: 290 FGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLN 332
>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 = 54.9 bits (133), Expect = 7e-10
Identities = 19/63 (30%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
++F+ LP+ T++ +++F Q+G+I +A ++ + GK +G GF+ + +K SA +A
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61
Query: 93 SNK 95
N
Sbjct: 62 PNP 64
Score = 41.8 bits (99), Expect = 2e-05
Identities = 16/52 (30%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNK 153
T++ +++F Q+G+I +A ++ + GK +G GF+ + +K SA +A N
Sbjct: 13 TDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPNP 64
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 54.5 bits (132), Expect = 8e-10
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L+++NLP +TEE+ +E F YG + +L++N D + +G F+ +A+ A A+ K N
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59
Query: 95 KKPYKGK 101
G+
Sbjct: 60 GLVLDGR 66
Score = 40.2 bits (95), Expect = 9e-05
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+TEE+ +E F YG + +L++N D + +G F+ +A+ A A+ K N G
Sbjct: 9 SVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLNGLVLDGR 66
>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 = 30/70 (42%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
R RLF+ NLP ITEEEFKE F +YG++ + L K KG GFI + +A KA
Sbjct: 1 RCRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKA 55
Query: 92 KSNKKPYKGK 101
+ + KG+
Sbjct: 56 ELDGIMRKGR 65
Score = 38.8 bits (91), Expect = 3e-04
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
ITEEEFKE F +YG++ + L K KG GFI + +A KA + + KG
Sbjct: 13 ITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELDGIMRKG 64
>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 = 53.5 bits (129), Expect = 2e-09
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
LF+ NL F E+ E FG+YG+I +L + D G+ KG G++ ++++ +A A+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57
Score = 39.7 bits (93), Expect = 1e-04
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
E+ E FG+YG+I +L + D G+ KG G++ ++++ +A A+
Sbjct: 10 ADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57
>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 = 53.6 bits (129), Expect = 2e-09
Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
RL + N+PF+ + + ++ FGQ+G I+D +++ N G KG GF+ +AN A +A K
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS-KGFGFVTFANSADADRAREKL 60
Query: 94 NKKPYKGKITE 104
+ +G+ E
Sbjct: 61 HGTVVEGRKIE 71
Score = 36.6 bits (85), Expect = 0.002
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
+ + + ++ FGQ+G I+D +++ N G KG GF+ +AN A +A
Sbjct: 11 RFRDPDLRQMFGQFGPILDVEIIFNERGS-KGFGFVTFANSADADRA 56
>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 = 53.7 bits (129), Expect = 2e-09
Identities = 17/57 (29%), Positives = 34/57 (59%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+LF+ L K E + + F +G I + +L++ +G+ +GC F+ +A++ A+ AI
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAI 59
Score = 49.0 bits (117), Expect = 8e-08
Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI-LKSNKKPYKGS 159
K E + + F +G I + +L++ +G+ +GC F+ +A++ A+ AI + + +G
Sbjct: 12 KCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMHHSQTMEGC 71
Query: 160 ENGLISPFHD 169
+ L+ F D
Sbjct: 72 SSPLVVKFAD 81
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 57.3 bits (137), Expect = 4e-09
Identities = 28/106 (26%), Positives = 58/106 (54%), Gaps = 1/106 (0%)
Query: 9 KVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA 68
K +E + + + ++ K + LF+ NLP+ +TEE+ +E F ++G + +L+++
Sbjct: 92 KEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR 151
Query: 69 D-GKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQ 113
+ GK +G F+ + ++ SA KAI + N K +G+ + + Q
Sbjct: 152 ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ 197
Score = 34.9 bits (79), Expect = 0.078
Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 1/101 (0%)
Query: 2 EKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID 61
+ + KK K K L++ NLP K EEE + F GDI+
Sbjct: 195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVR 254
Query: 62 AQLLKNADGKL-KGCGFINYANKISAVKAILKSNKKPYKGK 101
A L + DGK+ K F+ A+++ + NKK G+
Sbjct: 255 ASLPPSKDGKIPKSRSFVGNEASKDALESNSRGNKKKILGR 295
>gnl|CDD|179388 PRK02230, PRK02230, inorganic pyrophosphatase; Provisional.
Length = 184
Score = 55.4 bits (134), Expect = 5e-09
Identities = 43/156 (27%), Positives = 72/156 (46%), Gaps = 32/156 (20%)
Query: 179 KIFNMVVEIPRWTNAKMEINLNEPLNPIKQD-IKKGNLRYVANVFPHHGYIWNYGALPQT 237
KI + +EIP+ +N K E + N I D I +G+ Y P NYG + +
Sbjct: 3 KIIEVTIEIPKGSNIKYE--YDRKTNKIVVDRILRGDFVY-----PA-----NYGFIKEA 50
Query: 238 --WENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIA 295
W DGD +DVL ++ G ++ + +G + +ID+G+TD K+IA
Sbjct: 51 LDW--------------DGDELDVLVYSDQKFLPGTVLNARIIGAMKMIDDGETDTKLIA 96
Query: 296 INVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
++ +D +N + D+ H+ L +F YK
Sbjct: 97 VHDDDYRLDHINSLKDLPQHW---LDEIEYFFSNYK 129
>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 = 51.9 bits (125), Expect = 7e-09
Identities = 23/67 (34%), Positives = 43/67 (64%), Gaps = 1/67 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+F+ NL + + E+E ++ F + G+I D +L+KN GK KG ++ + N+ S +A LK +
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEA-LKLD 60
Query: 95 KKPYKGK 101
++ KG+
Sbjct: 61 RELIKGR 67
Score = 37.6 bits (88), Expect = 7e-04
Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ E+E ++ F + G+I D +L+KN GK KG ++ + N+ S +A LK +++ KG
Sbjct: 10 SVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEA-LKLDRELIKG 66
>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 = 52.2 bits (126), Expect = 7e-09
Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
LF++NLP+ T+E+ +E F + G I ++K+ K +G G++ +A + A +A+ +
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 94 NKKPYKGKITEEEFKEH 110
K + G+ EF +
Sbjct: 62 KKTKFGGRKIHVEFAKK 78
Score = 36.4 bits (85), Expect = 0.002
Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
T+E+ +E F + G I ++K+ K +G G++ +A + A +A+ + K + G
Sbjct: 11 TTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGG 68
>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 = 51.8 bits (125), Expect = 8e-09
Identities = 23/69 (33%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
L++ NLP+ +TEE+ K+ FGQ+G++ A+++ + + G+ +G GF+ A AI K
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 93 SNKKPYKGK 101
N + G+
Sbjct: 61 LNGTDFGGR 69
Score = 38.4 bits (90), Expect = 5e-04
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEE+ K+ FGQ+G++ A+++ + + G+ +G GF+ A AI K N + G
Sbjct: 12 TEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGG 68
>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 = 51.5 bits (124), Expect = 1e-08
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 93
L + NLP + T+E+F+E +G + L+ + KG GF+ YA+K SA+KA +
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 94 NKKPYKGKI 102
+ K G+
Sbjct: 62 DGKQIGGRK 70
Score = 37.3 bits (87), Expect = 0.001
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKSNKKPYKG 158
T+E+F+E +G + L+ + KG GF+ YA+K SA+KA + + K G
Sbjct: 12 TDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGG 68
>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 = 51.5 bits (124), Expect = 1e-08
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLK------GCGFINYANKISAVK 88
LF+KNL FK TEE K+HF + G + + K D K G GF+ + +K +A K
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 89 AI 90
A+
Sbjct: 63 AL 64
Score = 36.0 bits (84), Expect = 0.004
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLK------GCGFINYANKISAVKAI 148
K TEE K+HF + G + + K D K G GF+ + +K +A KA+
Sbjct: 11 KTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKAL 64
>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 = 51.1 bits (123), Expect = 1e-08
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+++ NLP +TEEE + F +G I + ++ K+ KG F+ + +A AI+ N
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAVN 57
Query: 95 KKPYKGKI 102
G+
Sbjct: 58 GTSINGQT 65
Score = 45.3 bits (108), Expect = 1e-06
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+TEEE + F +G I + ++ K+ KG F+ + +A AI+ N G
Sbjct: 12 LTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAVNGTSINGQ 64
>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 = 51.2 bits (123), Expect = 1e-08
Identities = 18/56 (32%), Positives = 35/56 (62%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+F+ NL +K+ ++ KE F G ++ A + ++ +GK +G G + + + I AV+AI
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAI 56
Score = 42.0 bits (99), Expect = 3e-05
Identities = 15/48 (31%), Positives = 29/48 (60%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
K+ ++ KE F G ++ A + ++ +GK +G G + + + I AV+AI
Sbjct: 9 KVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAI 56
>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 = 51.0 bits (123), Expect = 1e-08
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 94
F+ NLPF I EEE ++HF GD+ +++++ G KG G++ + K S A+ +
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62
Query: 95 KK 96
K
Sbjct: 63 IK 64
Score = 36.8 bits (86), Expect = 0.001
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
P+ I EEE ++HF GD+ +++++ G KG G++ + K S A+ + K
Sbjct: 8 PFD--IEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNGIK 64
>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 = 50.8 bits (122), Expect = 2e-08
Identities = 19/57 (33%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
L + LP+K TE++ K++F +G+++ Q+ K+ G+ KG GF+ +A+ VK +
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58
Score = 43.9 bits (104), Expect = 4e-06
Identities = 16/49 (32%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
K TE++ K++F +G+++ Q+ K+ G+ KG GF+ +A+ VK +
Sbjct: 10 KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58
>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 = 50.3 bits (121), Expect = 3e-08
Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 94
F+ N+P+ TEE+ E F + G ++ +L+ + D GK KG GF + + +A AI N
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 95 KKPYKGK 101
+ G+
Sbjct: 62 GYEFNGR 68
Score = 39.9 bits (94), Expect = 1e-04
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEE+ E F + G ++ +L+ + D GK KG GF + + +A AI N + G
Sbjct: 11 TEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNG 67
>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 = 50.3 bits (121), Expect = 3e-08
Identities = 21/70 (30%), Positives = 41/70 (58%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+F++NLPF +T ++ K+ F + G+++ A + + DG+ KG G + + + A +AI N
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60
Query: 95 KKPYKGKITE 104
+G+ E
Sbjct: 61 GYDLEGRELE 70
Score = 33.8 bits (78), Expect = 0.018
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 108 KEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
K+ F + G+++ A + + DG+ KG G + + + A +AI N +G E
Sbjct: 16 KDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRE 68
>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 = 50.3 bits (120), Expect = 4e-08
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
L++ NLP ++TE+E ++ F YG+I+ LL++ + G +G F+ Y + A AI
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAI 59
Score = 45.3 bits (107), Expect = 2e-06
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+TE+E ++ F YG+I+ LL++ + G +G F+ Y + A AI N GS
Sbjct: 12 LTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGST 71
Query: 161 NGL 163
L
Sbjct: 72 MPL 74
>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 = 50.3 bits (121), Expect = 4e-08
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 91
+LF+ L + TE+E + F ++G + + L+K+ G+ +G GF+ + + A AI
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61
Query: 92 KSNKKPYKGKI 102
N K +G++
Sbjct: 62 DLNGKELEGRV 72
Score = 36.0 bits (84), Expect = 0.004
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ TE+E + F ++G + + L+K+ G+ +G GF+ + + A AI N K +G
Sbjct: 12 RTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEG 70
>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 = 21/70 (30%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
R+F+ +P TEEE ++ F ++G + D +++ + G KG GF+ + + A K IL
Sbjct: 2 PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEK-IL 60
Query: 92 KSNKKPYKGK 101
++GK
Sbjct: 61 AMGNLNFRGK 70
Score = 38.8 bits (91), Expect = 3e-04
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
TEEE ++ F ++G + D +++ + G KG GF+ + + A K IL ++G
Sbjct: 12 PDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEK-ILAMGNLNFRG 69
>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 = 49.4 bits (118), Expect = 6e-08
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
LF+ NL F+ TE+E + HFG+ G I +++ D GK KG F+++ A A+
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57
Score = 37.8 bits (88), Expect = 6e-04
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
TE+E + HFG+ G I +++ D GK KG F+++ A A+
Sbjct: 10 TTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57
>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 = 49.3 bits (118), Expect = 7e-08
Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
+LFI L ++ T++ K +F Q+G+I D ++K+ + +G GF+ +A+ A+
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM-- 58
Query: 93 SNKKPYK--GKITE 104
N +P+K G+ E
Sbjct: 59 -NARPHKVDGREVE 71
Score = 40.0 bits (94), Expect = 1e-04
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYK 157
+ T++ K +F Q+G+I D ++K+ + +G GF+ +A+ A+ N +P+K
Sbjct: 10 ETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM---NARPHK 64
>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 = 49.2 bits (118), Expect = 7e-08
Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
L++ NL F ITE++ + F +G+I QL ++ + G+ KG GFI +A+ A KA+ +
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 94 N 94
N
Sbjct: 61 N 61
Score = 41.5 bits (98), Expect = 3e-05
Identities = 19/52 (36%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
ITE++ + F +G+I QL ++ + G+ KG GFI +A+ A KA+ + N
Sbjct: 10 ITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61
>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 = 49.3 bits (118), Expect = 7e-08
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAIL 91
GRLFI+NL + TEE+ ++ F +YG + + L + K KG F+ Y AVKA
Sbjct: 3 GRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFA 62
Query: 92 KSNKKPYKGKI 102
+ + ++G++
Sbjct: 63 ELDGTVFQGRL 73
Score = 29.3 bits (66), Expect = 0.76
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKA 147
TEE+ ++ F +YG + + L + K KG F+ Y AVKA
Sbjct: 15 TEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60
>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 = 48.8 bits (117), Expect = 7e-08
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 34 RLFIKNLP-FKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
R+F+ NL K+++E+ +E F +YG I+ L K G GF+ + N+ A A+
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK-------GYGFVQFDNEEDARAAVAG 54
Query: 93 SNKKPYKGK 101
N + G+
Sbjct: 55 ENGREIAGQ 63
Score = 38.0 bits (89), Expect = 4e-04
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
K+++E+ +E F +YG I+ L K G GF+ + N+ A A+ N + G
Sbjct: 12 KVSKEDLEEIFSKYGKILGISLHK-------GYGFVQFDNEEDARAAVAGENGREIAG 62
>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 = 48.8 bits (117), Expect = 8e-08
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 90
LFI +LP + T+++ + F +G++I A++ + + K GF++Y N SA AI
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAI 57
Score = 38.8 bits (91), Expect = 3e-04
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 148
T+++ + F +G++I A++ + + K GF++Y N SA AI
Sbjct: 11 TDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAI 57
>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 = 49.1 bits (117), Expect = 9e-08
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAIL 91
G+LFI L F E+ ++ F +YG I + ++K+ + + +G GF+ + N A A++
Sbjct: 1 GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60
Query: 92 KSNKKPYKGK 101
N K G+
Sbjct: 61 AMNGKSVDGR 70
Score = 37.5 bits (87), Expect = 0.001
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKSNKKPYKG 158
E+ ++ F +YG I + ++K+ + + +G GF+ + N A A++ N K G
Sbjct: 13 NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDG 69
>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 = 48.4 bits (116), Expect = 1e-07
Identities = 21/60 (35%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKS 93
LFI L + TEE +E+F +YG+++D ++K G+ +G GF+ +A+ S+V +L +
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADP-SSVDKVLAA 59
Score = 44.5 bits (106), Expect = 3e-06
Identities = 17/50 (34%), Positives = 33/50 (66%), Gaps = 2/50 (4%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKS 151
TEE +E+F +YG+++D ++K G+ +G GF+ +A+ S+V +L +
Sbjct: 11 TEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADP-SSVDKVLAA 59
>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 = 48.8 bits (117), Expect = 1e-07
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 93
L++ LP +T++E + F YG II +++L + L +G GFI + +I A +AI
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 94 NKK 96
N
Sbjct: 63 NGT 65
Score = 41.5 bits (98), Expect = 4e-05
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKSNKK 154
T++E + F YG II +++L + L +G GFI + +I A +AI N
Sbjct: 13 TQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGT 65
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L+++NLP TEE+ +E F +YG++ + K+K F+++ + AVKA+ + N
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVK-------KIKDYAFVHFEERDDAVKAMEEMN 56
Query: 95 KKPYKGKITE 104
K +G E
Sbjct: 57 GKELEGSPIE 66
Score = 39.9 bits (94), Expect = 1e-04
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
TEE+ +E F +YG++ + K+K F+++ + AVKA+ + N K +GS
Sbjct: 14 TEEQLRELFSEYGEVERVK-------KIKDYAFVHFEERDDAVKAMEEMNGKELEGSP 64
>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 = 48.0 bits (115), Expect = 2e-07
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+L ++N+PF+ T++E +E F +G + +L K DG +G F+ + K A A+
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAM 58
Score = 33.7 bits (78), Expect = 0.023
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
T++E +E F +G + +L K DG +G F+ + K A A+
Sbjct: 13 TKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAM 58
>gnl|CDD|179262 PRK01250, PRK01250, inorganic pyrophosphatase; Provisional.
