RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15852
(661 letters)
>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 = 112 bits (282), Expect = 6e-30
Identities = 39/75 (52%), Positives = 54/75 (72%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGGLSPE +E+I+ +F +FGNI+E E+P DK ++R+ FCFITF+ E V +L+
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 246 PKQKINDKEVDVKKA 260
I K+V+VKKA
Sbjct: 61 QFHVIGGKKVEVKKA 75
Score = 74.7 bits (184), Expect = 1e-16
Identities = 23/51 (45%), Positives = 33/51 (64%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
I+E E+P DK ++R+ FCFITF+ E V +L+ I K+V+VKKA
Sbjct: 25 NIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQFHVIGGKKVEVKKA 75
Score = 60.5 bits (147), Expect = 9e-12
Identities = 26/67 (38%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+++E+F K+G I + L D T + RGF FI F E V+ ++ HVI K
Sbjct: 14 EKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE-----PVKKILETQFHVIGGK 68
Query: 174 KIEAKKA 180
K+E KKA
Sbjct: 69 KVEVKKA 75
Score = 48.9 bits (117), Expect = 1e-07
Identities = 17/44 (38%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+++E+F K+G I + L D T + RGF FI F E ++K
Sbjct: 14 EKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57
>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 = 86.5 bits (215), Expect = 6e-21
Identities = 29/66 (43%), Positives = 43/66 (65%), Gaps = 5/66 (7%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
E L+E+FSKYGE+ + + DP TGRSRGF F+ F D +SV+ V+A HV++
Sbjct: 12 EESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFAD-----PSSVDKVLAAKPHVLDG 66
Query: 173 KKIEAK 178
++I+ K
Sbjct: 67 REIDPK 72
Score = 69.9 bits (172), Expect = 4e-15
Identities = 23/45 (51%), Positives = 31/45 (68%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E L+E+FSKYGE+ + + DP TGRSRGF F+ F D S++K
Sbjct: 12 EESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKV 56
Score = 62.2 bits (152), Expect = 2e-12
Identities = 19/72 (26%), Positives = 41/72 (56%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+F+GGLS + +E ++ +F+++G +++ + D + + F F+TF S V +L
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 247 KQKINDKEVDVK 258
++ +E+D K
Sbjct: 61 PHVLDGREIDPK 72
Score = 35.6 bits (83), Expect = 0.005
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 436 EVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVK 492
EV + V M+ D + + F F+TF S V +L ++ +E+D K
Sbjct: 24 EVVDCVIMK--------DPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGREIDPK 72
>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 = 77.8 bits (192), Expect = 8e-18
Identities = 28/75 (37%), Positives = 48/75 (64%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGGL P++ +EE K +F+QFG +++ ++ D + + F F+TF+ ES V +
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 246 PKQKINDKEVDVKKA 260
++ K+V+VK+A
Sbjct: 61 GMLELGGKQVEVKRA 75
Score = 67.4 bits (165), Expect = 3e-14
Identities = 31/75 (41%), Positives = 48/75 (64%), Gaps = 6/75 (8%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ +TE E KE+FS++G++ + L D +TGRSRGF F+ F D+ES +VE V +
Sbjct: 6 GLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF-DSES----AVERVFSA 60
Query: 166 GNHVINNKKIEAKKA 180
G + K++E K+A
Sbjct: 61 GMLELGGKQVEVKRA 75
Score = 51.6 bits (124), Expect = 1e-08
Identities = 21/51 (41%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
G+ +TE E KE+FS++G++ + L D +TGRSRGF F+ F ++E+
Sbjct: 6 GLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVER 56
Score = 42.0 bits (99), Expect = 3e-05
Identities = 13/51 (25%), Positives = 29/51 (56%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
++++ ++ D + + F F+TF+ ES V + ++ K+V+VK+A
Sbjct: 25 KVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAGMLELGGKQVEVKRA 75
>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 = 74.7 bits (184), Expect = 1e-16
Identities = 32/80 (40%), Positives = 50/80 (62%)
Query: 183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL 242
++ KIFVGGL P + + +++ +F+QFG + E + YD K + + F FITFE E V +
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60
Query: 243 LKNPKQKINDKEVDVKKATP 262
+ IN K+V+VK+A P
Sbjct: 61 VNEHFHDINGKKVEVKRAEP 80
Score = 63.9 bits (156), Expect = 8e-13
Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ +TE +L+++FS++G + V + D R RGF FI F+ + SV+ V+ E
Sbjct: 9 GLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESED-----SVDQVVNE 63
Query: 166 GNHVINNKKIEAKKA 180
H IN KK+E K+A
Sbjct: 64 HFHDINGKKVEVKRA 78
Score = 45.8 bits (109), Expect = 2e-06
Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G+ +TE +L+++FS++G + V + D R RGF FI F+ +S+++
Sbjct: 9 GLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60
Score = 45.4 bits (108), Expect = 3e-06
Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 437 VTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATP 496
VTE V M YD K + + F FITFE E V ++ IN K+V+VK+A P
Sbjct: 29 VTEVVVM--------YDHEKKRPRGFGFITFESEDSVDQVVNEHFHDINGKKVEVKRAEP 80
>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 = 72.5 bits (178), Expect = 6e-16
Identities = 32/68 (47%), Positives = 44/68 (64%), Gaps = 5/68 (7%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
E L+E+FSK+GEI+ + DP T RSRGF F+ F D ASV+ V+A+G H ++