Length = 176
Score = 50.3 bits (121), Expect = 2e-07
Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 19/108 (17%)
Query: 227 YIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDE 286
Y NYG +P T DGDP+DVL + G +I+ + +GV+ + DE
Sbjct: 52 YPCNYGFIPHTLS------------LDGDPVDVLVVTPYPLVPGSVIRCRPVGVLKMEDE 99
Query: 287 GQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNE-WFKIYK 331
D KIIA+ + P + DV D+ P LKA + +F+ YK
Sbjct: 100 SGEDAKIIAVPHDKLSPEYDHIKDVNDL----PELLKAQIKHFFEHYK 143
>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 = 47.7 bits (113), Expect = 3e-07
Identities = 18/58 (31%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
+LF+ ++P ITE+E + F ++G++++ ++K+ G +GC F+ Y+ + A +AI
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
Score = 40.3 bits (94), Expect = 1e-04
Identities = 15/48 (31%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 148
ITE+E + F ++G++++ ++K+ G +GC F+ Y+ + A +AI
Sbjct: 11 ITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
>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 = 47.4 bits (113), Expect = 3e-07
Identities = 26/77 (33%), Positives = 46/77 (59%), Gaps = 4/77 (5%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKS 93
LF+ NLP ITE+E KE F ++G++++ ++ K G+L GF+ + + AV+ IL +
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDP-EAVQKILAN 64
Query: 94 NKKPYKG--KITEEEFK 108
++G ++ EE K
Sbjct: 65 KPIYFRGDHRLNVEEKK 81
Score = 38.1 bits (89), Expect = 6e-04
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 3/63 (4%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
ITE+E KE F ++G++++ ++ K G+L GF+ + + AV+ IL NK Y +
Sbjct: 15 ITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDP-EAVQKILA-NKPIYFRGD 72
Query: 161 NGL 163
+ L
Sbjct: 73 HRL 75
>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 = 47.1 bits (112), Expect = 4e-07
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
LF++NL F +T+E+ + F I A ++ + + G+ +G GF+ +A A +A+ K
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 94 NKKPYKGKITEEEFKE 109
K G+I + E
Sbjct: 62 KNKKLHGRILRLDIAE 77
>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 = 48.0 bits (114), Expect = 4e-07
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
LF++NLP+ TEE HF ++G + A + + + G+ KG GF+ + ++ + A LK+
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTY-NACLKN 62
Query: 94 NK 95
Sbjct: 63 AP 64
Score = 36.1 bits (83), Expect = 0.005
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP 155
PY TEE HF ++G + A + + + G+ KG GF+ + ++ + A LK+ P
Sbjct: 10 PYDA--TEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTY-NACLKN--AP 64
Query: 156 YKGSENGLI 164
GS + L
Sbjct: 65 AAGSTSLLS 73
>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 = 46.9 bits (112), Expect = 4e-07
Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVKAI 90
++++NL FK+ E++ + F ++G++ ++ K D K G F+ + + SA A+
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62
Query: 91 LKSNKK 96
+ +
Sbjct: 63 QLNGTE 68
Score = 34.9 bits (81), Expect = 0.007
Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVKAILKSNKK 154
K+ E++ + F ++G++ ++ K D K G F+ + + SA A+ + +
Sbjct: 11 KLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQLNGTE 68
>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 = 47.2 bits (112), Expect = 4e-07
Identities = 21/57 (36%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
L++ LP +T++E ++ F QYG II +++L++ G +G GFI + +I A +AI
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAI 59
Score = 41.8 bits (98), Expect = 3e-05
Identities = 22/61 (36%), Positives = 38/61 (62%), Gaps = 2/61 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK-SNKKPYKGS 159
+T++E ++ F QYG II +++L++ G +G GFI + +I A +AI + +KP S
Sbjct: 12 MTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEGAS 71
Query: 160 E 160
E
Sbjct: 72 E 72
>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 = 46.9 bits (112), Expect = 4e-07
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 5/56 (8%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+F+ L +TE+E + FG +G+I+ +K GK GCGF+ + ++ +A AI
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVY---VKIPPGK--GCGFVQFVHRAAAEAAI 54
Score = 45.4 bits (108), Expect = 1e-06
Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+TE+E + FG +G+I+ +K GK GCGF+ + ++ +A AI + GS
Sbjct: 12 AVTEDELRSLFGPFGEIVY---VKIPPGK--GCGFVQFVHRAAAEAAIQQLQGTIIGGSR 66
Query: 161 NGL 163
L
Sbjct: 67 IRL 69
>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 = 46.5 bits (111), Expect = 5e-07
Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS- 93
L++ L ++TE++ ++HF Q+G+I ++ + C F+ + + +A KA +
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR-----QQCAFVTFTTREAAEKAAERLF 58
Query: 94 NKKPYKGK 101
NK G+
Sbjct: 59 NKLIINGR 66
Score = 39.6 bits (93), Expect = 2e-04
Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
++TE++ ++HF Q+G+I ++ + C F+ + + +A KA + K
Sbjct: 12 RVTEKDLRDHFYQFGEIRSITVVPR-----QQCAFVTFTTREAAEKAAERLFNK 60
>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 = 46.4 bits (111), Expect = 6e-07
Identities = 18/69 (26%), Positives = 37/69 (53%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
RL + NL + +TEE+ +E FG+ G++ ++ + G+ +G + + + A +AI +
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQF 61
Query: 94 NKKPYKGKI 102
N G+
Sbjct: 62 NGVLLDGQP 70
Score = 34.1 bits (79), Expect = 0.014
Identities = 14/59 (23%), Positives = 30/59 (50%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+TEE+ +E FG+ G++ ++ + G+ +G + + + A +AI + N G
Sbjct: 12 VTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQP 70
>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 = 46.6 bits (110), Expect = 8e-07
Identities = 24/74 (32%), Positives = 45/74 (60%), Gaps = 6/74 (8%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
+LFI L F+ T+E + HF Q+G + D ++++ + K +G GF+ Y++ + V A +
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSS-VEEVDAAM- 61
Query: 93 SNKKPYK--GKITE 104
N +P+K G++ E
Sbjct: 62 -NARPHKVDGRVVE 74
Score = 35.4 bits (81), Expect = 0.007
Identities = 17/56 (30%), Positives = 34/56 (60%), Gaps = 4/56 (7%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKSNKKPYK 157
T+E + HF Q+G + D ++++ + K +G GF+ Y++ + V A + N +P+K
Sbjct: 15 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSS-VEEVDAAM--NARPHK 67
>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 = 46.1 bits (110), Expect = 8e-07
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG----CGFINYANKISAVKA 89
RL+I NL ++TE + F +YG I L + G LKG F+ + K A KA
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 90 ILKSNKKPYKGKI 102
+ N K GK
Sbjct: 61 LKSLNGKTALGKK 73
Score = 36.1 bits (84), Expect = 0.004
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKG----CGFINYANKISAVKAILKSNKK 154
++TE + F +YG I L + G LKG F+ + K A KA+ N K
Sbjct: 10 RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGK 67
>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 = 46.2 bits (109), Expect = 9e-07
Identities = 20/56 (35%), Positives = 35/56 (62%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+F+ NL +K+ ++ KE F G ++ A +L++ DGK +G G + + I AV+AI
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAI 58
Score = 37.7 bits (87), Expect = 8e-04
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
K+ ++ KE F G ++ A +L++ DGK +G G + + I AV+AI
Sbjct: 11 KVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAI 58
>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 = 46.3 bits (110), Expect = 9e-07
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
++I N+ +TEE+ + F QYG+I L+ K C F+N+ N +A+KAI
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLRE-----KNCAFVNFTNISNAIKAIDGVK 60
Query: 95 KKPYKGKITEEEFKEHFG 112
P ++FK +G
Sbjct: 61 SHPLF-----KKFKISYG 73
Score = 40.9 bits (96), Expect = 6e-05
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
TEE+ + F QYG+I L+ K C F+N+ N +A+KAI P
Sbjct: 16 TEEKLRNDFSQYGEIESVNYLRE-----KNCAFVNFTNISNAIKAIDGVKSHPL 64
>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 = 46.2 bits (110), Expect = 1e-06
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+F+ L +T+EE E F ++G I++ L+K A+ FI + + +A +A+ N
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHT-NAFAFIKFEREQAAARAVESEN 64
Query: 95 KKPYKGKITEEEFKE 109
K K ++KE
Sbjct: 65 HSMLKNKTMHVQYKE 79
Score = 37.3 bits (87), Expect = 0.001
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
+T+EE E F ++G I++ L+K A+ FI + + +A +A+ N K
Sbjct: 14 DVTKEELNERFSRHGKILEVNLIKRANHT-NAFAFIKFEREQAAARAVESENHSMLKNK 71
>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 = 45.4 bits (107), Expect = 2e-06
Identities = 23/56 (41%), Positives = 38/56 (67%), Gaps = 1/56 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
++F++NLPF +T ++ KE F Q G ++ A+ +K +GK KGCG + + + SA KA
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAE-IKMENGKSKGCGTVRFDSPESAEKA 55
Score = 32.3 bits (73), Expect = 0.064
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+T ++ KE F Q G ++ A++ K +GK KGCG + + + SA KA N G E
Sbjct: 11 LTWQKLKEKFSQCGHVMFAEI-KMENGKSKGCGTVRFDSPESAEKACRLMNGIKINGRE 68
>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 = 45.0 bits (107), Expect = 2e-06
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
LF+ NLP+ T E+ HF G +LL + GK KGC F+ + + A+ LK
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEF-DTAEAMTKALKL 61
Query: 94 NKKPYKGK 101
+ KG+
Sbjct: 62 HHTLLKGR 69
Score = 32.3 bits (74), Expect = 0.071
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFI 136
PY T E+ HF G +LL + GK KGC F+
Sbjct: 9 PYD--TTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFV 47
>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 = 44.9 bits (107), Expect = 2e-06
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
L+++NLPFKI+ EE + FG+YG I Q+ + +G F+ Y + A A
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAI--RQIRIGNTKETRGTAFVVYEDIYDAKNA 57
Score = 27.6 bits (62), Expect = 2.7
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
P+K I+ EE + FG+YG I Q+ + +G F+ Y + A A
Sbjct: 11 PFK--ISSEELYDLFGKYGAI--RQIRIGNTKETRGTAFVVYEDIYDAKNA 57
>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 = 45.3 bits (108), Expect = 2e-06
Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
++I LP+++TE + F QYG+I+D L+++ GK KG F+ Y ++ S + A+
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAV 68
Score = 35.3 bits (82), Expect = 0.008
Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 111 FGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
F QYG+I+D L+++ GK KG F+ Y ++ S + A+
Sbjct: 30 FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAV 68
>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 = 45.1 bits (107), Expect = 2e-06
Identities = 18/57 (31%), Positives = 32/57 (56%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+LF+ L + TE++ + F +G I + +L+ DG KGC F+ +++ A AI
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAI 59
Score = 41.7 bits (98), Expect = 3e-05
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
TE++ + F +G I + +L+ DG KGC F+ +++ A AI
Sbjct: 14 TEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAI 59
>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 = 44.2 bits (105), Expect = 4e-06
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
R+++ ++ ++E++ K F +G I L + + GK KG GFI Y N SA AI
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAI 59
Score = 37.6 bits (88), Expect = 0.001
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
++E++ K F +G I L + + GK KG GFI Y N SA AI
Sbjct: 12 LSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAI 59
>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 = 44.1 bits (104), Expect = 4e-06
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
LF+KNLP+ IT +E KE F D +D +L DG KG +I + + A KA+
Sbjct: 6 LFVKNLPYNITVDELKEVF---EDAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKAL 58
Score = 29.0 bits (65), Expect = 0.97
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 5/52 (9%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
PY IT +E KE F D +D +L DG KG +I + + A KA+
Sbjct: 12 PYN--ITVDELKEVFE---DAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKAL 58
>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 = 43.7 bits (104), Expect = 5e-06
Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKS 93
+ ++ LPF TEE+ ++ F D ++ + DG+ G ++ +A+ A +A+ K
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61
Query: 94 NKK 96
N K
Sbjct: 62 NNK 64
Score = 31.8 bits (73), Expect = 0.090
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
P+ TEE+ ++ F D ++ + DG+ G ++ +A+ A +A+ K N K
Sbjct: 8 PFS--ATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNK 64
>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 = 43.9 bits (104), Expect = 5e-06
Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHF-GQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
R+FI N+P+ + ++ K+ F + G++ +L K+ +GK +GCG + + +K S KA+
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60
Query: 93 SNKKPYKGK 101
N+ KG+
Sbjct: 61 MNRYELKGR 69
Score = 32.4 bits (74), Expect = 0.057
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 113 QYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ G++ +L K+ +GK +GCG + + +K S KA+ N+ KG
Sbjct: 23 KVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETMNRYELKG 68
>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 = 43.9 bits (104), Expect = 6e-06
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANK 83
K D K LF+ +P + E++ + F Q+G I + +LK+ G KGC F+ Y +
Sbjct: 1 KDDDAIK---LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCAR 57
Query: 84 ISAVKA 89
SA+KA
Sbjct: 58 ESALKA 63
Score = 35.5 bits (82), Expect = 0.008
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKA 147
E++ + F Q+G I + +LK+ G KGC F+ Y + SA+KA
Sbjct: 18 EEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63
>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 = 43.5 bits (103), Expect = 7e-06
Identities = 18/69 (26%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
LF+ NL + + +E K F ++G ++ A+++ + + G+ +G G++++ + A KAI
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 93 SNKKPYKGK 101
+ K G+
Sbjct: 61 MDGKELDGR 69
Score = 34.7 bits (80), Expect = 0.011
Identities = 14/58 (24%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ +E K F ++G ++ A+++ + + G+ +G G++++ + A KAI + K G
Sbjct: 11 VDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDG 68
>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 = 43.5 bits (103), Expect = 7e-06
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK-S 93
L+I +L K+TEE+ K F +YG+I ++ +GC ++ + A +A+ K
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP-----RGCAYVCMETRQDAHRALQKLR 59
Query: 94 NKKPYKGKIT 103
N K KI
Sbjct: 60 NVKLAGKKIK 69
Score = 35.4 bits (82), Expect = 0.006
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 150
K+TEE+ K F +YG+I ++ +GC ++ + A +A+ K
Sbjct: 13 KVTEEDLKNLFEEYGEIQSIDMIPP-----RGCAYVCMETRQDAHRALQK 57
>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 = 43.4 bits (103), Expect = 7e-06
Identities = 17/75 (22%), Positives = 39/75 (52%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
+L + NL F +++++ KE F ++G + A + + G+ G + + + A+KA+ +
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60
Query: 93 SNKKPYKGKITEEEF 107
N P G+ + +
Sbjct: 61 YNGVPLDGRPMKIQL 75
Score = 30.3 bits (69), Expect = 0.36
Identities = 13/57 (22%), Positives = 30/57 (52%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+++++ KE F ++G + A + + G+ G + + + A+KA+ + N P G
Sbjct: 12 VSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYNGVPLDG 68
>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 = 42.9 bits (102), Expect = 1e-05
Identities = 21/62 (33%), Positives = 37/62 (59%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
G +FIKNL I + + F +G+I+ ++ + +G KG GF+++ + +AV+AI K
Sbjct: 3 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEK 62
Query: 93 SN 94
N
Sbjct: 63 VN 64
Score = 29.8 bits (68), Expect = 0.51
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 152
I + + F +G+I+ ++ + +G KG GF+++ + +AV+AI K N
Sbjct: 14 IDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64
>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 = 43.1 bits (101), Expect = 1e-05
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+LFI + K E + + F +G I + ++L+ DG +GC F+ + + A AI
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAI 59
Score = 38.9 bits (90), Expect = 4e-04
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
K E + + F +G I + ++L+ DG +GC F+ + + A AI
Sbjct: 12 KCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAI 59
>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 = 42.8 bits (101), Expect = 1e-05
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
LFI NL T + +E F ++G+IID + K FI YA+ S VKA+ K
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGN--PAYAFIQYADIASVVKAMRK 60
Score = 35.1 bits (81), Expect = 0.007
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 150
T + +E F ++G+IID + K FI YA+ S VKA+ K
Sbjct: 14 TTYSDLREAFERFGEIIDIDIKKQGGN--PAYAFIQYADIASVVKAMRK 60
>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 = 42.9 bits (101), Expect = 1e-05
Identities = 18/68 (26%), Positives = 39/68 (57%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+F+ + FK E + ++ F QYG + + +++ + G KG GF+ + + A K + ++
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEA 63
Query: 94 NKKPYKGK 101
N+ ++ K
Sbjct: 64 NRLCFRDK 71
Score = 34.4 bits (79), Expect = 0.015
Identities = 14/57 (24%), Positives = 32/57 (56%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK 157
K E + ++ F QYG + + +++ + G KG GF+ + + A K + ++N+ ++
Sbjct: 13 KTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEANRLCFR 69
>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 = 42.7 bits (101), Expect = 1e-05
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L+I NLP + E++ + YG +I ++L+++ G+ +G GF ++ I K N
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFN 62
Query: 95 KKPYKG 100
K KG
Sbjct: 63 GKYLKG 68
Score = 33.9 bits (78), Expect = 0.017
Identities = 18/68 (26%), Positives = 33/68 (48%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSEN 161
+ E++ + YG +I ++L+++ G+ +G GF ++ I K N K KG
Sbjct: 12 MDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFNGKYLKGEGE 71
Query: 162 GLISPFHD 169
L+ F D
Sbjct: 72 PLLVKFAD 79
>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 = 42.8 bits (100), Expect = 1e-05
Identities = 24/58 (41%), Positives = 39/58 (67%), Gaps = 1/58 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 91
+F+ +L +IT E+ K F +G I DA+++K+ A GK KG GF+++ NK+ A AI+
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61
Score = 39.3 bits (91), Expect = 3e-04
Identities = 22/50 (44%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 149
+IT E+ K F +G I DA+++K+ A GK KG GF+++ NK+ A AI+
Sbjct: 12 EITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61
>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 = 42.9 bits (101), Expect = 1e-05
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 34 RLFIKNLPFKITE-EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
+L I+NLP+ I + + K+ FG+YG + +A + + GKL G F+ + +A A+
Sbjct: 2 KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALEN 61
Query: 93 SN 94
+N
Sbjct: 62 TN 63
Score = 33.7 bits (77), Expect = 0.028
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 105 EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 152
+ K+ FG+YG + +A + + GKL G F+ + +A A+ +N
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTN 63
>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 = 42.5 bits (101), Expect = 1e-05
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 35 LFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
L+I NL KI ++E K F Q+G ++D K K++G F+ + + SA A+
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTL--KMRGQAFVVFKDVESATNAL 59
Query: 91 LKSNKKPYKGK 101
P+ K
Sbjct: 60 RALQGFPFYDK 70
Score = 31.0 bits (71), Expect = 0.20