Sbjct: 12 AEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSD-----PASVDKVLAQGPHELDG 66
Query: 173 KKIEAKKA 180
KKI+ K A
Sbjct: 67 KKIDPKVA 74
Score = 59.4 bits (144), Expect = 3e-11
Identities = 22/44 (50%), Positives = 30/44 (68%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
E L+E+FSK+GEI+ + DP T RSRGF F+ F D S++K
Sbjct: 12 AEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDK 55
Score = 50.1 bits (120), Expect = 5e-08
Identities = 22/74 (29%), Positives = 42/74 (56%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+F+GGLS + E ++ +F++FG I E + D + + + F F+TF + V +L
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 247 KQKINDKEVDVKKA 260
+++ K++D K A
Sbjct: 61 PHELDGKKIDPKVA 74
Score = 30.5 bits (69), Expect = 0.50
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 436 EVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
E+ E + M D + + + F F+TF + V +L +++ K++D K A
Sbjct: 24 EIKECMVMR--------DPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKIDPKVA 74
>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 = 71.8 bits (176), Expect = 1e-15
Identities = 31/67 (46%), Positives = 48/67 (71%), Gaps = 5/67 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
++LKE+FSK+GE+ + T+K DP TGRSRGF F++FKD S+EK V+ + H ++ +
Sbjct: 13 KDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEK-----VLDQKEHKLDGR 67
Query: 174 KIEAKKA 180
I+ K+A
Sbjct: 68 VIDPKRA 74
Score = 66.4 bits (162), Expect = 8e-14
Identities = 27/47 (57%), Positives = 37/47 (78%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
D ++LKE+FSK+GE+ + T+K DP TGRSRGF F++FKD S+EK
Sbjct: 9 DTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEK 55
Score = 45.6 bits (108), Expect = 2e-06
Identities = 20/74 (27%), Positives = 44/74 (59%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FVGGLS + +++K +F++FG +++ + D + + F F+ F+ + V +L
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 247 KQKINDKEVDVKKA 260
+ K++ + +D K+A
Sbjct: 61 EHKLDGRVIDPKRA 74
>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 = 71.6 bits (175), Expect = 2e-15
Identities = 32/67 (47%), Positives = 49/67 (73%), Gaps = 5/67 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD S+EK V+ + H ++ +
Sbjct: 14 KDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEK-----VLEQKEHRLDGR 68
Query: 174 KIEAKKA 180
I+ KKA
Sbjct: 69 LIDPKKA 75
Score = 65.4 bits (159), Expect = 2e-13
Identities = 27/47 (57%), Positives = 38/47 (80%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
D ++LK++F+K+GE+ + T+K DPNTGRSRGF FI+FKD S+EK
Sbjct: 10 DTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEK 56
Score = 49.2 bits (117), Expect = 1e-07
Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVGGLS + +++K +F +FG + + + D + + + F FI F+ S V +L+
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 246 PKQKINDKEVDVKKA 260
+ +++ + +D KKA
Sbjct: 61 KEHRLDGRLIDPKKA 75
Score = 27.3 bits (60), Expect = 5.9
Identities = 13/51 (25%), Positives = 28/51 (54%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
E+ + + D + + + F FI F+ S V +L+ + +++ + +D KKA
Sbjct: 25 EVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQKEHRLDGRLIDPKKA 75
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 69.5 bits (171), Expect = 7e-15
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+FVG L P+ +EE++ F++FG + + DK + K F F+ FE E L+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 246 -PKQKINDKEVDV 257
++++ + + V
Sbjct: 61 LNGKELDGRPLKV 73
Score = 68.8 bits (169), Expect = 1e-14
Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 4/63 (6%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
EEL+E FSK+G++E+V L D TG+S+GFAF+ F+ E EKA + A ++ +
Sbjct: 14 EELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKA----LEALNGKELDGR 69
Query: 174 KIE 176
++
Sbjct: 70 PLK 72
Score = 66.1 bits (162), Expect = 1e-13
Identities = 24/44 (54%), Positives = 33/44 (75%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL+E FSK+G++E+V L D TG+S+GFAF+ F+ E EKA
Sbjct: 14 EELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKA 57
Score = 35.6 bits (83), Expect = 0.005
Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN-PKQKINDKEVDV 491
++ + DK + K F F+ FE E L+ ++++ + + V
Sbjct: 25 KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
>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 = 68.9 bits (168), Expect = 1e-14
Identities = 32/67 (47%), Positives = 50/67 (74%), Gaps = 5/67 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K V+ + H +N K
Sbjct: 13 KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK-----VMDQKEHKLNGK 67
Query: 174 KIEAKKA 180
I+ K+A
Sbjct: 68 VIDPKRA 74
Score = 61.2 bits (148), Expect = 7e-12
Identities = 26/47 (55%), Positives = 39/47 (82%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
D ++LK++FSK+GE+ + TLK DP TGRSRGF F++FK++ES++K
Sbjct: 9 DTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK 55
Score = 47.3 bits (112), Expect = 5e-07
Identities = 20/74 (27%), Positives = 43/74 (58%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+F+GGLS + +++K +F++FG +++ + D + + F F+ F+ V ++
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 247 KQKINDKEVDVKKA 260
+ K+N K +D K+A
Sbjct: 61 EHKLNGKVIDPKRA 74
Score = 28.0 bits (62), Expect = 3.0
Identities = 12/51 (23%), Positives = 26/51 (50%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