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 101 KITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
KI ++E K F Q+G ++D K K++G F+ + + SA A
Sbjct: 10 KIKKDELKRSLYALFSQFGPVLDIVASKTL--KMRGQAFVVFKDVESATNA 58
>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 = 42.7 bits (100), Expect = 2e-05
Identities = 20/56 (35%), Positives = 33/56 (58%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+F+ NL FK+ ++ KE F G + A + ++ DGK +G G + + I AV+AI
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAI 58
Score = 33.1 bits (75), Expect = 0.041
Identities = 16/48 (33%), Positives = 27/48 (56%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
K+ ++ KE F G + A + ++ DGK +G G + + I AV+AI
Sbjct: 11 KVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAI 58
>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 = 42.7 bits (101), Expect = 2e-05
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
+F+ NLP E + F +G + + +++++ K KG GF+ N A AI
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63
Query: 94 NKKPYKGKITEEEFK 108
N G++ + FK
Sbjct: 64 NGYRLGGRVLQVSFK 78
Score = 27.7 bits (62), Expect = 3.3
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 111 FGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
F +G + + +++++ K KG GF+ N A AI N G
Sbjct: 22 FSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGG 70
>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 = 42.6 bits (101), Expect = 2e-05
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 9/75 (12%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQY-------GDIIDAQLLKNADGKLKGCGFINYANKISA 86
RL++KNL ++TEE+ FG++ ++ D +L+ +G++KG F+ + ++ A
Sbjct: 3 RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMT--EGRMKGQAFVTFPSEEIA 60
Query: 87 VKAILKSNKKPYKGK 101
KA+ N KGK
Sbjct: 61 TKALNLVNGYVLKGK 75
Score = 28.7 bits (65), Expect = 1.2
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 9/59 (15%)
Query: 101 KITEEEFKEHFGQY-------GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 152
++TEE+ FG++ ++ D +L+ +G++KG F+ + ++ A KA+ N
Sbjct: 12 RVTEEDLVYIFGRFVDSSSEEKNMFDIRLMT--EGRMKGQAFVTFPSEEIATKALNLVN 68
>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 = 42.2 bits (99), Expect = 2e-05
Identities = 27/70 (38%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
R RLF+ NLP ITE+EFK+ F +YG+ ++ N K KG GFI ++ A A
Sbjct: 1 RCRLFVGNLPADITEDEFKKLFAKYGE--PGEVFIN---KGKGFGFIKLESRALAEIAKA 55
Query: 92 KSNKKPYKGK 101
+ + P +G+
Sbjct: 56 ELDDTPMRGR 65
Score = 27.6 bits (61), Expect = 3.4
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
ITE+EFK+ F +YG+ ++ N K KG GFI ++ A A + + P +G +
Sbjct: 13 ITEDEFKKLFAKYGE--PGEVFIN---KGKGFGFIKLESRALAEIAKAELDDTPMRGRQ 66
>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 = 42.1 bits (99), Expect = 2e-05
Identities = 21/68 (30%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
+F+ N+P++ TEE+ K+ F + G ++ +L+ + + GK KG GF Y ++ +A+ A+
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 94 NKKPYKGK 101
N G+
Sbjct: 61 NGYELNGR 68
Score = 33.2 bits (76), Expect = 0.029
Identities = 18/53 (33%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
PY+ TEE+ K+ F + G ++ +L+ + + GK KG GF Y ++ +A+ A+
Sbjct: 7 PYE--ATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAM 57
>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 = 42.5 bits (100), Expect = 2e-05
Identities = 19/57 (33%), Positives = 34/57 (59%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+LF+ L + TE+E +E F YG + D ++++ + +GC F+ Y++K A AI
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAI 57
Score = 38.7 bits (90), Expect = 4e-04
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK-KPYKGSEN 161
TE+E +E F YG + D ++++ + +GC F+ Y++K A AI N +G +
Sbjct: 12 TEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALNGVYTMRGCDQ 71
Query: 162 GLISPFHD 169
LI F D
Sbjct: 72 PLIVRFAD 79
>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 = 42.0 bits (99), Expect = 2e-05
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
+ L + LP +T++E + F G+I +L+++ G+ G GF+NY + A KAI
Sbjct: 1 KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60
Query: 91 LKSNK 95
N
Sbjct: 61 NTLNG 65
Score = 37.8 bits (88), Expect = 8e-04
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNK 153
+T++E + F G+I +L+++ G+ G GF+NY + A KAI N
Sbjct: 13 MTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNG 65
>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 = 42.4 bits (99), Expect = 2e-05
Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKA 89
+ L++ LP +T++E ++ F QYG II +++L G +G GFI + +I A +A
Sbjct: 1 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60
Query: 90 ILKSN-KKP 97
I N +KP
Sbjct: 61 IKGLNGQKP 69
Score = 37.0 bits (85), Expect = 0.002
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKSN-KKPYKGS 159
+T++E ++ F QYG II +++L G +G GFI + +I A +AI N +KP +
Sbjct: 14 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAA 73
Query: 160 E 160
E
Sbjct: 74 E 74
>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 = 42.0 bits (99), Expect = 2e-05
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
+F+ +L +I E + F +G+I DA+++K+ GK KG GF+++ K A AI
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAI 58
Score = 38.9 bits (91), Expect = 3e-04
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
I E + F +G+I DA+++K+ GK KG GF+++ K A AI
Sbjct: 11 IDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAI 58
>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 = 42.0 bits (98), Expect = 3e-05
Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
+LFI L F+ T++ +EHF ++G + D ++++ K +G GF+ Y+ + V A +
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSC-VEEVDAAMS 62
Query: 93 SNKKPYKGKITE 104
+ G++ E
Sbjct: 63 ARPHKVDGRVVE 74
>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 = 41.4 bits (98), Expect = 4e-05
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 37 IKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNK 95
+ NL E++ +E F +G I L K+ + G+ +G F+ + + A +AI K N
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
Query: 96 KPYKGKITEEEF 107
Y I E+
Sbjct: 64 FGYDNLILSVEW 75
Score = 37.1 bits (87), Expect = 0.001
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYK 157
E++ +E F +G I L K+ + G+ +G F+ + + A +AI K N Y
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYD 67
>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 = 41.5 bits (97), Expect = 4e-05
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
++F++NLPF T + K+ F + G ++ A +K +GK KGCG + + + A +A
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHVLYAD-IKMENGKSKGCGVVRFESPEVAERACRMM 59
Query: 94 NKKPYKGK 101
N G+
Sbjct: 60 NGYKLNGR 67
Score = 28.8 bits (64), Expect = 1.4
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
T + K+ F + G ++ A + K +GK KGCG + + + A +A N G E
Sbjct: 12 TWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVRFESPEVAERACRMMNGYKLNGRE 68
>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 = 41.0 bits (97), Expect = 4e-05
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 49 FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
+ F +G++ +LLK G F+ ++ + +A KA+ N + G+
Sbjct: 1 LYKLFSPFGNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGGR 49
Score = 39.4 bits (93), Expect = 1e-04
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 107 FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ F +G++ +LLK G F+ ++ + +A KA+ N + G
Sbjct: 1 LYKLFSPFGNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGG 48
>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 = 41.4 bits (97), Expect = 4e-05
Identities = 26/64 (40%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
L + NLP T EEF+E YG+I L+ + G KG GF+ Y K SA KA L+
Sbjct: 2 LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61
Query: 94 NKKP 97
K
Sbjct: 62 LGKQ 65
>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 = 41.1 bits (97), Expect = 5e-05
Identities = 13/53 (24%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
++F+ L +TEE+ +++F Q+G++ D + K + F+ +A+ A
Sbjct: 2 KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP----FRAFAFVTFADPEVA 50
Score = 34.6 bits (80), Expect = 0.009
Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 144
+TEE+ +++F Q+G++ D + K + F+ +A+ A
Sbjct: 11 DMTEEDLRQYFSQFGEVTDVYIPKP----FRAFAFVTFADPEVA 50
>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 = 41.0 bits (96), Expect = 5e-05
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
R RLF+ NLP ITEEE ++ F +YG ++ + D KG GFI + A A
Sbjct: 1 RSRLFVGNLPPDITEEEMRKLFEKYGKA--GEIFIHKD---KGFGFIRLETRTLAEIAKA 55
Query: 92 KSNKKPYKGK 101
+ + P +GK
Sbjct: 56 ELDNMPLRGK 65
>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 = 41.3 bits (96), Expect = 5e-05
Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
+ L + LP +T+EEFK FG G+I +L+++ G+ G GF+NY + A KAI
Sbjct: 3 KTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62
Score = 36.6 bits (84), Expect = 0.002
Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 148
+T+EEFK FG G+I +L+++ G+ G GF+NY + A KAI
Sbjct: 15 MTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62
>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 = 41.2 bits (96), Expect = 5e-05
Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
+LFI L F+ TEE + ++ Q+G + D ++++ A + +G GF+ ++ ++ V A +
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSC-MNEVDAAMA 62
Query: 93 SNKKPYKGKITE 104
+ G++ E
Sbjct: 63 ARPHTIDGRVVE 74
>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 = 41.0 bits (96), Expect = 5e-05
Identities = 15/49 (30%), Positives = 33/49 (67%), Gaps = 1/49 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYAN 82
+FI L ++ T++ +E+FGQ+G++ D ++++ A G+ +G GF+ +
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49
Score = 36.0 bits (83), Expect = 0.003
Identities = 12/39 (30%), Positives = 27/39 (69%), Gaps = 1/39 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYAN 140
T++ +E+FGQ+G++ D ++++ A G+ +G GF+ +
Sbjct: 11 TDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49
>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 = 41.2 bits (97), Expect = 5e-05
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKS 93
L++ L + K+ F +YG ++ A+++ NA C GF+ A+ A K I
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 94 NKKPYKGKI 102
++ G++
Sbjct: 62 HRTELHGRV 70
Score = 35.4 bits (82), Expect = 0.005
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 106 EFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYKGS 159
+ K+ F +YG ++ A+++ NA C GF+ A+ A K I ++ G
Sbjct: 15 DLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGR 69
>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 = 41.2 bits (96), Expect = 5e-05
Identities = 23/57 (40%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
+F+ +L +IT ++ K F +G I DA+++K+ A GK KG GF+++ NK A AI
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60
Score = 37.8 bits (87), Expect = 0.001
Identities = 21/49 (42%), Positives = 32/49 (65%), Gaps = 1/49 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
+IT ++ K F +G I DA+++K+ A GK KG GF+++ NK A AI
Sbjct: 12 EITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60
>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 = 41.5 bits (98), Expect = 6e-05
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKIS 85
P T LF+ L + TEE +E F +YGDI +L+++ G KG F+ Y ++
Sbjct: 2 PYLT----LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERD 57
Query: 86 AVKAILKSNK 95
A++A ++K
Sbjct: 58 ALRAYRDAHK 67
Score = 35.3 bits (82), Expect = 0.009
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
TEE +E F +YGDI +L+++ G KG F+ Y ++ A++A ++K GSE
Sbjct: 16 TEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSE 74
>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 = 41.3 bits (96), Expect = 6e-05
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKA 89
+ L++ LP +T++E ++ F QYG II +++L G +G GFI + +I A +A
Sbjct: 4 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63
Query: 90 I--LKSNKKP 97
I L K P
Sbjct: 64 IKGLNGQKPP 73
Score = 36.3 bits (83), Expect = 0.003
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+T++E ++ F QYG II +++L G +G GFI + +I A +AI N + G+
Sbjct: 17 MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPPGAT 76
Query: 161 NGLISPFHDIP 171
+ F + P
Sbjct: 77 EPITVKFANNP 87
>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 = 41.0 bits (96), Expect = 6e-05
Identities = 14/50 (28%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
+LF+ L ++ T+E + +F QYG+++D ++K+ + +G GF+ + +
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50
Score = 35.2 bits (81), Expect = 0.007
Identities = 11/39 (28%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 140
T+E + +F QYG+++D ++K+ + +G GF+ + +
Sbjct: 12 TQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50
>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 = 40.7 bits (95), Expect = 7e-05
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 5/55 (9%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
R RLF+ NLP ITEE+FK+ F +YG+ +++ N D +G GFI ++ A
Sbjct: 1 RCRLFVGNLPTDITEEDFKKLFEKYGE--PSEVFINRD---RGFGFIRLESRTLA 50
>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 = 40.6 bits (95), Expect = 8e-05
Identities = 15/58 (25%), Positives = 32/58 (55%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
++ +KNLPF+ T+++ + F YG + ++ K D +G F+ ++ A+ A+
Sbjct: 1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAM 58
>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 = 40.5 bits (95), Expect = 8e-05
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
++I NLP +EEE +E ++G I +++K K F+++ + +A+K +
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTLP 60
Query: 95 KKPY 98
+P
Sbjct: 61 CEPD 64
Score = 32.8 bits (75), Expect = 0.053
Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
+EEE +E ++G I +++K K F+++ + +A+K + +P
Sbjct: 15 YSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTLPCEPD 64
>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 = 40.8 bits (95), Expect = 9e-05
Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
L++ LP ++++E ++ F QYG II +++L + G +G GFI + +I A +AI
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63
Query: 94 N-KKP 97
N +KP
Sbjct: 64 NGQKP 68
Score = 35.7 bits (82), Expect = 0.004
Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN-KKPYKGS 159
++++E ++ F QYG II +++L + G +G GFI + +I A +AI N +KP +
Sbjct: 13 MSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGLNGQKPLGAA 72
Query: 160 E 160
E
Sbjct: 73 E 73
>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 = 40.4 bits (95), Expect = 1e-04
Identities = 19/56 (33%), Positives = 32/56 (57%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
LF+ NL ++TEE E F Q G + ++ K+ +GK K F+ + +++S AI
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAI 59
Score = 34.2 bits (79), Expect = 0.012
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
++TEE E F Q G + ++ K+ +GK K F+ + +++S AI
Sbjct: 12 RVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAI 59
>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 = 40.0 bits (94), Expect = 1e-04
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
L + LP +T+EE + F G I +++++ G+ G GF++Y ++ A KAI
Sbjct: 3 LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAI 59
Score = 35.8 bits (83), Expect = 0.004
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
+T+EE + F G I +++++ G+ G GF++Y ++ A KAI
Sbjct: 12 MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAI 59
>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 = 40.1 bits (94), Expect = 1e-04
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
RLF+ +P TEE+ +E F ++GDI ++K+ + G+ KG G++ + A A+
Sbjct: 3 RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59
Score = 37.0 bits (86), Expect = 0.001
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
TEE+ +E F ++GDI ++K+ + G+ KG G++ + A A+
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59
>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 = 39.9 bits (94), Expect = 1e-04
Identities = 13/59 (22%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
L +++LP +++E++ ++ +G +++ GKLK F + N+ +A +A+ +
Sbjct: 1 TLLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSR-RGKLKNTAFATFDNEQAASQALSR 57
Score = 28.7 bits (65), Expect = 0.97
Identities = 10/49 (20%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 150
++E++ ++ +G +++ GKLK F + N+ +A +A+ +
Sbjct: 11 LSEDDKEDLLKHFG-ASSVRVMSR-RGKLKNTAFATFDNEQAASQALSR 57
>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 = 43.5 bits (102), Expect = 1e-04
Identities = 28/111 (25%), Positives = 52/111 (46%), Gaps = 16/111 (14%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
+ K++K + + G + I K L++ NLP IT+++ FG+YG I+ +L
Sbjct: 175 RNKRLKVSYARPGGESI--------KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNIL 226
Query: 66 KNA-DGKLKGCGFINYANKISAVKAILKSNK-------KPYKGKITEEEFK 108
++ G +G F+ + + A +AI N +P ++ EE K
Sbjct: 227 RDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK 277
Score = 35.0 bits (80), Expect = 0.070
Identities = 29/143 (20%), Positives = 58/143 (40%), Gaps = 29/143 (20%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
L + LP +T+ E F G I +++++ G G F+++ ++ + +AI
Sbjct: 110 LIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNL 169
Query: 94 NKKPYKGK---------------------------ITEEEFKEHFGQYGDIIDAQLLKNA 126
N + K IT+++ FG+YG I+ +L++
Sbjct: 170 NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK 229
Query: 127 -DGKLKGCGFINYANKISAVKAI 148
G +G F+ + + A +AI
Sbjct: 230 LTGTPRGVAFVRFNKREEAQEAI 252
>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 = 43.7 bits (103), Expect = 1e-04
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
R++I NLP + E++ KE +GD+ L+K+ A G KG F Y + AI
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356
Query: 93 SNKKPYKGKI 102
N K
Sbjct: 357 LNGKDTGDNK 366
Score = 31.0 bits (70), Expect = 1.6
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 83 KISAVKAILKSNKKPYKGKI----TEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFIN 137
K+ +L S + Y G + E++ KE +GD+ L+K+ A G KG F
Sbjct: 284 KLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCE 343
Query: 138 YANKISAVKAI 148
Y + AI
Sbjct: 344 YKDPSVTDVAI 354
>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 = 40.1 bits (93), Expect = 2e-04
Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
+ L + LP +T+EEF+ FG G+I +L+++ G+ G GF+NY + A KAI
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Score = 35.1 bits (80), Expect = 0.008
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 148
+T+EEF+ FG G+I +L+++ G+ G GF+NY + A KAI
Sbjct: 14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
>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 = 39.8 bits (93), Expect = 2e-04
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISA 86
++I +LP E+E K++F Q+G + + ++ ++ G K GFI + N A
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVA 54
Score = 34.8 bits (80), Expect = 0.009
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 104 EEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISA 144
E+E K++F Q+G + + ++ ++ G K GFI + N A
Sbjct: 13 EKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVA 54
>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 = 39.6 bits (93), Expect = 2e-04
Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+ + ++E++ KE F G++ +L + + F+ +A+ SA+ A+ S
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFA-FVEFADAESALSALNLS 60
Score = 35.0 bits (81), Expect = 0.007
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 151
G ++E++ KE F G++ +L + + F+ +A+ SA+ A+ S
Sbjct: 10 GSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFA-FVEFADAESALSALNLS 60
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+LF+ L +TEE+ +E+F QYG++ +++ + + GK +G F+ + + K +L+
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Score = 38.0 bits (89), Expect = 5e-04
Identities = 15/53 (28%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 99 KGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 150
K +TEE+ +E+F QYG++ +++ + + GK +G F+ + + K +L+
Sbjct: 8 KEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
>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 = 39.4 bits (92), Expect = 2e-04
Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAI 90
+LF+ L K ++ + HF +YG + + ++ + + K GFI +++ A +A+
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
Score = 32.8 bits (75), Expect = 0.045
Identities = 11/49 (22%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAI 148
K ++ + HF +YG + + ++ + + K GFI +++ A +A+
Sbjct: 13 KTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 40.8 bits (95), Expect = 3e-04
Identities = 19/69 (27%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
+LFI L + + ++ F +GD++DA+++ + + G+ +G GF+N+ ++ +A AI +
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
Query: 93 SNKKPYKGK 101
+ K G+
Sbjct: 96 MDGKELNGR 104
Score = 34.2 bits (78), Expect = 0.041
Identities = 15/56 (26%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 104 EEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ ++ F +GD++DA+++ + + G+ +G GF+N+ ++ +A AI + + K G
Sbjct: 48 DASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNG 103
>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 = 39.0 bits (91), Expect = 3e-04
Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
RL+++ P +E +E F YG + + +++ N F+ + + SA++A
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISNF-------AFVEFESLESAIRAKDSV 53
Query: 94 NKKPYKG 100
+ K
Sbjct: 54 HGKVLNN 60
Score = 28.2 bits (63), Expect = 1.4
Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 96 KPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
+P+ +E +E F YG + + +++ N F+ + + SA++A + K
Sbjct: 5 RPFPPDTSESAIREIFSPYGAVKEVKMISNF-------AFVEFESLESAIRAKDSVHGKV 57
Query: 156 YKG 158
Sbjct: 58 LNN 60
>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 = 38.7 bits (90), Expect = 3e-04
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 7/57 (12%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+LF+ NLP + TE+E + F QYG +++ ++KN GF++ +K +A +AI
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNY-------GFVHMDDKTAADEAI 51
Score = 28.7 bits (64), Expect = 1.2
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 7/46 (15%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
TE+E + F QYG +++ ++KN GF++ +K +A +AI
Sbjct: 13 TEQEIRSLFEQYGKVLECDIIKNY-------GFVHMDDKTAADEAI 51
>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 = 39.2 bits (91), Expect = 3e-04
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
+LF+ NLP I E E KE F +G++++ ++ K GKL GF+ + + V+ IL
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDS-EPVQRILG 65
Query: 93 SNKKPYKGKI 102
+ ++G++
Sbjct: 66 AKPIMFRGEV 75
Score = 27.2 bits (60), Expect = 4.7
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
I E E KE F +G++++ ++ K GKL GF+ + + V+ IL + ++G
Sbjct: 17 IDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDS-EPVQRILGAKPIMFRG 73
>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 = 38.8 bits (91), Expect = 3e-04
Identities = 16/51 (31%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
+LF+ NLP+ + +E KE+F Q+G + + + + G KG GF++++++
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51
Score = 27.3 bits (61), Expect = 3.3
Identities = 11/37 (29%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 106 EFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 141
E KE+F Q+G + + + + G KG GF++++++
Sbjct: 15 ELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51
>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 = 14/55 (25%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
LF++NLP + T+E + F Q+ + +L+ +G F+ + + A A
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR-----RGIAFVEFETEEQATVA 54
Score = 26.4 bits (59), Expect = 7.2
Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
T+E + F Q+ + +L+ +G F+ + + A A
Sbjct: 14 TTKEMLEMLFNQFPGFKEVRLVPR-----RGIAFVEFETEEQATVA 54
>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 = 39.1 bits (91), Expect = 3e-04
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
G + + E+E ++ +YG+I ++L+ K C FIN+ N +A+ A+
Sbjct: 8 GNVSDVGDERNLPEKELRKECEKYGEIESIRILRE-----KACAFINFMNIPNAIAALQT 62
Query: 93 SN-KKPY 98
N KKPY
Sbjct: 63 LNGKKPY 69
Score = 38.0 bits (88), Expect = 9e-04
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 6/56 (10%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN-KKPY 156
+ E+E ++ +YG+I ++L+ K C FIN+ N +A+ A+ N KKPY
Sbjct: 19 LPEKELRKECEKYGEIESIRILRE-----KACAFINFMNIPNAIAALQTLNGKKPY 69
>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 = 38.8 bits (91), Expect = 4e-04
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG-KLKGCGFINYANKISAVKAILKS 93
+++ NLPF +T + + F +YG ++ ++K+ + K KG FI + ++ A K +
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63
Query: 94 NKK 96
N K
Sbjct: 64 NNK 66
Score = 27.3 bits (61), Expect = 3.9
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 111 FGQYGDIIDAQLLKNADG-KLKGCGFINYANKISAVKAILKSNKK 154
F +YG ++ ++K+ + K KG FI + ++ A K + N K
Sbjct: 22 FSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNK 66
>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 = 38.4 bits (89), Expect = 4e-04
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
LF++NL +TEE ++ FGQ+G + + KLK FI++ + AVKA+ + N
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMN 56
Query: 95 KKPYKGKITEEEF 107
K +G+ E F
Sbjct: 57 GKELEGENIEIVF 69
Score = 30.0 bits (67), Expect = 0.42
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+TEE ++ FGQ+G + + KLK FI++ + AVKA+ + N K +G
Sbjct: 13 VTEEILEKAFGQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNGKELEG 62
>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 = 38.8 bits (90), Expect = 4e-04
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKS 93
LFI +LP + T+ + + F +G++I A++ + L C GF++Y N SA AI
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66
Query: 94 N 94
N
Sbjct: 67 N 67
>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 = 38.9 bits (90), Expect = 4e-04
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
+ L + LP +T+EE K FG G+I +L+++ G+ G GF+NY + A KAI
Sbjct: 4 KTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63
Score = 33.9 bits (77), Expect = 0.019
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 148
+T+EE K FG G+I +L+++ G+ G GF+NY + A KAI
Sbjct: 16 MTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63
>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 = 38.8 bits (90), Expect = 4e-04
Identities = 22/69 (31%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+LF+ NLP + + E KE F QYG++++ ++ N+ GKL GF+ + + V+ IL +
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRI--NSGGKLPNFGFVVFDDS-EPVQKILSN 61
Query: 94 NKKPYKGKI 102
++G +
Sbjct: 62 RPIMFRGDV 70
Score = 26.8 bits (59), Expect = 6.2
Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI 136
+ + E KE F QYG++++ ++ N+ GKL GF+
Sbjct: 15 VDKSELKEFFQQYGNVVELRI--NSGGKLPNFGFV 47
>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 = 38.1 bits (89), Expect = 4e-04
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
RLFI P + ++ F ++G +ID L+ K G+ YA++ SA +AI
Sbjct: 1 RLFIVCNPSPPPDYILEDVFCRFGGLIDVYLVPG-----KNYGYAKYADRESAERAI 52
Score = 33.8 bits (78), Expect = 0.014
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 108 KEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
++ F ++G +ID L+ K G+ YA++ SA +AI
Sbjct: 17 EDVFCRFGGLIDVYLVPG-----KNYGYAKYADRESAERAI 52
>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 = 38.3 bits (89), Expect = 4e-04
Identities = 21/51 (41%), Positives = 32/51 (62%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
LF+ NL K+TEE E F Q G +I ++ K+ DGK K F+N+ +++S
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVS 54
Score = 31.8 bits (72), Expect = 0.086
Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 143
K+TEE E F Q G +I ++ K+ DGK K F+N+ +++S
Sbjct: 12 KVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVS 54
>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 = 38.4 bits (90), Expect = 5e-04
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAI 90
L++ L ++ E+ F +GDI D Q+ L K +G F+ + A AI
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57
Score = 33.0 bits (76), Expect = 0.031
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAI 148
+ E+ F +GDI D Q+ L K +G F+ + A AI
Sbjct: 10 VDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57
>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 = 38.1 bits (89), Expect = 5e-04
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
++F+ L + TEE+ +E+FG++G+I++ +L + K +G FI + ++ VK IL+
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSE-EPVKKILE 59
Query: 93 SNKKPYKGKITE 104
+ GK E
Sbjct: 60 TQFHVIGGKKVE 71
Score = 34.3 bits (79), Expect = 0.013
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
TEE+ +E+FG++G+I++ +L + K +G FI + ++ VK IL++ G +
Sbjct: 11 TTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSE-EPVKKILETQFHVIGGKK 69
>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 = 38.2 bits (89), Expect = 6e-04
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
L++ NLP + EE EHF +YG + ++L F+++ + SA KA
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA 56
Score = 30.1 bits (68), Expect = 0.41
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
+ EE EHF +YG + ++L F+++ + SA KA
Sbjct: 11 VREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA 56
>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 = 37.6 bits (88), Expect = 7e-04
Identities = 12/62 (19%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKSN 94
F+ L K+ E + E F + G + D ++++ + KG ++ + ++ S A+ +
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLTG 62
Query: 95 KK 96
++
Sbjct: 63 QR 64
Score = 31.8 bits (73), Expect = 0.092
Identities = 10/55 (18%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKSNKK 154
K+ E + E F + G + D ++++ + KG ++ + ++ S A+ + ++
Sbjct: 10 KVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLTGQR 64
>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 = 38.2 bits (88), Expect = 7e-04
Identities = 14/43 (32%), Positives = 26/43 (60%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
L+I NLP + E+E + +G +I ++L+++ G +G GF
Sbjct: 3 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGF 45
>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 = 38.1 bits (88), Expect = 8e-04
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAILKS 93
L+I LP +T+++ ++ F ++G II+++ L+ A G +G FI + + A +AI
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62
Query: 94 N-KKP 97
N KP
Sbjct: 63 NGHKP 67
Score = 31.9 bits (72), Expect = 0.099
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAILKSN-KKPYKGS 159
+T+++ ++ F ++G II+++ L+ A G +G FI + + A +AI N KP S
Sbjct: 12 MTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSS 71
Query: 160 E 160
E
Sbjct: 72 E 72
>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM1 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 = 37.7 bits (87), Expect = 8e-04
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHF-GQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
R+FI N+P+ + + K+ + G++ +L K+A+GK +GCG + + ++ KA+
Sbjct: 1 RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEV 60
Query: 93 SNKKPYKGK 101
NK G+
Sbjct: 61 MNKYDLNGR 69
Score = 29.6 bits (66), Expect = 0.73
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 115 GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
G++ +L K+A+GK +GCG + + ++ KA+ NK G
Sbjct: 25 GEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVMNKYDLNG 68
>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 = 38.2 bits (88), Expect = 9e-04
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
L+I NLP + E+E + +G +I ++L++A+G +G GF
Sbjct: 4 LYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGF 46
>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 = 37.7 bits (87), Expect = 0.001
Identities = 15/43 (34%), Positives = 26/43 (60%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
L+I NLP + E+E + +G +I ++L++A G +G GF
Sbjct: 3 LYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGF 45
>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM1 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 = 76
Score = 37.7 bits (87), Expect = 0.001
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
R FI N+PF + + K+ + G++ +LL +A+GK +GC + + + S KA+
Sbjct: 1 RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEV 60
Query: 93 SNKKPYKGK 101
NK G+
Sbjct: 61 LNKHVLNGR 69
Score = 28.1 bits (62), Expect = 2.3
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 115 GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
G++ +LL +A+GK +GC + + + S KA+ NK G
Sbjct: 25 GEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEVLNKHVLNG 68
>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 = 37.2 bits (87), Expect = 0.001
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
++I +LP E E +++F Q+G + +L ++ GK KG F+ + +
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51
Score = 31.4 bits (72), Expect = 0.11
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 104 EEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 141
E E +++F Q+G + +L ++ GK KG F+ + +
Sbjct: 13 EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51
>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 = 37.6 bits (88), Expect = 0.001
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 5/65 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD---GKLKGCGFINYANKISAVKAIL 91
+F+ + + EE+ + F ++G+I + L N D G +KG I Y K A AI
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHL--NLDRRTGFVKGYALIEYETKKEAQAAIE 66
Query: 92 KSNKK 96
N K
Sbjct: 67 GLNGK 71
Score = 34.1 bits (79), Expect = 0.019
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD---GKLKGCGFINYANKISAVKAILKSNKK 154
EE+ + F ++G+I + L N D G +KG I Y K A AI N K
Sbjct: 18 AQEEDVHDKFAEFGEIKNLHL--NLDRRTGFVKGYALIEYETKKEAQAAIEGLNGK 71
>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 = 37.6 bits (87), Expect = 0.001
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
+LF+ L + E + EHF Q+G + A+++ + GK +G GF+ + N SA KA +
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV 59
Score = 36.4 bits (84), Expect = 0.003
Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 99 KGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 149
KG + E + EHF Q+G + A+++ + GK +G GF+ + N SA KA +
Sbjct: 8 KGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV 59
>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 = 37.2 bits (87), Expect = 0.001
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 44 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGKI 102
TE + +E F +YG I Q++ + G+ +G GF+ + + A +A + N G+
Sbjct: 11 TTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRR 70
Query: 103 TEEEF 107
++
Sbjct: 71 IRVDY 75
Score = 36.8 bits (86), Expect = 0.002
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSN 152
TE + +E F +YG I Q++ + G+ +G GF+ + + A +A + N
Sbjct: 11 TTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLN 62
>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 = 37.0 bits (86), Expect = 0.001
Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKA 89
++ ++N+PF+ T +E +E F +G++ +L K G +G GF+++ K A +A
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59
>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 = 37.3 bits (87), Expect = 0.001
Identities = 17/72 (23%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
++F+ LP +TE + +++F Q+G + + ++ + + K +G GFI + ++ +V ++
Sbjct: 4 KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESE-DSVDQVVN 62
Query: 93 SNKKPYKGKITE 104
+ GK E
Sbjct: 63 EHFHDINGKKVE 74
Score = 30.8 bits (70), Expect = 0.26
Identities = 11/49 (22%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAIL 149
+TE + +++F Q+G + + ++ + + K +G GFI + ++ +V ++
Sbjct: 14 VTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESE-DSVDQVV 61
>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 = 37.1 bits (87), Expect = 0.001
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS 93
L++ +L +TE E F G ++ ++ ++ + G ++N+ N A +A+
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61
Query: 94 NKKPYKGK 101
N KGK
Sbjct: 62 NFDVIKGK 69
Score = 28.3 bits (64), Expect = 1.7
Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+TE E F G ++ ++ ++ + G ++N+ N A +A+ N KG
Sbjct: 11 VTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKG 68
>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 = 37.3 bits (86), Expect = 0.001
Identities = 19/56 (33%), Positives = 32/56 (57%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
L +KNLP ++ E +E F +G + A ++ + G+ G G + +A K SA KA+
Sbjct: 2 LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKAL 57
Score = 29.2 bits (65), Expect = 1.00
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
++ E +E F +G + A ++ + G+ G G + +A K SA KA+
Sbjct: 11 VSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKAL 57
>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 = 36.9 bits (86), Expect = 0.002
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 8/61 (13%)
Query: 34 RLFI---KNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKA 89
RLFI K+ +TE++ +E F +G+I D ++K+ K KG ++ +A SA +A
Sbjct: 5 RLFIVCGKS----VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60
Query: 90 I 90
+
Sbjct: 61 M 61
Score = 35.4 bits (82), Expect = 0.005
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 148
+TE++ +E F +G+I D ++K+ K KG ++ +A SA +A+
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61
>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 = 36.4 bits (85), Expect = 0.002
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDI 59
+ +KNLPF TEEE +E F ++G +
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSL 27
>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 = 37.2 bits (87), Expect = 0.002
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKIS 85
LF+ L + TE + + F +YG I +L+++ GK +G FI + ++
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERD 55
Score = 29.1 bits (66), Expect = 1.3
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKIS 143
TE + + F +YG I +L+++ GK +G FI + ++
Sbjct: 14 TESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERD 55
>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 = 36.9 bits (86), Expect = 0.002
Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 4/70 (5%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLL--KNADGKLKG--CGFINYANKISAVKAI 90
L++ NL K+TEE + FG++G + +++ + + + + CGF+ + N+ A +A+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 91 LKSNKKPYKG 100
+ + K G
Sbjct: 64 DELDGKDVMG 73
Score = 29.5 bits (67), Expect = 0.63
Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLL--KNADGKLKG--CGFINYANKISAVKAILKSNKKPY 156
K+TEE + FG++G + +++ + + + + CGF+ + N+ A +A+ + + K
Sbjct: 12 KVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERALDELDGKDV 71
Query: 157 KGSE 160
G E
Sbjct: 72 MGYE 75
>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 = 36.6 bits (85), Expect = 0.002
Identities = 17/68 (25%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 93
+FI L ++ T E +E+F ++G+I + ++++ K +G GF+ +++ ++V +L
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDP-ASVDKVLAQ 59
Query: 94 NKKPYKGK 101
GK
Sbjct: 60 GPHELDGK 67
Score = 30.1 bits (68), Expect = 0.37
Identities = 12/50 (24%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 151
T E +E+F ++G+I + ++++ K +G GF+ +++ ++V +L
Sbjct: 11 TAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDP-ASVDKVLAQ 59
>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 = 36.6 bits (85), Expect = 0.002
Identities = 18/55 (32%), Positives = 28/55 (50%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
LF+ NL ITEEE + F +YG + D + + G+ F+ + N A +A
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRA 59