E+++ + D + + F F+ F+ V ++ + K+N K +D K+A
Sbjct: 24 EVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA 74
>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 = 68.1 bits (166), Expect = 2e-14
Identities = 30/75 (40%), Positives = 47/75 (62%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVGGLSP+ +E+IK +F FG I E+P D ++R+ FCF+T+ E V LL++
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 246 PKQKINDKEVDVKKA 260
+I + ++K A
Sbjct: 61 RYHQIGSGKCEIKVA 75
Score = 49.2 bits (117), Expect = 1e-07
Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ TEE +KE+F +GEIEN+ L D T RGF F+ + D E ++K ++
Sbjct: 6 GLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQK-----LLES 60
Query: 166 GNHVINNKKIEAKKA 180
H I + K E K A
Sbjct: 61 RYHQIGSGKCEIKVA 75
Score = 48.5 bits (115), Expect = 2e-07
Identities = 22/51 (43%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
G+ TEE +KE+F +GEIEN+ L D T RGF F+ + D E ++K
Sbjct: 6 GLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQK 56
Score = 38.5 bits (89), Expect = 6e-04
Identities = 17/51 (33%), Positives = 29/51 (56%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
EI E+P D ++R+ FCF+T+ E V LL++ +I + ++K A
Sbjct: 25 EIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLESRYHQIGSGKCEIKVA 75
>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 = 66.2 bits (162), Expect = 1e-13
Identities = 26/78 (33%), Positives = 46/78 (58%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+F+GGLS E D+ +K +F+Q+G I + + D + + + F F+TF S V +
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 246 PKQKINDKEVDVKKATPK 263
K++ +EV+ K+A P+
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
Score = 63.9 bits (156), Expect = 8e-13
Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 6/78 (7%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ ++ T++ LK +FS++GEI + + DPNT RSRGF F+ F + V+ +
Sbjct: 6 GLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFAS-----ASEVDAAMNA 60
Query: 166 GNHVINNKKIEAKKAKAK 183
H ++ +++E K+A +
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
Score = 54.7 bits (132), Expect = 1e-09
Identities = 21/52 (40%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G+ + T++ LK +FS++GEI + + DPNT RSRGF F+ F ++ A
Sbjct: 6 GLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAA 57
Score = 32.3 bits (74), Expect = 0.12
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 436 EVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKAT 495
E+T+ V M+ D + + + F F+TF S V + K++ +EV+ K+A
Sbjct: 25 EITDCVVMK--------DPNTKRSRGFGFVTFASASEVDAAMNARPHKVDGREVEPKRAV 76
Query: 496 PK 497
P+
Sbjct: 77 PR 78
>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 = 65.5 bits (160), Expect = 2e-13
Identities = 29/74 (39%), Positives = 48/74 (64%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGGLS ++++K +F+QFG + + + +DK ++ + F F+TFE E VV + +
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 246 PKQKINDKEVDVKK 259
+IN+K V+ KK
Sbjct: 61 HFHEINNKMVECKK 74
Score = 57.8 bits (140), Expect = 9e-11
Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
+++K++FS++G++E+ L D T R RGF F+ F+ + ++K V H INNK
Sbjct: 14 DDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDK-----VCEIHFHEINNK 68
Query: 174 KIEAKK 179
+E KK
Sbjct: 69 MVECKK 74
Score = 48.2 bits (115), Expect = 3e-07
Identities = 15/44 (34%), Positives = 30/44 (68%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+++K++FS++G++E+ L D T R RGF F+ F+ + ++K
Sbjct: 14 DDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57
Score = 34.7 bits (80), Expect = 0.014
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 447 ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKK 493
+ + +DK ++ + F F+TFE E VV + + +IN+K V+ KK
Sbjct: 28 DAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIHFHEINNKMVECKK 74
>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 = 65.5 bits (160), Expect = 2e-13
Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 7/78 (8%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ K TE +LK++FS +GE+ V +K DP TG+S+GF F+ F D E K
Sbjct: 6 GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV------LS 59
Query: 166 GNHVINNKKIEAKKAKAK 183
H+I+ + + K +K
Sbjct: 60 QRHMIDGRWCDVKIPNSK 77
Score = 61.6 bits (150), Expect = 4e-12
Identities = 24/52 (46%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G+ K TE +LK++FS +GE+ V +K DP TG+S+GF F+ F D E K
Sbjct: 6 GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57
Score = 37.0 bits (86), Expect = 0.002
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+ V GL + ++++K +F+ FG ++ ++ D Q K F F+ F + +L
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60
Query: 246 PKQKINDKEVDVKKATPK 263
+ I+ + DVK K
Sbjct: 61 -RHMIDGRWCDVKIPNSK 77
>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 = 63.8 bits (156), Expect = 6e-13
Identities = 25/63 (39%), Positives = 39/63 (61%), Gaps = 5/63 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+LK+ FSK+G IE++ + D TGRS+GFAF+ F+D E EKA + A + +
Sbjct: 13 EDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKA----LEALNGKELGGR 67
Query: 174 KIE 176
++
Sbjct: 68 ELR 70
Score = 60.7 bits (148), Expect = 9e-12
Identities = 24/44 (54%), Positives = 33/44 (75%), Gaps = 1/44 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+LK+ FSK+G IE++ + D TGRS+GFAF+ F+D E EKA
Sbjct: 13 EDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKA 55
Score = 59.9 bits (146), Expect = 1e-11
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 2/70 (2%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN- 245
+FVG L P+ +E++K F++FG I + D++ + K F F+ FE E L+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETG-RSKGFAFVEFEDEEDAEKALEAL 59
Query: 246 PKQKINDKEV 255
+++ +E+
Sbjct: 60 NGKELGGREL 69
Score = 29.1 bits (66), Expect = 1.2
Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN-PKQKINDKEV 489
I + D++ + K F F+ FE E L+ +++ +E+
Sbjct: 24 PIESIRIVRDETG-RSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 66.2 bits (161), Expect = 7e-13
Identities = 37/118 (31%), Positives = 57/118 (48%), Gaps = 8/118 (6%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
S K+F+GGLS D ++ FA FG++++ ++ D+ + + F F+ F E +
Sbjct: 34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93
Query: 244 KNPKQK-INDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGY 300
K +N + + V A +P GG GG G G GGYGG G GGG+
Sbjct: 94 SEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGG-------GGYGGGGDGGGGF 144
Score = 43.9 bits (103), Expect = 4e-05
Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 8/107 (7%)
Query: 429 GTDMMHMEVTEAVPMEIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQK-INDK 487
GTD + A ++++ ++ D+ + + F F+ F E + K +N +
Sbjct: 45 GTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGR 104
Query: 488 EVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGY 534
+ V A +P GG GG G GG GYGG G GGG+
Sbjct: 105 HIRVNPANDRPSAPRAYGGGGGYSGGGG-------GYGGGGDGGGGF 144
Score = 39.6 bits (92), Expect = 0.001
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
L++ F+ +G++ + + D TGRSRGF F+ F D + A E
Sbjct: 51 LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
Score = 39.6 bits (92), Expect = 0.001
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
L++ F+ +G++ + + D TGRSRGF F+ F D + A E
Sbjct: 51 LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
>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 = 63.4 bits (155), Expect = 1e-12
Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 5/68 (7%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
+ L+++FS++GEIE + +D TG+SRG+ F+ FKD ES E+A + N +I+
Sbjct: 14 DDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA-----CKDPNPIIDG 68
Query: 173 KKIEAKKA 180
+K A
Sbjct: 69 RKANVNLA 76
Score = 62.2 bits (152), Expect = 3e-12
Identities = 21/45 (46%), Positives = 33/45 (73%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ L+++FS++GEIE + +D TG+SRG+ F+ FKD ES E+A
Sbjct: 14 DDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58
Score = 60.7 bits (148), Expect = 8e-12
Identities = 23/75 (30%), Positives = 41/75 (54%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGGL D+ ++ +F+QFG I E + D+ + + + F+TF+ + K+
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61
Query: 246 PKQKINDKEVDVKKA 260
P I+ ++ +V A
Sbjct: 62 PNPIIDGRKANVNLA 76
Score = 33.0 bits (76), Expect = 0.056
Identities = 12/51 (23%), Positives = 25/51 (49%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
EI E + D+ + + + F+TF+ + K+P I+ ++ +V A
Sbjct: 26 EIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPNPIIDGRKANVNLA 76
>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 = 62.7 bits (152), Expect = 2e-12
Identities = 29/68 (42%), Positives = 47/68 (69%), Gaps = 5/68 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD S++K V+ H ++ K
Sbjct: 14 KDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDK-----VLELKEHKLDGK 68
Query: 174 KIEAKKAK 181
I+ K+AK
Sbjct: 69 LIDPKRAK 76
Score = 57.7 bits (139), Expect = 1e-10
Identities = 23/47 (48%), Positives = 36/47 (76%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
D ++L E+ S++GE+ + T+K+DP TGRSRGF F++FKD S++K
Sbjct: 10 DTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDK 56
Score = 41.9 bits (98), Expect = 4e-05
Identities = 19/75 (25%), Positives = 44/75 (58%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+F+GGLS + +++ + ++FG +++ + D + + F F+ F+ + V +L+
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 246 PKQKINDKEVDVKKA 260
+ K++ K +D K+A
Sbjct: 61 KEHKLDGKLIDPKRA 75
>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 = 62.3 bits (151), Expect = 2e-12
Identities = 28/75 (37%), Positives = 46/75 (61%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGGLSP+ +E+I+ +F FG + E+P D ++R+ FCFITF+ E V +++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 246 PKQKINDKEVDVKKA 260
+ + ++K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
Score = 44.2 bits (104), Expect = 6e-06
Identities = 19/47 (40%), Positives = 31/47 (65%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
D E+++E+F +GE+E++ L D T + RGF FI FK+ E ++K
Sbjct: 10 DTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56
Score = 44.2 bits (104), Expect = 6e-06
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 5/67 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+++E+F +GE+E++ L D T + RGF FI FK+ E ++K ++ + H +
Sbjct: 14 EKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK-----IMEKKYHNVGLS 68
Query: 174 KIEAKKA 180
K E K A