Score = 29.3 bits (66), Expect = 0.76
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
ITEEE + F +YG + D + + G+ F+ + N A +A
Sbjct: 14 ITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRA 59
>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 = 37.0 bits (85), Expect = 0.002
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKS 93
LFI +LP + +++ + F +G+++ A++ + L C GF++Y N +SA AI
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69
Query: 94 N 94
N
Sbjct: 70 N 70
Score = 28.9 bits (64), Expect = 1.5
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 104 EEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSN 152
+++ + F +G+++ A++ + L C GF++Y N +SA AI N
Sbjct: 21 DQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAMN 70
>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 = 36.4 bits (84), Expect = 0.003
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
LFI +LP + + E + F +G++I A++ + A + K GF+++ N SA AI
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66
Query: 94 N 94
N
Sbjct: 67 N 67
Score = 27.1 bits (60), Expect = 4.5
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSN 152
+ E + F +G++I A++ + A + K GF+++ N SA AI N
Sbjct: 17 GDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMN 67
>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 = 36.6 bits (84), Expect = 0.003
Identities = 18/56 (32%), Positives = 33/56 (58%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
L +KNL ++ E ++ F Q+G + A ++ + G+ G GF+ +A K +A KA+
Sbjct: 2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKAL 57
Score = 31.5 bits (71), Expect = 0.13
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
++ E ++ F Q+G + A ++ + G+ G GF+ +A K +A KA+
Sbjct: 11 VSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKAL 57
>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 = 36.5 bits (85), Expect = 0.003
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDI-IDA-------QLLKNADGKLKGCGFINYANKISA 86
++I LP +TE+ E FG G I D ++ + + + KG + Y + +A
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60
Query: 87 VKAILKSNKKPYKGK 101
AI N ++G
Sbjct: 61 QAAIEWFNGYEFRGN 75
Score = 28.8 bits (65), Expect = 1.2
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 102 ITEEEFKEHFGQYGDI-IDA-------QLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
+TE+ E FG G I D ++ + + + KG + Y + +A AI N
Sbjct: 10 VTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAAQAAIEWFNG 69
Query: 154 KPYKGSE 160
++G++
Sbjct: 70 YEFRGNK 76
>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 = 36.0 bits (84), Expect = 0.003
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+++K P T ++ +E F ++G + + ++ ++ D K KG F+ + + A K L+
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDA-KKFLEKE 60
Query: 95 KKPYKGK 101
K YK K
Sbjct: 61 KLKYKEK 67
Score = 31.0 bits (71), Expect = 0.15
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
T ++ +E F ++G + + ++ ++ D K KG F+ + + A K L+ K YK E
Sbjct: 12 TLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDA-KKFLEKEKLKYKEKE 68
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 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 = 92
Score = 36.4 bits (85), Expect = 0.003
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIID--------AQLLKNADGKLKGCGFINYA 81
+++ LP IT EEF E F + G I + +L ++ +G LKG Y
Sbjct: 4 VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYL 58
Score = 31.0 bits (71), Expect = 0.26
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 102 ITEEEFKEHFGQYGDIID--------AQLLKNADGKLKGCGFINYA 139
IT EEF E F + G I + +L ++ +G LKG Y
Sbjct: 13 ITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYL 58
>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 = 36.2 bits (84), Expect = 0.003
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDI-IDAQLLK--------NADGKLKGCGFINYANKIS 85
+F+ NLP TE++ EHFG G I ID + K G+ KG + Y + +
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 86 AVKAILKSNKKPYKG 100
A AI N K + G
Sbjct: 61 ASAAIEWFNNKDFMG 75
Score = 29.7 bits (67), Expect = 0.70
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 9/66 (13%)
Query: 103 TEEEFKEHFGQYGDI-IDAQLLK--------NADGKLKGCGFINYANKISAVKAILKSNK 153
TE++ EHFG G I ID + K G+ KG + Y + +A AI N
Sbjct: 11 TEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHAASAAIEWFNN 70
Query: 154 KPYKGS 159
K + G+
Sbjct: 71 KDFMGN 76
>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 = 36.2 bits (83), Expect = 0.003
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
R L + LP +T++E + F G++ A+L+++ G G GF+NY N A +AI
Sbjct: 1 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60
Score = 30.4 bits (68), Expect = 0.36
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
+T++E + F G++ A+L+++ G G GF+NY N A +AI
Sbjct: 13 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60
>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 = 36.1 bits (83), Expect = 0.004
Identities = 18/60 (30%), Positives = 32/60 (53%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+F+ +P + E+E F G I + +L+ + DGK +G F+ Y K A +A+ + N
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63
Score = 30.7 bits (69), Expect = 0.31
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 152
+ E+E F G I + +L+ + DGK +G F+ Y K A +A+ + N
Sbjct: 13 VYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63
>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 = 35.7 bits (82), Expect = 0.004
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKA 89
L I NLP T+++F+E +G++ L+ + G KG GF+ Y K SA +A
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARA 57
>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 = 35.7 bits (83), Expect = 0.004
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
G L + NL I+++E + F Q+G++ D ++ + F+ + + +A A+
Sbjct: 2 GTLLVFNLDSPISDQELRSLFSQFGEVKD---IRETPLR-PSQKFVEFYDIRAAEAALDA 57
Query: 93 SNKKPYKGK 101
N +P+ G
Sbjct: 58 LNGRPFLGG 66
Score = 27.6 bits (62), Expect = 3.3
Identities = 12/58 (20%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
I+++E + F Q+G++ D ++ + F+ + + +A A+ N +P+ G
Sbjct: 13 ISDQELRSLFSQFGEVKD---IRETPLR-PSQKFVEFYDIRAAEAALDALNGRPFLGG 66
>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 = 35.6 bits (83), Expect = 0.005
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDI--IDAQLLKNADGKLKGCG--FINYANKISAVKAI 90
L++ NL F TEE+ E F + GDI I L + CG F+ Y + A A+
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRF---TKTPCGFCFVEYYTREDAENAV 57
>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM2 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 78
Score = 35.5 bits (82), Expect = 0.005
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAI 90
LF++ LPF +TE+ ++ F G +D LKN G G + +A K A++ +
Sbjct: 2 LFLRGLPFSVTEDNVRDFFS--GLKVDGVIFLKNRRGLNNGNSMVKFATKEDAIEGL 56
>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 = 35.4 bits (82), Expect = 0.005
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
L +KNL ++ E ++ F Q+G++ A ++ + G+ G G + ++ K A AI
Sbjct: 2 LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAI 57
Score = 31.1 bits (71), Expect = 0.18
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 89 AILKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
A+ N P+ ++ E ++ F Q+G++ A ++ + G+ G G + ++ K A AI
Sbjct: 1 ALRVKNLSPF---VSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAI 57
>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 = 35.2 bits (82), Expect = 0.005
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 90
L + L + ++ KE F YG + D L + + L +G ++ + + A KAI
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAI 57
Score = 32.9 bits (76), Expect = 0.032
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 148
+ ++ KE F YG + D L + + L +G ++ + + A KAI
Sbjct: 10 VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAI 57
>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 = 35.2 bits (82), Expect = 0.006
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
RLF+ L +TE + +E F ++G + D ++ K G +G +I+ + +K
Sbjct: 1 RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60
Query: 93 S-NKKPYKG 100
+ N +KG
Sbjct: 61 TLNGTKWKG 69
Score = 26.8 bits (60), Expect = 7.1
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS-NKKPYKGS 159
+TE + +E F ++G + D ++ K G +G +I+ + +K + N +KGS
Sbjct: 11 VTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKSTLNGTKWKGS 70
Query: 160 E 160
Sbjct: 71 V 71
>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 = 34.9 bits (81), Expect = 0.007
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
RL + NL +TE++ E F G + A+L++ G + Y K A+ AI K
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVRP------GVAEVVYVRKDDALTAIDK 54
Query: 93 SNKKPYKGK 101
N + G+
Sbjct: 55 YNNRELDGQ 63
>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 = 35.0 bits (81), Expect = 0.007
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L+I NL + E + ++ F ++ + + L+K G F++ ++ A KAI K N
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG-----GYAFVDCPDQSWADKAIEKLN 55
Query: 95 KKPYKGKITEEEFK 108
K +GK+ E E
Sbjct: 56 GKILQGKVIEVEHS 69
>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 = 35.3 bits (82), Expect = 0.007
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKL-KGCGFINYANKISAVKAI 90
LFI NL ++ E+ + F +G I+ +++++ D KG FI+Y + ++ AI
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAI 61
Score = 28.4 bits (64), Expect = 1.7
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 111 FGQYGDIIDA-QLLKNADGKL-KGCGFINYANKISAVKAI 148
F +G I+ +++++ D KG FI+Y + ++ AI
Sbjct: 22 FSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAI 61
>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 = 35.0 bits (80), Expect = 0.007
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
LF++NL +TEE ++ F ++G + + KLK F+++ + +AV+A+ + N
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVK-------KLKDYAFVHFEERDAAVRAMDEMN 56
Query: 95 KKPYKGKITE 104
K +G+ E
Sbjct: 57 GKEIEGEEIE 66
Score = 28.1 bits (62), Expect = 2.2
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 7/59 (11%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+TEE ++ F ++G + + KLK F+++ + +AV+A+ + N K +G E
Sbjct: 13 VTEEILEKSFSEFGKLERVK-------KLKDYAFVHFEERDAAVRAMDEMNGKEIEGEE 64
>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 = 35.2 bits (81), Expect = 0.007
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 3/50 (6%)
Query: 32 RGRL-FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINY 80
GR+ +I+NL ++ E K+ F +G+I + ++L + G + GFI Y
Sbjct: 1 EGRVIYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRG--EKYGFITY 48
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 75
Score = 35.1 bits (81), Expect = 0.007
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 37 IKNLPFKITEEEFKEHFGQYGDIID-AQLLKNADGKLKGCGFINYANKISAVKAILKSNK 95
++NLPF T EE + F Y I LL N +G G + + A+ A+ + N
Sbjct: 5 VQNLPFTATIEEILDFFYGYRVIPGSVSLLYNDNGAPTGEATVAFDTHREAMAAVRELNG 64
Query: 96 KP 97
+P
Sbjct: 65 RP 66
>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 = 35.0 bits (80), Expect = 0.008
Identities = 16/61 (26%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
++FI L ++ T+E +E+FGQ+G++ + ++++ K +G GF+ + ++ K + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 93 S 93
S
Sbjct: 62 S 62
Score = 28.0 bits (62), Expect = 2.1
Identities = 13/52 (25%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 151
+ T+E +E+FGQ+G++ + ++++ K +G GF+ + ++ K + +S
Sbjct: 11 QTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
>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 = 35.0 bits (81), Expect = 0.008
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSN 94
F+ N+ + T EE +EHF G I +L + G+ KG +I + +K S A+L +
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62
Score = 30.0 bits (68), Expect = 0.37
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSN 152
T EE +EHF G I +L + G+ KG +I + +K S A+L +
Sbjct: 12 TPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62
>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 = 34.9 bits (80), Expect = 0.008
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
LF+ NL ++ EE E F Q G + + K+ +GK K GF+ + + S AI
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAI 59
Score = 28.0 bits (62), Expect = 2.1
Identities = 15/48 (31%), Positives = 24/48 (50%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
++ EE E F Q G + + K+ +GK K GF+ + + S AI
Sbjct: 12 RVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAI 59
>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 = 34.7 bits (80), Expect = 0.009
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKA 89
++F+ L TE++ K++F Q+G + DA L+ + +G GF+ + ++ K
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57
Score = 31.6 bits (72), Expect = 0.11
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKA 147
TE++ K++F Q+G + DA L+ + +G GF+ + ++ K
Sbjct: 12 TEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57
>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 = 34.6 bits (80), Expect = 0.009
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 42 FKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+ +TEE K+ F +G+II+ + K K CGF+ + SA +AI
Sbjct: 12 YGLTEEILKKAFSPFGNIINISMEKE-----KNCGFVTFEKMESADRAI 55
Score = 33.8 bits (78), Expect = 0.020
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
+TEE K+ F +G+II+ + K K CGF+ + SA +AI
Sbjct: 13 GLTEEILKKAFSPFGNIINISMEKE-----KNCGFVTFEKMESADRAI 55
>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 = 34.4 bits (79), Expect = 0.011
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 149
P + TEE+ E+FGQ+G ++D ++ + GF+ + N VK IL
Sbjct: 6 PADSRFTEEDVSEYFGQFGPVLDVRIPYQQK---RMFGFVTFENA-ETVKRIL 54
Score = 32.0 bits (73), Expect = 0.082
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 45 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
TEE+ E+FGQ+G ++D ++ + GF+ + N VK IL
Sbjct: 12 TEEDVSEYFGQFGPVLDVRIPYQQK---RMFGFVTFENA-ETVKRIL 54
>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 = 34.6 bits (79), Expect = 0.012
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
LF++N+ E+ + FG+YG I+D + L + +G +I + + A A+
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 94 NKKPYKGKITEEEFKE 109
N+K G+ E +F +
Sbjct: 63 NRKWVCGRQIEIQFAQ 78
>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 = 34.3 bits (79), Expect = 0.013
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
++I NL + ITE++ +E F +I +L + + G+ KG G +++A++ S A LK
Sbjct: 1 TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAA-LK 58
Query: 93 SNKKPYKGK 101
+ G+
Sbjct: 59 LDGTVLCGR 67
>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 = 34.3 bits (79), Expect = 0.014
Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 37 IKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 96
++ PF + E+ +E F + +++KN G+ G F++ ++ +K LK NK
Sbjct: 5 MRGAPFNVKEKHIREFFSPL-KPVAIRIVKNDHGRKTGFAFVDLKSE-EDLKKALKRNKD 62
Query: 97 PYKGKITE 104
G+ E
Sbjct: 63 YMGGRYIE 70
Score = 26.2 bits (58), Expect = 9.5
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+ E+ +E F + +++KN G+ G F++ ++ +K LK NK G
Sbjct: 11 NVKEKHIREFFSPL-KPVAIRIVKNDHGRKTGFAFVDLKSE-EDLKKALKRNKDYMGG 66
>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 = 34.4 bits (78), Expect = 0.017
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISA 86
D+ + L+I+ LP T+++ + YG I+ + +L K KG GF+++ + +A
Sbjct: 3 DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAA 62
Query: 87 VKAI 90
KA+
Sbjct: 63 QKAV 66
>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 = 34.0 bits (78), Expect = 0.018
Identities = 14/59 (23%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+F+ + ++ E E + F +YG + + +++ + G KG GF+++ + + V+ I++S
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVD-VQKIVES 65
Score = 31.3 bits (71), Expect = 0.18
Identities = 13/51 (25%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 151
++ E E + F +YG + + +++ + G KG GF+++ + + V+ I++S
Sbjct: 16 RMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVD-VQKIVES 65
>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 = 34.1 bits (79), Expect = 0.018
Identities = 16/63 (25%), Positives = 33/63 (52%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+F+ +P + E+E F + G I + +L+ + G +G F+ Y NK +A +A+ + +
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63
Query: 95 KKP 97
Sbjct: 64 NYE 66
>gnl|CDD|241046 cd12602, RRM2_SF2_plant_like, RNA recognition motif 2 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subfamily corresponds to the RRM2 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 = 76
Score = 33.6 bits (77), Expect = 0.020
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 12/78 (15%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+ + LP + ++ K+H + GD+ +Q+ ++ G G +++ N AI
Sbjct: 2 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGRGTT---GIVDFTNYDDMKYAI--- 55
Query: 94 NKKPYKGKITEEEFKEHF 111
K+ + EF+ F
Sbjct: 56 ------RKLDDTEFRNPF 67
>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 = 33.8 bits (78), Expect = 0.020
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAI 90
++I+ LP T+E+ ++ +G II + L K KG GF+++ + +A+KAI
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAI 59
Score = 28.4 bits (64), Expect = 1.4
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAI 148
T+E+ ++ +G II + L K KG GF+++ + +A+KAI
Sbjct: 13 TDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAI 59
>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 = 34.2 bits (79), Expect = 0.020
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 35 LFIKNLP--FKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
LF+ LP F+ ++ F Q G QL +G+ +G F+ YA A +A
Sbjct: 5 LFVDRLPKTFRDVSI-LRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEA 60
Score = 30.7 bits (70), Expect = 0.39
Identities = 15/56 (26%), Positives = 23/56 (41%)
Query: 105 EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
++ F Q G QL +G+ +G F+ YA A +A N +GS
Sbjct: 18 SILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSP 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 = 33.7 bits (78), Expect = 0.020
Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 35 LFIKNLPFKI-TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
L ++N+P ++ + EHF ++G I++ Q+ N + ++ A KA
Sbjct: 4 LEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYN-----PESALVQFSTSEEAKKAY 55
Score = 29.8 bits (68), Expect = 0.49
Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
+ EHF ++G I++ Q+ N + ++ A KA
Sbjct: 15 NITKLNEHFSKFGTIVNIQVNYN-----PESALVQFSTSEEAKKAY 55
>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 = 33.4 bits (77), Expect = 0.021
Identities = 13/69 (18%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+ + LP + ++ K+ Q GD+ A + ++ +G+ G + + ++ +A+ K
Sbjct: 2 RVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGE----GVVEFTSQEDMERALRKL 57
Query: 94 NKKPYKGKI 102
+ ++G+
Sbjct: 58 DGTEFRGRR 66
>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 = 33.7 bits (77), Expect = 0.022
Identities = 16/71 (22%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
+F+ L + T+++ KE+F ++G+++D + + G+ +G GF+ + + S V+ +L
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAAS-VEKVLDQ 59
Query: 94 NKKPYKGKITE 104
+ G++ +
Sbjct: 60 KEHKLDGRVID 70
Score = 27.1 bits (60), Expect = 3.8
Identities = 12/47 (25%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAI 148
T+++ KE+F ++G+++D + + G+ +G GF+ + + S K +
Sbjct: 11 TKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVL 57
>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 = 33.4 bits (77), Expect = 0.023
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L++ NL +TE+ E F Q G I +L++ + F+ Y + SA A+ N
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIR--EHGNDPYAFVEYYDHRSAAAALQTMN 58
Query: 95 KKPYKGKI 102
+ G+
Sbjct: 59 GRLILGQE 66
Score = 28.8 bits (65), Expect = 1.1
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
+TE+ E F Q G I +L++ + F+ Y + SA A+ N + G E
Sbjct: 9 TVTEDLLAELFSQIGPIKSCKLIR--EHGNDPYAFVEYYDHRSAAAALQTMNGRLILGQE 66
>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 = 33.5 bits (76), Expect = 0.025
Identities = 18/61 (29%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
++F+ L TEE+ KE+FG +G+I + +L + + +G F+ Y ++ V+ +L+
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDE-EPVQKLLE 59
Query: 93 S 93
S
Sbjct: 60 S 60
Score = 30.4 bits (68), Expect = 0.37
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 102 ITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 151
TEE+ KE+FG +G+I + +L + + +G F+ Y ++ V+ +L+S
Sbjct: 11 TTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDE-EPVQKLLES 60
>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 = 33.5 bits (76), Expect = 0.026
Identities = 17/56 (30%), Positives = 32/56 (57%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
L ++NL ++ E +E F Q+G + A ++ + G+ G G + +A+K +A KA
Sbjct: 2 LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAF 57
Score = 31.2 bits (70), Expect = 0.20
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 94 NKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
N PY ++ E +E F Q+G + A ++ + G+ G G + +A+K +A KA
Sbjct: 6 NLSPY---VSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAF 57
>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 = 33.7 bits (77), Expect = 0.026
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 93
+F+ NL F+ EE FG+ G I +++++ + KG ++ + ++ + KA+L
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALL-L 60
Query: 94 NKKPYKGKITEE 105
N+K + + E
Sbjct: 61 NEKKFPPMLPRE 72
>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 = 36.5 bits (84), Expect = 0.028
Identities = 30/138 (21%), Positives = 57/138 (41%), Gaps = 25/138 (18%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK-- 92
+F+ +P + E+E F + G I + +L+ + G+ +G F+ + K A +A+
Sbjct: 61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120
Query: 93 ----------------SNKKPYKGKI----TEEEFKEHFGQYGD-IIDAQLLKNADGKLK 131
N + + G I EE E F + + ++D + +A K K
Sbjct: 121 NYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKK 180
Query: 132 --GCGFINYANKISAVKA 147
G F+ Y + +A A
Sbjct: 181 NRGFAFVEYESHRAAAMA 198
Score = 30.7 bits (69), Expect = 1.6
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 35 LFIKNLPFKITEEEFKEHFGQY--GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
L+++NL TEE ++ F ++ G + + K++ F+++ ++ AVKA+ +
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVK-------KIRDYAFVHFEDREDAVKAMDE 288
Query: 93 SNKKPYKGKITE 104
N K +G E
Sbjct: 289 LNGKELEGSEIE 300
Score = 30.7 bits (69), Expect = 1.8
Identities = 13/49 (26%), Positives = 25/49 (51%)
Query: 104 EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 152
E+E F + G I + +L+ + G+ +G F+ + K A +A+ N
Sbjct: 72 EDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120
>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 = 33.5 bits (77), Expect = 0.029
Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDI---IDAQLL---KNADGKLKGCGFINYANKISAV 87
R++I NL + +EE+ +E + + I +Q + ++ + G + +++ A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 88 KAILKSNKKPYKGK 101
K + N K +K +
Sbjct: 61 KVVKDLNGKVFKNR 74
>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 = 33.4 bits (76), Expect = 0.029
Identities = 17/71 (23%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
+FI L + T+++ K++F ++G+++D L L G+ +G GF+ + + +V ++
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF-KESESVDKVMDQ 59
Query: 94 NKKPYKGKITE 104
+ GK+ +
Sbjct: 60 KEHKLNGKVID 70
Score = 28.4 bits (63), Expect = 1.7
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKK 154
T+++ K++F ++G+++D L L G+ +G GF+ + S K + + K
Sbjct: 11 TKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHK 63
>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 = 33.5 bits (77), Expect = 0.030
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 35 LFIKNLPFKITEEEF----KEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+F+ +LP +++E EHF +YG ++ ++L+ D + + F+ + N A A+
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLR--DWRQRPYAFVQFTNDDDAKNAL 62
Query: 91 LK 92
K
Sbjct: 63 AK 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 = 33.1 bits (76), Expect = 0.035
Identities = 15/57 (26%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
+++ +P+ TE+E + +F G+I + L+ D G+ +G FI + + +A +A+
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL 57
>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 = 33.1 bits (76), Expect = 0.037
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
L I LP +T+EEF+ F G + + +++++ G G GF++Y + A +AI
Sbjct: 3 LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62
Query: 94 N 94
N
Sbjct: 63 N 63
Score = 28.1 bits (63), Expect = 2.0
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN 152
+T+EEF+ F G + + +++++ G G GF++Y + A +AI N
Sbjct: 12 LTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLN 63
>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 = 36.2 bits (83), Expect = 0.040
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 22 IERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG-KLKGCGFINY 80
I+ + + K R+++ ++ ++E + K F +G+I+ QL + G KG GFI Y
Sbjct: 194 IDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEY 253
Query: 81 ANKISAVKAILKSN 94
N S +AI N
Sbjct: 254 NNLQSQSEAIASMN 267
Score = 33.5 bits (76), Expect = 0.24
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADG-KLKGCGFINYANKISAVKAILKSN 152
++E + K F +G+I+ QL + G KG GFI Y N S +AI N
Sbjct: 216 LSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN 267
>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 = 33.0 bits (75), Expect = 0.040
Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
LF++N+ E+ + FG+YG I+D + L + +G ++ + + A A+
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 94 NKKPYKGKITEEEFKE 109
++K G+ E +F +
Sbjct: 63 DRKWICGRQIEIQFAQ 78
>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 = 32.6 bits (75), Expect = 0.042
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
+LF+ NLP T EE + F +YG + + ++KN GF++ + A AI
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKNY-------GFVHMEEEEDAEDAIKAL 53
Query: 94 NKKPYKGK 101
N + GK
Sbjct: 54 NGYEFMGK 61
>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 = 33.0 bits (75), Expect = 0.044
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 35 LFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
++I NL K+ +EE K+ F Q+G I+D LK K++G F+ + + SA A+
Sbjct: 2 IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALKTL--KMRGQAFVVFKDISSATNAL 59
Query: 91 LKSNKKPYKGK 101
P+ K
Sbjct: 60 RSMQGFPFYDK 70
>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 = 32.5 bits (74), Expect = 0.048
Identities = 13/68 (19%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
++F+ N+ ++EE + F YG ++ +++ F++ + +A +AI +
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQF-------AFVHLRGEAAADRAIEEL 54
Query: 94 NKKPYKGK 101
N + G+
Sbjct: 55 NGRELHGR 62
>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 = 32.7 bits (75), Expect = 0.049
Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 93
L + NL ++ T ++ + F +YG++ D + ++ + +G F+ + +K A A+
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Query: 94 NKKPYKGK 101
+ K G+
Sbjct: 61 DGKELDGR 68
>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 = 32.6 bits (75), Expect = 0.053
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
G + + K EE + HFG++GDI D ++L + KG F+ Y + SA
Sbjct: 7 GGIKAGSAL-KQIEEILRRHFGEWGDIEDIRVLPS-----KGIAFVRYKYRASA 54
Score = 32.2 bits (74), Expect = 0.082
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 144
K EE + HFG++GDI D ++L + KG F+ Y + SA
Sbjct: 15 LKQIEEILRRHFGEWGDIEDIRVLPS-----KGIAFVRYKYRASA 54
>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 = 32.7 bits (74), Expect = 0.053
Identities = 13/58 (22%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 90
++FI L ++ + + +++F ++G+I + ++++ K +G GF+ +A+ S K +
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58
>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 = 32.7 bits (75), Expect = 0.059
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 45 TEEEFKEHFGQYG-DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGKI 102
E K F G ++ ++++N G G F+ +A++ +A + + K N KP G
Sbjct: 12 DENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPIPGSN 71
Query: 103 TEEEFKEHFGQYG 115
+ FK + YG
Sbjct: 72 PPKRFKLNRATYG 84
Score = 30.0 bits (68), Expect = 0.56
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 97 PYKGKITEEEFKEHFGQYG-DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
PY + E K F G ++ ++++N G G F+ +A++ +A + + K N K
Sbjct: 9 PY---MDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGK 65
Query: 155 PYKGS 159
P GS
Sbjct: 66 PIPGS 70
>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 = 32.8 bits (75), Expect = 0.060
Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 5/55 (9%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
F+ + + E + +++F Q+G ++ N K CGF+ + + +A K
Sbjct: 5 FFLFGVEDDLPEYKIRDYFEQFGKSK--SVIVNHRAK---CGFVRFETREAAEKF 54
Score = 30.1 bits (68), Expect = 0.49
Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
+ E + +++F Q+G ++ N K CGF+ + + +A K
Sbjct: 13 DLPEYKIRDYFEQFGKSK--SVIVNHRAK---CGFVRFETREAAEKF 54
>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 = 32.5 bits (74), Expect = 0.062
Identities = 15/59 (25%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN---ADGKLKGCGFINYANKISAVKA 89
++F+ +P +E++ +E F QYG + +L++ + KGC F+ + + +A++A
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61
>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 = 32.6 bits (74), Expect = 0.064
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
LF+ NL +TE + + F ++G I + + + G+ GF+ + N A +A L +
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69
Query: 95 KK 96
K
Sbjct: 70 GK 71
>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 = 32.3 bits (74), Expect = 0.069
Identities = 15/76 (19%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
L+++N+ ++ + FG+YG I+D + L + +G ++ + + A A+
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 94 NKKPYKGKITEEEFKE 109
++ + G+ E +F +
Sbjct: 63 DRTRFLGREIEIQFAQ 78
>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 = 32.3 bits (73), Expect = 0.069
Identities = 14/51 (27%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANK 83
++F+ L T E+ K++F Q+G + DA L+ + +G GF+ + ++
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51
Score = 28.1 bits (62), Expect = 2.1
Identities = 12/40 (30%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 103 TEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANK 141
T E+ K++F Q+G + DA L+ + +G GF+ + ++
Sbjct: 12 TVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51
>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 = 32.5 bits (75), Expect = 0.073
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 36 FIKNLPFKITEEEF---KEHFGQYGDIIDAQLLKNA--DGKLKGCG--FINYANKISAVK 88
++ LP ++ +EE E+FGQYG I + +N +G ++ Y+ K A++
Sbjct: 9 YVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALR 68
Query: 89 AILKSNKKPYKGKI 102
I + G++
Sbjct: 69 CIQAVDGFYLDGRL 82
Score = 28.3 bits (64), Expect = 2.9
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 108 KEHFGQYGDIIDAQLLKNA--DGKLKGCG--FINYANKISAVKAILKSNKKPYKG 158
E+FGQYG I + +N +G ++ Y+ K A++ I + G
Sbjct: 26 PEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDGFYLDG 80
>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 = 32.2 bits (73), Expect = 0.075
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+F+ +P + E+E F + G I + +L+ G+ +G F+ Y K A AI
Sbjct: 4 VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAI 59
Score = 27.2 bits (60), Expect = 4.8
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
+ E+E F + G I + +L+ G+ +G F+ Y K A AI
Sbjct: 13 MYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAI 59
>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 = 32.2 bits (73), Expect = 0.083
Identities = 17/60 (28%), Positives = 32/60 (53%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+FI LP + E+E + G I + +++ + +G +G F+ ++NK A AI + N
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63
>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 = 32.0 bits (73), Expect = 0.089
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 34 RLFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVK 88
L++ + K+TEEE E F Q+G + ++ NA G F+ + + +A +
Sbjct: 2 TLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASR 61
Query: 89 AILKSNKK 96
A N K
Sbjct: 62 AQKACNGK 69
Score = 28.1 bits (63), Expect = 2.3
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 100 GKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKK 154
K+TEEE E F Q+G + ++ NA G F+ + + +A +A N K
Sbjct: 10 PKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASRAQKACNGK 69
>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 = 31.7 bits (72), Expect = 0.092
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+++ NLP + E++ ++ F +YG I D + LKN G L F+ + + A A+
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIE-LKNRRG-LVPFAFVRFEDPRDAEDAVFGR 58
Query: 94 N 94
N
Sbjct: 59 N 59
>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 = 32.0 bits (72), Expect = 0.097
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINY 80
T+ ++F+ L E+ K++F Q+G + DA L+ + +G GF+ +
Sbjct: 1 TRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52
Score = 27.3 bits (60), Expect = 4.7
Identities = 11/35 (31%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 105 EEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINY 138
E+ K++F Q+G + DA L+ + +G GF+ +
Sbjct: 18 EDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTF 52
>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 = 32.2 bits (74), Expect = 0.12
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 16/80 (20%)
Query: 34 RLFIKNLPFKITEEEFKEHF---------GQYGDIIDAQLLKNAD-------GKLKGCGF 77
RL I+NLP + E++ KE F + I +++++ GK KG GF
Sbjct: 2 RLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGF 61
Query: 78 INYANKISAVKAILKSNKKP 97
+ + N A+KA+ N P
Sbjct: 62 VEFTNHEHALKALRALNNNP 81
>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 = 31.6 bits (71), Expect = 0.14
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
+FI NL E + FG +G + + +++++ + K KG GF+ N A AI
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 94 NKKPYKGKITEEEFK 108
N KI + FK
Sbjct: 64 NGYRLGDKILQVSFK 78
>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 = 31.5 bits (72), Expect = 0.15
Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
LF+ L T+E+ + F ++G I +++++ G FI + K +A K
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65
Query: 94 N 94
+
Sbjct: 66 D 66
Score = 30.3 bits (69), Expect = 0.38
Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 103 TEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN 152
T+E+ + F ++G I +++++ G FI + K +A K +
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMD 66
>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 = 31.6 bits (71), Expect = 0.17
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
+F+ NL + E + FG +G + + +++++ K KG GF+ N A AI
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 94 NKKPYKGKITEEEFK 108
N ++ + FK
Sbjct: 64 NGYRLGDRVLQVSFK 78
>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 = 31.2 bits (70), Expect = 0.18
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
+F+ NL E + FG +G + + +++++ + K KG GF+ N A AI
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 94 NKKPYKGKITEEEFK 108
N ++ + FK
Sbjct: 66 NGYRLGDRVLQVSFK 80
>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 = 31.1 bits (70), Expect = 0.20
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK- 92
+L+I NL +T E+ ++ FG + Q+L + G F++Y ++ A++AI
Sbjct: 3 KLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKS-----GYAFVDYPDQNWAIRAIETL 57
Query: 93 SNKKPYKGKITEEEF 107
S K GK+ E ++
Sbjct: 58 SGKVELHGKVMEVDY 72
>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 = 30.8 bits (70), Expect = 0.24
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
++++ LP T E K F +YG ++ L + G +KG FI + A KA
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKAC 58
Score = 26.6 bits (59), Expect = 7.2
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
T E K F +YG ++ L + G +KG FI + A KA
Sbjct: 11 ATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKAC 58
>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 = 30.7 bits (70), Expect = 0.24
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYA 81
++FI LP ++E++ KE +G + L+K+ A G KG F Y
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYL 50
>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 = 30.7 bits (69), Expect = 0.25
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R++I L + + E++ + FG YG +++ LKN G GF+ + + A A+ +
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEID-LKN------GYGFVEFEDSRDADDAVYEL 53
Query: 94 NKKPYKGK 101
N K G+
Sbjct: 54 NGKDLCGE 61
>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 = 30.2 bits (68), Expect = 0.30
Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 35 LFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
LF+ N P + + HF YG +++ ++ +N F+ Y + A KA+ +
Sbjct: 2 LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNF-------AFVQYETQEDATKALEST 54
Query: 94 NKKPYKGKITEEEF 107
N ++ E+
Sbjct: 55 NMSKVLDRVISVEY 68
>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 = 30.4 bits (69), Expect = 0.30
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R++I LP++ E + + F YG I + LKN G GF+ + + A A+ +
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREI-NLKN------GFGFVEFEDPRDADDAVYEL 53
Query: 94 NKK 96
N K
Sbjct: 54 NGK 56
>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 = 30.4 bits (69), Expect = 0.35
Identities = 17/57 (29%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNAD-GKLKGCGFINYANKISAVKAI 90
++ NLP+ +TEE+ KE F ++ +L + D G+L+G G+ + ++ S ++A+
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQAL 60
>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 = 30.5 bits (69), Expect = 0.35
Identities = 14/56 (25%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+ + NLP +TEE+ H ++G I++ ++ + ++GK + + +A + A +A+
Sbjct: 10 IHVSNLPSDVTEEDVINHLAEHGVIVNVKVFE-SNGKKQ--ALVEFATEEQATEAL 62
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B shows high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 30.1 bits (68), Expect = 0.35
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+F+ LP+ E + KE F D+ D LK +G+ G + +A A K LK +
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGL-DVEDVIFLKRHNGRNNGNAIVKFATFQDA-KEALKRH 59
Query: 95 K 95
+
Sbjct: 60 R 60
>gnl|CDD|223368 COG0291, RpmI, Ribosomal protein L35 [Translation, ribosomal
structure and biogenesis].
Length = 65
Score = 29.9 bits (68), Expect = 0.36
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDK----TKRGRLFIKNL 40
M K+ KK K FK G KI+RK K TK+ ++L
Sbjct: 1 MPKMKTKKGAAKRFKITGTGKIKRKHAGKRHILTKKSTKRKRHL 44
>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 = 30.0 bits (68), Expect = 0.37
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+ +KN P+ T EE ++ F +G + ++L G + + +AN A A
Sbjct: 3 ILVKNFPYGTTAEELRDLFEPHGKL--TRVLMPPAGTI---AIVEFANPQQARLAFKALA 57
Query: 95 KKPYKGKI 102
+ +K I
Sbjct: 58 YRRFKDSI 65
>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 = 30.2 bits (68), Expect = 0.39
Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
+++ N+ + T EE + HF G + +L + G KG +I +++K S V+ L
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES-VRTALAL 60
Query: 94 NKKPYKGK 101
++ ++G+
Sbjct: 61 DESLFRGR 68
>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 = 30.1 bits (68), Expect = 0.42
Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 37 IKNLPFKITEEEFKEHF-GQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+ NLP +TE + +E+F Q G I L N GK G I + A KA K N
Sbjct: 4 VSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFN 62
>gnl|CDD|214367 CHL00103, rpl35, ribosomal protein L35.