Sbjct: 69 KCEIKVA 75
Score = 35.4 bits (81), Expect = 0.010
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
E+ E+P D ++R+ FCFITF+ E V +++ + + ++K A
Sbjct: 25 EVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA 75
>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 = 68.8 bits (168), Expect = 3e-12
Identities = 61/260 (23%), Positives = 96/260 (36%), Gaps = 41/260 (15%)
Query: 111 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV 169
K E +L E FSK G++ +V D N+ RS+G A++ F D ES+ KA + G +
Sbjct: 100 KARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKA----LALTGQML 155
Query: 170 IN----------NKKIEAKKAKAKSG------KIFVGGLSPEMKDEEIKAHFAQFGNIIE 213
+ K AK A + G K++VG L + ++E++ F FG+I +
Sbjct: 156 LGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIED 215
Query: 214 TEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEV-----------DVK---K 259
++ D + K F FI F + L + +N E+ D
Sbjct: 216 VQLHRDPETGRSKGFGFIQFHDAEEAKEAL----EVMNGFELAGRPIKVGYAQDSTYLLD 271
Query: 260 ATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLFYELNELGIS 319
A E + G R M G G G K L +L GI
Sbjct: 272 AANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGII 331
Query: 320 GRSLVCRTGPMVQATPPLAE 339
++ + A +A
Sbjct: 332 DPNI--PSRYATGALAIMAR 349
Score = 53.4 bits (128), Expect = 2e-07
Identities = 25/52 (48%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ ITE EL++ F +G+IE+V L DP TGRS+GF FI F D E ++A
Sbjct: 193 NLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA 244
Score = 53.0 bits (127), Expect = 3e-07
Identities = 25/47 (53%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 606 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
ITE EL++ F +G+IE+V L DP TGRS+GF FI F D E ++A
Sbjct: 198 ITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA 244
Score = 45.7 bits (108), Expect = 5e-05
Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 605 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
K E +L E FSK G++ +V D N+ RS+G A++ F D ES+ KA
Sbjct: 100 KARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKA 147
>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 = 68.3 bits (167), Expect = 5e-12
Identities = 41/156 (26%), Positives = 73/156 (46%), Gaps = 24/156 (15%)
Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN--- 172
L + FSK+G I + + +D N G+SRG+ F+ F+ ES + A I + N ++ N
Sbjct: 105 LFDTFSKFGNILSCKVATDEN-GKSRGYGFVHFEKEESAKAA-----IQKVNGMLLNDKE 158
Query: 173 --------KKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQ 224
K K ++V L P + +++++ FA+FG I + D S +
Sbjct: 159 VYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GR 217
Query: 225 RKNFCFITFE-HESVVIDLLKNPKQKINDKEVDVKK 259
+ F F+ FE HE +++N K++ + K
Sbjct: 218 SRGFAFVNFEKHEDA-----AKAVEEMNGKKIGLAK 248
Score = 66.4 bits (162), Expect = 3e-11
Identities = 40/156 (25%), Positives = 71/156 (45%), Gaps = 29/156 (18%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV-------IAEG 166
++L+E F+K+GEI + + D + GRSRGFAF+ F+ E KA VE++ EG
Sbjct: 193 DKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKA-VEEMNGKKIGLAKEG 250
Query: 167 NHV------------------INNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQF 208
+ + E +K KA+ ++V L + DE+++ F++
Sbjct: 251 KKLYVGRAQKRAEREAELRRKFEELQQE-RKMKAQGVNLYVKNLDDTVTDEKLRELFSEC 309
Query: 209 GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
G I ++ D+ K + F F+ F + +
Sbjct: 310 GEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVT 344
Score = 56.7 bits (137), Expect = 3e-08
Identities = 44/171 (25%), Positives = 76/171 (44%), Gaps = 28/171 (16%)
Query: 111 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV 169
+TE +L + F +G + +V + D T RS G+ ++ F++ E+A +
Sbjct: 11 DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERA----LETMNFKR 66
Query: 170 INNKKIEAKK-----AKAKSGK--IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYD--- 219
+ K I + +SG IFV L + ++ + F++FGNI+ ++ D
Sbjct: 67 LGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENG 126
Query: 220 KSKSQRKNFCFITFEHESVVIDLLKNPKQKIN-----DKEVDVKKATPKPE 265
KS+ + F+ FE E + QK+N DKEV V + K E
Sbjct: 127 KSRG----YGFVHFEKEESAKAAI----QKVNGMLLNDKEVYVGRFIKKHE 169
Score = 48.3 bits (115), Expect = 9e-06
Identities = 22/49 (44%), Positives = 34/49 (69%), Gaps = 2/49 (4%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV 656
++L+E F+K+GEI + + D + GRSRGFAF+ F+ E KA VE++
Sbjct: 193 DKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKA-VEEM 239
Score = 47.1 bits (112), Expect = 2e-05
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 604 DKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
D +T+E L+E FS+ GEI + + D G SRGF F+ F + E +A E
Sbjct: 295 DTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTE 345
Score = 46.7 bits (111), Expect = 3e-05
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
E+L+E FS+ GEI + + D G SRGF F+ F + E +A E
Sbjct: 300 EKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTE 345
Score = 41.3 bits (97), Expect = 0.001
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
L + FSK+G I + + +D N G+SRG+ F+ F+ ES + A +
Sbjct: 105 LFDTFSKFGNILSCKVATDEN-GKSRGYGFVHFEKEESAKAAIQK 148
Score = 36.3 bits (84), Expect = 0.051
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 605 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+TE +L + F +G + +V + D T RS G+ ++ F++ E+A