Length = 65
Score = 29.7 bits (67), Expect = 0.43
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDK 29
M KL +K K +KK G K R+K K
Sbjct: 1 MPKLKTRKAAAKRYKKTGNGKFLRRKAFK 29
>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 = 30.2 bits (68), Expect = 0.45
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+R ++I +P ++T E K+ F +G+I + + ++G GF+ Y A AI
Sbjct: 1 ERRVVYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEG--DNYGFVTYRYTEEAFAAI 58
Query: 91 LKSNK 95
+K
Sbjct: 59 ENGHK 63
>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 = 30.0 bits (67), Expect = 0.46
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 44 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKIT 103
+TE+ ++ F +G I++ ++ KG FI ++ SA AI+ N +G +
Sbjct: 12 LTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESAAHAIVSVNGTTIEGHVV 66
Query: 104 E 104
+
Sbjct: 67 K 67
Score = 28.8 bits (64), Expect = 1.0
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
+TE+ ++ F +G I++ ++ KG FI ++ SA AI+ N +G
Sbjct: 12 LTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESAAHAIVSVNGTTIEG 63
>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 = 30.3 bits (69), Expect = 0.49
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDI 59
+F+ NLP +++ K+ F Q+G I
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPI 27
>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 = 29.7 bits (67), Expect = 0.49
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
+++ NLP I E E ++ F +YG I+D L + G FI + + A AI
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDL--KLPPRPPGYAFIEFEDARDAEDAI 55
>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 = 29.9 bits (68), Expect = 0.56
Identities = 18/64 (28%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILK 92
R+F+ +L ++T+E F +Y A+++++ GK KG GF+++++ +KA+ +
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67
Query: 93 SNKK 96
N K
Sbjct: 68 MNGK 71
>gnl|CDD|241194 cd12750, RRM5_RBM12B, RNA recognition motif 5 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM5 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 77
Score = 29.9 bits (67), Expect = 0.56
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 37 IKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNK 95
++NLPFK T E + F Y I D+ + N G G + N A+ AI + N
Sbjct: 5 LENLPFKATINEILDFFHGYRVIPDSVSMQYNEQGLPTGTAIVAMENYYEAMAAINELND 64
Query: 96 KP 97
+P
Sbjct: 65 RP 66
>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 = 29.6 bits (66), Expect = 0.56
Identities = 15/72 (20%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
++F+ L + ++++ K++F ++G++ D + + + G+ +G GFI + + S+V+ +L+
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDA-SSVEKVLE 59
Query: 93 SNKKPYKGKITE 104
+ G++ +
Sbjct: 60 QKEHRLDGRLID 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 = 29.8 bits (67), Expect = 0.57
Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
+F+ +L ++T+ F + DA+++ + G+ +G GF+++ ++ A AI +
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 94 NKK 96
N K
Sbjct: 62 NGK 64
>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 = 29.4 bits (66), Expect = 0.58
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG 70
LF+ N+P +TE + F YGD+ Q + ++G
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEG 39
>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 = 29.9 bits (68), Expect = 0.58
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGD-IIDAQLLKNADGKLK--GCGFINYANKISAVKAI 90
RLF+ +P T+EE E F + + ++D + ++ D K K G F+ Y + +A A
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMAR 62
Query: 91 LK 92
K
Sbjct: 63 RK 64
>gnl|CDD|113924 pfam05172, Nup35_RRM, Nup53/35/40-type RNA recognition motif.
Members of this family belong to the nucleor pore
complex, NPC, the only gateway between the nucleus and
the cytoplasm. The NPC consists of several subcomplexes
each one of which is made up of multiple copies of
several individual Nup, Nic or Sec protein subunits. In
yeast, this Nup or nucleoporin subunit is numbered
Nup53, Nup40 in Schizo. pombe and in vertebrates as
Nup35. This subunit forms part of the inner ring within
the membrane and interacts directly with Nup-Ndc1,
considered to be an anchor for the NPC in the pore
membrane. This region of the Nup is the RNA-recognition
region.
Length = 87
Score = 29.7 bits (67), Expect = 0.61
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 51 EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
HF ++G+I+ + + Y + SA KA+ K
Sbjct: 25 LHFSRFGEILKHVQGPTNGNWMH----LTYQSPSSARKALSK 62
Score = 29.7 bits (67), Expect = 0.61
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 109 EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 150
HF ++G+I+ + + Y + SA KA+ K
Sbjct: 25 LHFSRFGEILKHVQGPTNGNWMH----LTYQSPSSARKALSK 62
>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 = 29.9 bits (67), Expect = 0.64
Identities = 16/55 (29%), Positives = 27/55 (49%)
Query: 28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
D+ LFI NL ++E E + F +YG I + + + A G+ F+ + N
Sbjct: 4 DQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQN 58
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 31.7 bits (73), Expect = 0.67
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFK 43
++K K K + KK K+K E K + RLF+ L FK
Sbjct: 61 LDKKELKAWHKAQ--KK-KEKQEAKAAKAKSKPRLFV--LDFK 98
>gnl|CDD|129113 TIGR00001, rpmI_bact, ribosomal protein L35. This ribosomal
protein is found in bacteria and organelles only. It is
not closely related to any eukaryotic or archaeal
ribosomal protein [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 63
Score = 29.2 bits (66), Expect = 0.70
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 3 KLAKKKKVKKEFKKKGKKKIERKKPDK 29
K+ K K FK G KI+RKK K
Sbjct: 2 KMKTHKAAAKRFKITGSGKIKRKKAGK 28
>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 = 29.5 bits (66), Expect = 0.71
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L + NL + +E+ +E F + I Q +G+ KG F+ + + A +A+ N
Sbjct: 4 LVVNNLSYSASEDSLQEVFEKATSIRIPQ----NNGRPKGYAFVEFESAEDAKEALNSCN 59
Query: 95 KKPYKGKITEEEF 107
+G+ EF
Sbjct: 60 NTEIEGRSIRLEF 72
>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 = 29.1 bits (65), Expect = 0.74
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
++F+ N+ T +E + F ++G +++ K+K F++ + A+ AI
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECD-------KVKDYAFVHMEREEEALAAIEAL 54
Query: 94 NKKPYKGK 101
N K KG+
Sbjct: 55 NGKEVKGR 62
>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 = 29.6 bits (67), Expect = 0.78
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+++ +P T E ++ F +G+I + L DG GF+ Y A +AI N
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDG--DNYGFVTYRYACDAFRAIEHGN 62
Query: 95 KKP 97
P
Sbjct: 63 DDP 65
Score = 28.8 bits (65), Expect = 1.6
Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 98 YKGKI----TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
Y GKI T E ++ F +G+I + L DG GF+ Y A +AI N
Sbjct: 6 YVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGD--NYGFVTYRYACDAFRAIEHGND 63
Query: 154 KP 155
P
Sbjct: 64 DP 65
>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 = 29.4 bits (66), Expect = 0.79
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC------GFINYANKISAVK 88
LF+KNL F T + + F + A++ D K G GF+ + K A
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 89 AI 90
A+
Sbjct: 63 AL 64
>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 = 29.1 bits (66), Expect = 0.84
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 10/69 (14%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA----- 89
LF+ NL TEEE ++ F + ++ G F+ + + A +A
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGP---VCFVEFEDVSFATQALNSLQ 61
Query: 90 --ILKSNKK 96
+L S+ +
Sbjct: 62 GAVLSSSDR 70
>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 = 29.0 bits (65), Expect = 0.86
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
+G L + NL ++ ++ + FG YG+I + + N + FI + + SA A+
Sbjct: 1 QGTLVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNK----RHHKFIEFYDVRSAEAALK 56
Query: 92 KSNKKPYKGK 101
N+ GK
Sbjct: 57 ALNRSEIAGK 66
>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 = 29.3 bits (65), Expect = 0.88
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKS 93
L++ L + K F +YG ++ A+++ NA C GF+ + A K I
Sbjct: 4 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63
Query: 94 NKKPYKGKITEEE 106
++ G++ E
Sbjct: 64 HRTELHGRMISVE 76
>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 = 29.2 bits (66), Expect = 0.90
Identities = 18/71 (25%), Positives = 38/71 (53%), Gaps = 5/71 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK----NADGKLKGCGFINYANKISAVKAI 90
L++ NL + T+E+ + + G ++D + +K A+GK KG ++ +A++ +A
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAG-VVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVK 59
Query: 91 LKSNKKPYKGK 101
K + + GK
Sbjct: 60 EKLEGREFNGK 70
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist 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 = 75
Score = 29.1 bits (66), Expect = 0.99
Identities = 16/88 (18%), Positives = 30/88 (34%), Gaps = 22/88 (25%)
Query: 35 LFIKNLP---FKITE--EEFKEHFGQYGDIIDAQLLKNADGKLKGCGF----INYANKIS 85
L + N+P F E + F YG+I L + F + +++
Sbjct: 1 LIVTNVPSEVFTNAELKAALESLFSSYGEIATFVYLPS---------FRRARVVFSSPEE 51
Query: 86 AVKAILKSNKKPYKGKITEEEFKEHFGQ 113
A A ++ + + +FGQ
Sbjct: 52 AALARIELHGT----VFEGSVLRVYFGQ 75
>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 = 29.3 bits (65), Expect = 1.0
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
+F+ NL E + FG +G + + +++++ + K KG GF+ N A AI
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 94 NKKPYKGKITEEEFK 108
N ++ + FK
Sbjct: 66 NGYRLGDRVLQVSFK 80
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It is an essential yeast protein involved in pre-rRNA
processing and ribosome assembly, and is speculated to
be required for correct assembly of rpS27 into the
pre-ribosomal particle. Rrp7p contains an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal RRP7 domain. .
Length = 96
Score = 29.3 bits (66), Expect = 1.0
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 9/62 (14%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
LF+ NLP TE ++ FG G II++ + ++ + L +
Sbjct: 3 LFLVNLPVDTTERHLRKLFGSGGGIIESVVFVEELL---------EEDEEALDLDDLVAQ 53
Query: 95 KK 96
Sbjct: 54 LV 55
>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 = 28.8 bits (64), Expect = 1.1
Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
L+++NL + +E+ K+ FGQ+ ++ K++ F+++ ++ AV A+ N
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERV-----KKIRDYAFVHFTSREDAVHAMNNLN 58
Query: 95 KKPYKGKITE 104
+G E
Sbjct: 59 GTELEGSCIE 68
>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 = 29.0 bits (64), Expect = 1.1
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAI 90
L+I+ L T+++ + YG I+ + +L K KG GF+++ + +A KA+
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60
>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 = 28.8 bits (65), Expect = 1.1
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDI 59
LF++N+ + +EE + F Q+GDI
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDI 28
>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 = 28.8 bits (64), Expect = 1.2
Identities = 15/72 (20%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
++FI L + ++++ E+ ++G+++D + + G+ +G GF+ + + S V +L+
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAAS-VDKVLE 59
Query: 93 SNKKPYKGKITE 104
+ GK+ +
Sbjct: 60 LKEHKLDGKLID 71
>gnl|CDD|223534 COG0458, CarB, Carbamoylphosphate synthase large subunit (split
gene in MJ) [Amino acid transport and metabolism /
Nucleotide transport and metabolism].
Length = 400
Score = 31.1 bits (71), Expect = 1.2
Identities = 19/66 (28%), Positives = 26/66 (39%), Gaps = 7/66 (10%)
Query: 239 ENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV-KALGVIG------LIDEGQTDW 291
EN D HTG P L E R I+V + +G+ G +D G +
Sbjct: 222 ENLDPMGVHTGDSITVAPAQTLTDKEYQMLRDAAIKVIREIGIEGGCNIQFAVDPGGGEL 281
Query: 292 KIIAIN 297
+I IN
Sbjct: 282 YVIEIN 287
>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 = 28.6 bits (64), Expect = 1.2
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
R+ I+NLP +T++E + Y +K D K K + N A +AI K
Sbjct: 1 RIVIRNLPADVTKQEVHDLLSDYQ-------VKYCDVDKSKRTAQVTLLNGDQASRAIAK 53
Query: 93 SNKKPYKGK 101
++ YK +
Sbjct: 54 LHQSSYKER 62
>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 = 28.7 bits (65), Expect = 1.3
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL--LK-NADGKLKGCGFINYANKISAVKAIL 91
L++ N P + + ++ F QYG+I+ + L+ N + C ++ + + SA A+
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRF--C-YVQFTSPESAAAAVA 59
Query: 92 KSNKK 96
N K
Sbjct: 60 LLNGK 64
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 31.1 bits (71), Expect = 1.3
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 2 EKLAKKKKVKKEFKKKGKKKI-ERKKPDKT 30
+K +K+K K + + + K I +R+KP T
Sbjct: 402 KKEKEKEKPKVKKRHRDTKNIGKRRKPSGT 431
Score = 29.9 bits (68), Expect = 3.3
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 3 KLAKKKKVKKEFKKKGKKKIERKKPDKTKRGR 34
K+ K+ KKE K+K K K++++ D G+
Sbjct: 394 KVLAKRAEKKE-KEKEKPKVKKRHRDTKNIGK 424
Score = 29.1 bits (66), Expect = 5.6
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 2 EKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGR 34
EK K K K+ KK+ E++KP KR R
Sbjct: 385 EKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRHR 417
Score = 28.4 bits (64), Expect = 9.8
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 4 LAKKKKVKKEFKKKGKKKIERKKPDKTKRGR 34
LAK+ + K++ K+K K K + + R
Sbjct: 396 LAKRAEKKEKEKEKPKVKKRHRDTKNIGKRR 426
>gnl|CDD|241165 cd12721, RRM_Nup53p_fungi, RNA recognition motif in yeast
nucleoporin Nup53p and similar proteins. This subgroup
corresponds to the RRM of Saccharomyces cerevisiae
Nup53p, the 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. Like
vertebrate Nup35, yeast Nup53p contains 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. The RRM
domain lacks the conserved residues that typically bind
RNA in canonical RRM domains.
Length = 86
Score = 28.9 bits (65), Expect = 1.4
Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 51 EHFGQYGDIIDA-QLLKNADGKLKGCGF-------INYANKISAVKAILK 92
EHF +G+II+ ++ +++ G K F + Y +SA +A+ +
Sbjct: 19 EHFSGFGEIIEDFEVPRSSSGLQKPPIFEGSNWVKLTYKEPLSAARALRE 68
Score = 28.9 bits (65), Expect = 1.4
Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 109 EHFGQYGDIIDA-QLLKNADGKLKGCGF-------INYANKISAVKAILK 150
EHF +G+II+ ++ +++ G K F + Y +SA +A+ +
Sbjct: 19 EHFSGFGEIIEDFEVPRSSSGLQKPPIFEGSNWVKLTYKEPLSAARALRE 68
>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 = 28.3 bits (64), Expect = 1.5
Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 14/73 (19%)
Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK-SNKKPYKGSE 160
++ EE F +YG + D + K F++Y++ A A + K+ +
Sbjct: 15 VSREELLRVFEKYGTVEDLVMPPG-----KPYCFVSYSSIEDAAAAYDALNGKELELPQQ 69
Query: 161 NGLISPFHDIPLY 173
N PLY
Sbjct: 70 N--------KPLY 74
Score = 27.2 bits (61), Expect = 5.1
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 44 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
++ EE F +YG + D + K F++Y++ A A
Sbjct: 15 VSREELLRVFEKYGTVEDLVMPPG-----KPYCFVSYSSIEDAAAA 55
>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 = 28.2 bits (63), Expect = 1.9
Identities = 13/63 (20%), Positives = 27/63 (42%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+FI +P + E+ F G + + +L+ G +G + Y+++ A AI +
Sbjct: 4 VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATLH 63
Query: 95 KKP 97
Sbjct: 64 NYE 66
>gnl|CDD|241195 cd12751, RRM5_RBM12, RNA recognition motif 5 in RNA-binding protein
12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM5 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RBMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 76
Score = 28.0 bits (62), Expect = 2.2
Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 37 IKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKSNK 95
++N+PF +T +E + F Y I + LK + G G + + ++ A+ A++ N
Sbjct: 6 VQNMPFTVTVDEILDFFYGYQVIPGSVCLKFSDKGMPTGEAMVAFESRDEAMAAVVDLND 65
Query: 96 KPYKGK 101
+P +
Sbjct: 66 RPIGSR 71
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 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 = 81
Score = 28.0 bits (62), Expect = 2.3
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
L ++NLP++ TEEE E +G I++ + A+ + F+ +A+ A+ +
Sbjct: 5 LHLRNLPWECTEEELIELCKPFGKIVNTKCNVGAN---RNQAFVEFADLNQAIAMV 57
>gnl|CDD|181682 PRK09184, PRK09184, acyl carrier protein; Provisional.
Length = 89
Score = 28.1 bits (63), Expect = 2.3
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 240 NPDETDAHTGQKGDG---DPIDVLEIGERIAKR 269
P+ DA G+G D ID+LEI I+KR
Sbjct: 25 QPESIDADAPLYGEGLGLDSIDILEIALVISKR 57
>gnl|CDD|240957 cd12513, RRM3_RBM12B, RNA recognition motif 3 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM3 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 81
Score = 28.1 bits (63), Expect = 2.4
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 37 IKNLPFKITEEEFKEHFGQYGDIIDAQL--LKNADGKLKGCGFINYANKISAVKAILKSN 94
++NLPF + + + + FG D+ D+Q+ L + GK F+ + + + A L +
Sbjct: 5 LENLPFSVEKRDIRAFFGDL-DLPDSQITFLSDKKGKRTRSAFVMFKS-LRDYCAALAHH 62
Query: 95 KKPYKGK 101
K+ +
Sbjct: 63 KRVLYNR 69
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 30.3 bits (69), Expect = 2.4
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 2 EKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGR 34
EK K K K+E KK K+K ++K+ K K+ +
Sbjct: 377 EKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRK 409
Score = 29.6 bits (67), Expect = 3.4
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 6 KKKKVKKEFKKKGKKKIERKKPDKTKRGR 34
KKK+ +K+ +K+ KKK +KK K K+
Sbjct: 384 KKKREEKKPQKRKKKKKRKKKGKKRKKKG 412
Score = 29.2 bits (66), Expect = 5.6
Identities = 14/35 (40%), Positives = 24/35 (68%), Gaps = 1/35 (2%)
Query: 1 MEKLAKK-KKVKKEFKKKGKKKIERKKPDKTKRGR 34
E+L K+ +++K+++ K KKK E KKP K K+ +
Sbjct: 365 KEELNKRIEEIKEKYPKPPKKKREEKKPQKRKKKK 399
>gnl|CDD|239658 cd03687, Dehydratase_LU, Dehydratase large subunit. This family
contains the large (alpha) subunit of B12-dependent
glycerol dehydratases (GDHs) and B12-dependent diol
dehydratases (DDHs). GDH is isofunctional with DDH.
These enzymes can each catalyze the conversion of
1,2-propanediol, glycerol, and 1,2-ethanediol to the
corresponding aldehydes via a coenzyme B12
(adenosylcobalamin)-dependent radical mechanism. Both
enzymes exhibit a subunit composition of
alpha2beta2gamma2. The enzymes differ in substrate
specificity; glycerol is the preferred substrate for GDH
and 1,2-propanediol for DDH. GDH shows almost equal
affinity for both (R) and (S)-isomers while DDH prefers
the (S) isomer. GDH plays a key role in the
dihydroxyacetone (DHA) pathway and DDH in the anaerobic
degradation of 1,2-diols. The radical mechanism has been
well studied for Klebsiella oxytoca DDH and involves
binding of 1,2-propanediol to the enzyme to induce
hemolytic cleavage of the Co-C5' bond of the coenzyme to
form cob(II)alamin and the adenosyl radical. Hydrogen
abstraction from the substrate follows producing a
substrate generated radical and 5'-deoxyadenosine.