Sbjct: 11 DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERA 58
>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 = 61.1 bits (149), Expect = 6e-12
Identities = 25/65 (38%), Positives = 42/65 (64%), Gaps = 5/65 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+L+E+FS+YG +E+V + +D TG+ RGFAF+ F D + ++K + + H IN
Sbjct: 14 EDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKI-----VLQKYHTINGH 68
Query: 174 KIEAK 178
++E K
Sbjct: 69 RVEVK 73
Score = 56.5 bits (137), Expect = 3e-10
Identities = 23/52 (44%), Positives = 38/52 (73%), Gaps = 1/52 (1%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G+ + +TEE L+E+FS+YG +E+V + +D TG+ RGFAF+ F D + ++K
Sbjct: 6 GLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKI 57
Score = 51.9 bits (125), Expect = 1e-08
Identities = 24/73 (32%), Positives = 44/73 (60%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVGGL ++ +E+++ +F+Q+GN+ E+ DK +++ F F+TF+ V ++
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 246 PKQKINDKEVDVK 258
IN V+VK
Sbjct: 61 KYHTINGHRVEVK 73
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 66.9 bits (162), Expect = 6e-12
Identities = 47/176 (26%), Positives = 73/176 (41%), Gaps = 26/176 (14%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVIAEGNHVIN 171
E+L+E F K+G ++ V L D TG+SRGFAF+ F+ ES EKA + EG +
Sbjct: 130 EDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRV 189
Query: 172 NKKIEAKKAKA-----------------------KSGKIFVGGLSPEMKDEEIKAHFAQF 208
K A + ++ KS ++VG L + +EE+ F
Sbjct: 190 QKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSR 249
Query: 209 GNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKP 264
G+I+ +P K K+ F+ E S + K +KA +P
Sbjct: 250 GDIVRASLPPSKDGKIPKSRSFVGNEA-SKDALESNSRGNKKKILGRGPRKAFSQP 304
Score = 59.6 bits (143), Expect = 1e-09
Identities = 21/101 (20%), Positives = 49/101 (48%), Gaps = 1/101 (0%)
Query: 167 NHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRK 226
+ +K+K ++ +FVG L ++ +E+++ F +FG + + D+ + +
Sbjct: 98 LFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR 157
Query: 227 NFCFITFEHESVVIDLLKN-PKQKINDKEVDVKKATPKPEP 266
F F+ FE E ++ +++ + + V+KA P +P
Sbjct: 158 GFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQP 198
Score = 54.6 bits (130), Expect = 6e-08
Identities = 23/44 (52%), Positives = 31/44 (70%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+L+E F K+G ++ V L D TG+SRGFAF+ F+ ES EKA
Sbjct: 130 EDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA 173
Score = 33.4 bits (75), Expect = 0.33
Identities = 11/58 (18%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN-PKQKINDKEVDVKKATPKPEP 500
+ + D+ + + F F+ FE E ++ +++ + + V+KA P +P
Sbjct: 141 PVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQP 198
>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 = 61.1 bits (149), Expect = 7e-12
Identities = 32/77 (41%), Positives = 45/77 (58%), Gaps = 7/77 (9%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ + TE EL+ FSK+G +E V L DP TG SRGF F+ F ES+E A + I +
Sbjct: 8 GLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTF---ESVEDA--DAAIRD 62
Query: 166 GN-HVINNKKIEAKKAK 181
N + + I+ +KAK
Sbjct: 63 LNGKELEGRVIKVEKAK 79
Score = 56.1 bits (136), Expect = 4e-10
Identities = 24/52 (46%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G+ + TE EL+ FSK+G +E V L DP TG SRGF F+ F+ E + A
Sbjct: 8 GLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59
Score = 49.1 bits (118), Expect = 1e-07
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
K+FV GLS ++E++A F++FG + E + D + + F F+TFE
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFE 51
>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 = 60.8 bits (148), Expect = 9e-12
Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
+ TEE L+E FSK+GEIE+V + D + G+S+GFAF+ F+ E EKA + A
Sbjct: 5 NLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKA----LEAL 59
Query: 166 GNHVINNKKIEAK 178
++ +K++
Sbjct: 60 NGKELDGRKLKVS 72
Score = 60.4 bits (147), Expect = 1e-11
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE-HESVVIDLLKN 245
+FVG L P+ +E+++ F++FG I + DK + K F F+ FE E L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDG-KSKGFAFVEFESPEDAEKALEAL 59
Query: 246 PKQKINDKEVDVK 258
++++ +++ V
Sbjct: 60 NGKELDGRKLKVS 72
Score = 57.7 bits (140), Expect = 1e-10
Identities = 25/52 (48%), Positives = 35/52 (67%), Gaps = 2/52 (3%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ TEE L+E FSK+GEIE+V + D + G+S+GFAF+ F+ E EKA
Sbjct: 5 NLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKA 55
Score = 28.4 bits (64), Expect = 1.9
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFE-HESVVIDLLKNPKQKINDKEVDVK 492
EI + DK + K F F+ FE E L ++++ +++ V
Sbjct: 24 EIESVRIVRDKDG-KSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72
>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 = 60.8 bits (147), Expect = 9e-12
Identities = 29/75 (38%), Positives = 47/75 (62%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGGL+PE +E+I+ +F +FG I E+P D ++R+ F FITF+ E V +L+
Sbjct: 6 KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEK 65
Query: 246 PKQKINDKEVDVKKA 260
++ + ++K A
Sbjct: 66 KFHNVSGSKCEIKVA 80
Score = 50.4 bits (120), Expect = 5e-08
Identities = 25/67 (37%), Positives = 41/67 (61%), Gaps = 5/67 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+++E+F ++GEIE + L DP T + RGF FI FK+ + ++K V+ + H ++
Sbjct: 19 EKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK-----VLEKKFHNVSGS 73
Query: 174 KIEAKKA 180
K E K A
Sbjct: 74 KCEIKVA 80
Score = 47.3 bits (112), Expect = 5e-07
Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
E+++E+F ++GEIE + L DP T + RGF FI FK+ + ++K
Sbjct: 19 EKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61
Score = 32.7 bits (74), Expect = 0.080
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
EI E+P D ++R+ F FITF+ E V +L+ ++ + ++K A
Sbjct: 30 EIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEKKFHNVSGSKCEIKVA 80
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 59.7 bits (145), Expect = 2e-11
Identities = 24/48 (50%), Positives = 31/48 (64%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
D I L EHFS GEI V++ +D TG S+GFA+I FK + +EKA
Sbjct: 14 DDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61
Score = 57.8 bits (140), Expect = 1e-10
Identities = 23/47 (48%), Positives = 30/47 (63%)
Query: 111 KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
I L EHFS GEI V++ +D TG S+GFA+I FK + +EKA
Sbjct: 15 DIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61
Score = 30.4 bits (69), Expect = 0.43
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 186 KIFVGGLSPEMKDEEIKA----HFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
IFV G + +++I+ HF+ G I +P D+ K F +I F+
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFK 53
>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 = 59.3 bits (143), Expect = 3e-11
Identities = 31/78 (39%), Positives = 51/78 (65%)
Query: 183 KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDL 242
++ KIFVGGLS E++K +F QFG + + + +DK+ ++ + F F+TFE+E VV +
Sbjct: 2 RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61
Query: 243 LKNPKQKINDKEVDVKKA 260
+ +IN+K V+ KKA
Sbjct: 62 CEIHFHEINNKMVECKKA 79
Score = 52.4 bits (125), Expect = 9e-09
Identities = 26/69 (37%), Positives = 42/69 (60%), Gaps = 5/69 (7%)
Query: 112 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN 171
+ E++K++F ++G++E+ L D T R RGF F+ F++ + +EK V H IN
Sbjct: 16 VVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK-----VCEIHFHEIN 70
Query: 172 NKKIEAKKA 180
NK +E KKA
Sbjct: 71 NKMVECKKA 79
Score = 44.3 bits (104), Expect = 6e-06
Identities = 18/56 (32%), Positives = 38/56 (67%), Gaps = 2/56 (3%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY 659
+ + E++K++F ++G++E+ L D T R RGF F+ F++ + +EK V +++F+
Sbjct: 14 NTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK--VCEIHFH 67
Score = 33.9 bits (77), Expect = 0.033
Identities = 17/43 (39%), Positives = 29/43 (67%)
Query: 452 YDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
+DK+ ++ + F F+TFE+E VV + + +IN+K V+ KKA
Sbjct: 37 FDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECKKA 79
>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 = 59.3 bits (144), Expect = 3e-11
Identities = 21/44 (47%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E LK FSKYG + V+L +TG +GFAFI F+ E +KA
Sbjct: 14 EWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57
Score = 59.3 bits (144), Expect = 3e-11
Identities = 21/44 (47%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E LK FSKYG + V+L +TG +GFAFI F+ E +KA
Sbjct: 14 EWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57
Score = 39.3 bits (92), Expect = 3e-04
Identities = 15/48 (31%), Positives = 24/48 (50%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++V L E +KA F+++G ++ +P K K F FI FE
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFE 49
>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 = 58.9 bits (142), Expect = 4e-11
Identities = 29/74 (39%), Positives = 47/74 (63%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGGLS E++K +F QFG + + + +DK+ ++ + F F+TFE E +V + +
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 246 PKQKINDKEVDVKK 259
+IN+K V+ KK
Sbjct: 61 HFHEINNKMVECKK 74
Score = 49.2 bits (117), Expect = 1e-07
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 109 VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH 168
V+ E++K++F ++G++++ L D T R RGF F+ F+ + +EK V H
Sbjct: 9 VNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-----VCEIHFH 63
Query: 169 VINNKKIEAKK 179
INNK +E KK
Sbjct: 64 EINNKMVECKK 74
Score = 42.7 bits (100), Expect = 2e-05
Identities = 18/57 (31%), Positives = 37/57 (64%), Gaps = 2/57 (3%)
Query: 603 VDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYFY 659
V+ E++K++F ++G++++ L D T R RGF F+ F+ + +EK V +++F+
Sbjct: 9 VNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK--VCEIHFH 63
Score = 33.4 bits (76), Expect = 0.038
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 452 YDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKK 493
+DK+ ++ + F F+TFE E +V + + +IN+K V+ KK
Sbjct: 33 FDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK 74
>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 = 58.4 bits (142), Expect = 5e-11
Identities = 25/47 (53%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 112 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
ITE+ L+ F +GEIE V L+ DP TGRS+G+ FI F D E +KA