Rearrangement to the product radical is then followed by
abstraction of a hydrogen atom from 5'-deoxyadenosine to
produce the hydrated propionaldehyde and regenerate the
adenosyl radical. After the Co-C5' bond is reformed and
the hydrated aldehyde dehydrated, the process is
complete. GDH has a higher affinity for coenzyme B12
than DDH. Both GDH and DDH are activated by various
monovalent cations with K+, NH4+, and Rb+ being the most
effective. However, DDH differs from GDH in that it is
partially active with Cs+ and Na+. In general, the alpha
and beta subunits for both enzymes are on different
chains. However, for a subset of the GDHs, alpha and
beta subunits appear to be on a single chain.
Length = 545
Score = 30.2 bits (68), Expect = 2.5
Identities = 23/96 (23%), Positives = 37/96 (38%), Gaps = 15/96 (15%)
Query: 254 GDPIDVLEIGERIAKRG--EIIQVKALGVIGLIDEGQTDWKII------------AINVN 299
+P++ ++ E I R + VKAL G DE + ++ AI +
Sbjct: 444 RNPVEDIKAAEEIINRNITGLDVVKALARGGFTDEAENILNMLKQRLTGDYLQTSAIIDD 503
Query: 300 DPNA-AKLNDVADIETHFPGYLKATNEWFKIYKIPD 334
D + +ND D GY + W +I IP
Sbjct: 504 DFQVLSAVNDPNDYAGPGTGYRLSGERWEEIKNIPG 539
>gnl|CDD|219621 pfam07890, Rrp15p, Rrp15p. Rrp15p is required for the formation
of 60S ribosomal subunits.
Length = 132
Score = 28.9 bits (65), Expect = 2.6
Identities = 13/44 (29%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 5 AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEE 48
AKKK ++ +KK K+++ +K ++GR +K + + E+E
Sbjct: 33 AKKKLKSEKLEKKAKRQLRAEKRQALEKGR--VKPVLPEDLEKE 74
>gnl|CDD|235197 PRK04007, rps28e, 30S ribosomal protein S28e; Validated.
Length = 70
Score = 27.6 bits (62), Expect = 2.6
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 253 DGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDP 301
+G P +V+EI R GE+ QVK I EG+ +II NV P
Sbjct: 5 EGTPAEVIEIIGRTGMTGEVTQVKC-----RILEGRDKGRIITRNVKGP 48
>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 = 27.7 bits (61), Expect = 2.7
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
++F+ L EE+ +E+FG +G++ +L + N K +G FI + + VK I++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEE-EPVKKIME 59
>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 = 27.7 bits (62), Expect = 2.7
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYG 57
+F+ +EE+ ++F +G
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFG 27
>gnl|CDD|234225 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter
like protein HpnN. The genomes containing members of
this family share the machinery for the biosynthesis of
hopanoid lipids. Furthermore, the genes of this family
are usually located proximal to other components of
this biological process. The proteins appear to be
related to the RND family of export proteins,
particularly the hydrophobe/amphiphile efflux-3 (HAE3)
family represented by TIGR00921.
Length = 862
Score = 30.0 bits (68), Expect = 2.9
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 30 TKRGRLFIKNLPFKITEEEFKEHFGQYGD----IIDAQ 63
T L +LPF+ E +++ F Q D +I+
Sbjct: 39 TDTSDLLSPDLPFRQDERAYEKAFPQDEDTIVVVIEGP 76
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 29.3 bits (66), Expect = 3.0
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 2 EKLAKKKKVKKEFKKKGKKKIERKKPDKTKR 32
+++ K+KK KK+ K+K + KK K K+
Sbjct: 161 KEVKKEKKEKKDKKEKMVEPKGSKKKKKKKK 191
>gnl|CDD|234676 PRK00172, rpmI, 50S ribosomal protein L35; Reviewed.
Length = 65
Score = 27.0 bits (61), Expect = 3.3
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 10/42 (23%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIER----------KKPDKTKR 32
M K+ K K FK G K++R KK K KR
Sbjct: 1 MPKMKTKSGAAKRFKVTGSGKVKRKHAGKRHILTKKSTKRKR 42
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 27.3 bits (61), Expect = 3.4
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 37 IKNLPFKITEEEFKEHFGQYGDIIDAQ---LLKNADGKLKGCGFINYANKISAVKAILKS 93
IKN+PF +T+ E F G I Q +L + GK G ++ + ++ A++A +
Sbjct: 4 IKNIPFDVTKGEVLAFFA--GIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAE-RL 60
Query: 94 NKKPYKGKI 102
++K KG+
Sbjct: 61 HRKKLKGRE 69
>gnl|CDD|241153 cd12709, RRM_RCAN2, RNA recognition motif in vertebrate regulator
of calcineurin 2 (RCAN2). This subgroup corresponds to
the RRM of RCAN2, also termed calcipressin-2, or Down
syndrome candidate region 1-like 1 (DSCR1L1), or
myocyte-enriched calcineurin-interacting protein 2
(MCIP2), or thyroid hormone-responsive protein ZAKI-4,
encoded by a novel thyroid hormone-responsive gene
ZAKI-4 that is abundantly expressed in human brain,
heart and muscles. RCAN2 binds to the catalytic subunit
of Ca2+/calmodulin-dependent phosphatase calcineurin
(also termed PP2B or PP3C), calcineurin A, and inhibits
its phosphatase activity through its C-terminal region.
RCAN2 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 = 27.6 bits (61), Expect = 3.4
Identities = 18/69 (26%), Positives = 38/69 (55%), Gaps = 9/69 (13%)
Query: 45 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITE 104
+E+F+ F Y D + QL K+ +++ IN++N +A +A ++ ++ ++GK
Sbjct: 18 VKEKFEGLFRAYDDCVTFQLFKSFR-RVR----INFSNPKAAARARIELHETQFRGK--- 69
Query: 105 EEFKEHFGQ 113
+ K +F Q
Sbjct: 70 -KLKLYFAQ 77
>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 = 27.2 bits (61), Expect = 3.4
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIID 61
++++ NL + T+ E ++ F +YG +
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRS 28
>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 = 27.4 bits (61), Expect = 3.5
Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 5/77 (6%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN---ADGKLKGCGFINYANKISAVKAIL 91
+ IKN+PF + +E+ + G I N +G +G F N+ + A +
Sbjct: 4 IVIKNIPFSLRKEQLLDIIEDLG--IPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVE 61
Query: 92 KSNKKPYKGKITEEEFK 108
N G+ E+K
Sbjct: 62 ALNGYEISGRRLRVEYK 78
>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 = 27.3 bits (60), Expect = 3.8
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 34 RLFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
R+FI NL + + + + F +YG I+ + K G F+ Y N+ +A A+
Sbjct: 3 RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQYVNERNARAAVAG 55
Query: 93 SNKKPYKGKITE 104
+ + G++ +
Sbjct: 56 EDGRMIAGQVLD 67
>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 = 27.7 bits (61), Expect = 3.8
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI-LK 92
+F+ +P + E+E F + G I D +L+ + G +G F+ + K +A +A+ L
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63
Query: 93 SNKKPYKGK 101
+N + GK
Sbjct: 64 NNHEIRPGK 72
>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 = 28.0 bits (63), Expect = 3.9
Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 45 TEEEFKE-------HFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 97
+F+E F ++G+++ ++ N + L+G ++ Y ++ A+ A N +
Sbjct: 34 LYSDFEEFYDDVLPEFEKFGEVVQFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMFNGRW 93
Query: 98 YKGK 101
Y GK
Sbjct: 94 YAGK 97
>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 = 27.4 bits (61), Expect = 3.9
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 9/79 (11%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
+F+ LP TEE +E F Q G+II ++ K K I +A + + KAI S
Sbjct: 9 VFVGGLPENATEEIIREVFEQCGEIIAIRMSK------KNFCHIRFAEEFAVDKAIYLSG 62
Query: 95 KKPYKGKITEEEFKEHFGQ 113
Y+ +I ++ G+
Sbjct: 63 ---YRVRIGSSTDPKNSGR 78
>gnl|CDD|215038 PLN00040, PLN00040, Protein MAK16 homolog; Provisional.
Length = 233
Score = 29.0 bits (65), Expect = 3.9
Identities = 25/114 (21%), Positives = 41/114 (35%), Gaps = 16/114 (14%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKE--HFGQYGD 58
M KLA K + K + K ER++ K ++ K++ E+E E G YGD
Sbjct: 122 MRKLALKTREKIVTTPRKLLKRERRRESKAQKAAQLEKSI-----EKELLERLKSGTYGD 176
Query: 59 II---DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKE 109
I K + + + K+ N K E E+++
Sbjct: 177 IYNFPSKSYNKVLEME------EVEEAEEELPKSDKNPNSKKKSRVHVEIEYED 224
>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 = 27.2 bits (61), Expect = 4.0
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 95
+KNLP TE + ++ F G+I + +++++ G + I + + A+ A+ K +K
Sbjct: 4 KVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLV---AVIEFETEDEALAALTKDHK 60
Query: 96 K 96
+
Sbjct: 61 R 61
>gnl|CDD|145004 pfam01632, Ribosomal_L35p, Ribosomal protein L35.
Length = 61
Score = 26.9 bits (60), Expect = 4.1
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 3 KLAKKKKVKKEFKKKGKKKIERKKPDKTK 31
K+ K K FK+ KI+R+K K
Sbjct: 2 KMKTVKAAAKRFKRTASGKIKRRKAGKRH 30
>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 = 27.4 bits (61), Expect = 4.2
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDII 60
++F+ LP I E+E F ++G ++
Sbjct: 2 KVFVGGLPPDIDEDEITASFRRFGPLV 28
>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 = 27.2 bits (60), Expect = 4.2
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKA 89
LF+K L TEE KE F I A+++ + D G KG GF++++++ A A
Sbjct: 3 LFVKGLSEDTTEETLKESF---DGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAA 55
>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 = 27.2 bits (61), Expect = 4.3
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 91 LKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 150
+K +K G +E+E ++ F +YGD+ D + K KG + +A+K +A A+
Sbjct: 5 VKWKRKKGNGDYSEDELRKIFSKYGDVSDVVVSS----KKKGSAIVEFASKKAAEAAVEN 60
Query: 151 SNKKP 155
P
Sbjct: 61 ECGLP 65
Score = 26.5 bits (59), Expect = 7.5
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 45 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 97
+E+E ++ F +YGD+ D + K KG + +A+K +A A+ P
Sbjct: 17 SEDELRKIFSKYGDVSDVVVSS----KKKGSAIVEFASKKAAEAAVENECGLP 65
>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 = 27.3 bits (60), Expect = 4.5
Identities = 13/60 (21%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
++F+ + E +++F QYG I +++ + GK +G F+ + + S K +++
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61
>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM2 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 = 93
Score = 27.6 bits (62), Expect = 4.6
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYG 57
++ LP K+T+E+ +E F Y
Sbjct: 4 TVYCGKLPKKVTDEDLREFFKDYN 27
>gnl|CDD|203922 pfam08377, MAP2_projctn, MAP2/Tau projection domain. This domain is
found in the MAP2/Tau family of proteins which includes
MAP2, MAP4, Tau, and their homologs. All isoforms contain
a conserved C-terminal domain containing tubulin-binding
repeats (pfam00418), and a N-terminal projection domain
of varying size. This domain has a net negative charge
and exerts a long-range repulsive force. This provides a
mechanism that can regulate microtubule spacing which
might facilitate efficient organelle transport.
Length = 1134
Score = 29.3 bits (65), Expect = 5.2
Identities = 12/35 (34%), Positives = 24/35 (68%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRL 35
+E + K+++ +KE ++ +K ++KP KT RGR+
Sbjct: 1033 LETIPKEERAEKEARRPSLEKHRKEKPFKTGRGRI 1067
>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 = 27.0 bits (60), Expect = 6.0
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 39 NLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
LP EE K+ F +G+I+D + KL C I +A+ SA++A
Sbjct: 1 VLPSDFDVEELKDDFTVFGEIVDISPI--ISRKL--CVSIFFADIRSAIRAK 48
>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 = 26.9 bits (59), Expect = 6.1
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
++F+ L + TEE+ +E+FG++G+I +L + K +G FI + + VK +L+
Sbjct: 6 KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEE-DPVKKVLE 64
>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 = 26.7 bits (59), Expect = 6.3
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R+++ NLP I ++ ++ F +YG I D LKN G F+ + + A A+
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDID-LKNRRG--PPFAFVEFEDPRDAEDAVYGR 57
Query: 94 NKKPYKGKITEEEF 107
+ Y G EF
Sbjct: 58 DGYDYDGYRLRVEF 71
>gnl|CDD|202804 pfam03909, BSD, BSD domain. This domain contains a distinctive
-FW- motif. It is found in a family of eukaryotic
transcription factors as well as a set of proteins of
unknown function.
Length = 60
Score = 26.0 bits (58), Expect = 6.6
Identities = 11/43 (25%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 7 KKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEF 49
+ + KK+ + + ++ P+ K L+ + +P K++EEEF
Sbjct: 5 DNEFDADEKKEEIQALLKEDPELRK---LYNELVPKKLSEEEF 44
>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 = 26.5 bits (58), Expect = 6.9
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
R++I L ++ E + + F YG I++ LKN G GF+ + + A A+ +
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVD-LKN------GYGFVEFDDLRDADDAVYEL 53
Query: 94 NKKPYKGK 101
N K G+
Sbjct: 54 NGKDLCGE 61
>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 = 26.8 bits (60), Expect = 7.1
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 56 YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 97
G I+ + + GK KG F+ +A A +A+ N
Sbjct: 33 VGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYK 74
Score = 26.8 bits (60), Expect = 7.1
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 114 YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
G I+ + + GK KG F+ +A A +A+ N
Sbjct: 33 VGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYK 74
>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal. This
domain is found to the N-terminus of bacterial signal
peptidases of the S49 family (pfam01343).
Length = 154
Score = 27.9 bits (63), Expect = 7.6
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 1 MEKLAKK---KKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFK 43
++K K K KK K K K + ++ K ++ K RLF+ L FK
Sbjct: 63 LDKKELKAWEKAEKKAEKAKAKAEKKKAKKEEPK-PRLFV--LDFK 105
>gnl|CDD|214778 smart00697, DM8, Repeats found in several Drosophila proteins.
Length = 93
Score = 27.0 bits (60), Expect = 7.9
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 69 DGKLKGCGFINYANKISAVKAILKSNKKP 97
+ C + N+I ++ ILKS K
Sbjct: 7 NVTTDVCKLLKSRNQIPLIRIILKSLLKF 35
Score = 27.0 bits (60), Expect = 7.9
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 127 DGKLKGCGFINYANKISAVKAILKSNKKP 155
+ C + N+I ++ ILKS K
Sbjct: 7 NVTTDVCKLLKSRNQIPLIRIILKSLLKF 35
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 28.7 bits (65), Expect = 7.9
Identities = 14/51 (27%), Positives = 23/51 (45%)
Query: 1 MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKE 51
+KK ++E K+K KK KK ++ + K + EEE +E
Sbjct: 414 KIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEE 464
>gnl|CDD|217636 pfam03606, DcuC, C4-dicarboxylate anaerobic carrier.
Length = 456
Score = 28.4 bits (64), Expect = 8.1
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 133 CGFINYANKISAVKAILKSNKKPYKGSENGLI 164
GF N+ A+ A +K+ KP KG E+ I
Sbjct: 84 GGFAGVMNRTGAIDAGVKALVKPLKGIESPYI 115
>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 = 26.6 bits (58), Expect = 8.3
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILK 92
+LF+ + E +++F +YG I +++ + GK +G GF+ + + K +L+
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61
>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional.
Length = 135
Score = 27.3 bits (61), Expect = 9.1
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 2 EKLAKKKKVKKEFKKKGKKKIERKKPDKT 30
EK +KK+ KK+ KKK KK ++ K
Sbjct: 107 EKAKQKKQKKKKKKKKKKKTSKKAAKKKK 135
>gnl|CDD|241324 cd13170, RanBD_NUP50, Nucleoporin 50 Ran-binding domain. NUP50
acts as a cofactor for the importin-alpha:importin-beta
heterodimer, which allows for transportation of many
nuclear-targeted proteins through nuclear pore
complexes. It is thought to function primarily at the
terminal stages of nuclear protein import to coordinate
import complex disassembly and importin recycling.
NUP50 is composed of a N-terminal NUP50 domain which
binds the C-terminus of importin-beta, a central domain
which binds importin-beta, and a C-terminal RanBD which
binds importin-beta through Ran-GTP.
NUP50:importin-alpha then binds cargo and can stimulate
nuclear import. The N-terminal domain of NUP50 is also
able to displace nuclear localization signals from
importin-alpha. NUP50 interacts with cyclin-dependent
kinase inhibitor 1B which binds to cyclin E-CDK2 or
cyclin D-CDK4 complexes and prevents its activation,
thereby controling the cell cycle progression at G1.
Ran is a Ras-like nuclear small GTPase, which regulates
receptor-mediated transport between the nucleus and the
cytoplasm. RanGTP hydrolysis is stimulated by RanGAP
together with the Ran-binding domain containing
acessory proteins RanBP1 and RanBP2. These accessory
proteins stabilize the active GTP-bound form of Ran.
RabBD shares structural similarity to the PH domain,
but lacks detectable sequence similarity.
Length = 109
Score = 26.9 bits (60), Expect = 9.8
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 3 KLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKN 39
KL KK E+K KG + KK T + RL ++
Sbjct: 10 KLFVKKD-DGEWKDKGVGTLYLKKVKDTSKARLLVRA 45
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 0.137 0.406
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,530,234
Number of extensions: 2342432
Number of successful extensions: 3566
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3255
Number of HSP's successfully gapped: 619
Length of query: 451
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 351
Effective length of database: 6,502,202
Effective search space: 2282272902
Effective search space used: 2282272902
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: 42 (22.0 bits)
S2: 61 (27.3 bits)