Sbjct: 10 ITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKA 56
Score = 58.4 bits (142), Expect = 5e-11
Identities = 25/47 (53%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
ITE+ L+ F +GEIE V L+ DP TGRS+G+ FI F D E +KA
Sbjct: 10 ITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKA 56
Score = 37.6 bits (88), Expect = 0.001
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
++VG L + +++++ F FG I ++ D + K + FI F
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQF 47
>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 = 63.4 bits (154), Expect = 1e-10
Identities = 40/126 (31%), Positives = 60/126 (47%), Gaps = 9/126 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
EE++ F+ GEIE+ L D TG+S G+ F+ + E EKA V + + NK
Sbjct: 18 EEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA----VNSLNGLRLQNK 73
Query: 174 KIEAKKAKAKSGKI-----FVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
I+ A+ S I +V GL M E+++ F+ FG II + + D K
Sbjct: 74 TIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGV 133
Query: 229 CFITFE 234
FI F+
Sbjct: 134 GFIRFD 139
Score = 39.9 bits (93), Expect = 0.004
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EE++ F+ GEIE+ L D TG+S G+ F+ + E EKA
Sbjct: 18 EEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61
Score = 32.2 bits (73), Expect = 0.94
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 96 MEAKNKMVSHPGIVHKI--------TEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAF 145
+ A ++ + G + I T+E L + F +G ++NV + D T + +G+ F
Sbjct: 256 LAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGF 315
Query: 146 I 146
+
Sbjct: 316 V 316
Score = 31.4 bits (71), Expect = 1.3
Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 607 TEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFI 640
T+E L + F +G ++NV + D T + +G+ F+
Sbjct: 281 TDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFV 316
Score = 31.4 bits (71), Expect = 1.4
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EL+ FS +G+I + SD TG S+G FI F + ++A
Sbjct: 104 HELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRA 147
Score = 31.4 bits (71), Expect = 1.4
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EL+ FS +G+I + SD TG S+G FI F + ++A
Sbjct: 104 HELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRA 147
Score = 30.3 bits (68), Expect = 3.7
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFIT 232
IFV LSP+ + + F FG + ++ D + +Q K + F++
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVS 317
>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 = 56.9 bits (138), Expect = 2e-10
Identities = 21/78 (26%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+IFVGG+ P+ +EE++ F++FG++ + ++ D++ K + F+TFE + +L
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKILAM 62
Query: 246 PKQKINDKEVDVKKATPK 263
K++++ A K
Sbjct: 63 GNLNFRGKKLNIGPAIRK 80
Score = 45.0 bits (107), Expect = 4e-06
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
GI TE EL++ FS++G +++V + +D G S+G+ F+ F+ E EK ++A
Sbjct: 9 GIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEK-----ILAM 62
Query: 166 GNHVINNKKIEAKKA 180
GN KK+ A
Sbjct: 63 GNLNFRGKKLNIGPA 77
Score = 38.0 bits (89), Expect = 9e-04
Identities = 19/52 (36%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
GI TE EL++ FS++G +++V + +D G S+G+ F+ F+ E EK
Sbjct: 9 GIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKI 59
>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 = 56.8 bits (137), Expect = 2e-10
Identities = 23/67 (34%), Positives = 42/67 (62%), Gaps = 6/67 (8%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
+ L+E+F ++GE+ + T+ D TGRSRGF F+ FK +S+ + + + H+++ K
Sbjct: 13 DSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSV------NEVMKKEHILDGK 66
Query: 174 KIEAKKA 180
I+ K+A
Sbjct: 67 IIDPKRA 73
Score = 51.4 bits (123), Expect = 2e-08
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF 658
+ + L+E+F ++GE+ + T+ D TGRSRGF F+ FK +S+ + ++
Sbjct: 9 ETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEHIL 63
Score = 49.9 bits (119), Expect = 7e-08
Identities = 25/78 (32%), Positives = 47/78 (60%), Gaps = 3/78 (3%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+F+GGL+ E D+ ++ +F QFG + + + D + + + F F+TF+ V +++K
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMK-- 58
Query: 247 KQKIND-KEVDVKKATPK 263
K+ I D K +D K+A P+
Sbjct: 59 KEHILDGKIIDPKRAIPR 76
Score = 28.3 bits (63), Expect = 2.8
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKIND-KEVDVKKATPK 497
E+ + + D + + + F F+TF+ V +++K K+ I D K +D K+A P+
Sbjct: 24 EVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMK--KEHILDGKIIDPKRAIPR 76
>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 = 56.2 bits (135), Expect = 4e-10
Identities = 28/75 (37%), Positives = 47/75 (62%), Gaps = 6/75 (8%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ + T+E L+E+F ++GE++ + DP T RSRGF F+ F D +A V+ V+A+
Sbjct: 7 GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD-----QAGVDKVLAQ 61
Query: 166 GNHVINNKKIEAKKA 180
H +++K I+ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 46.9 bits (111), Expect = 8e-07
Identities = 23/75 (30%), Positives = 42/75 (56%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+F+GGLS + E ++ +F QFG + E + D + + F F+TF ++ V +L
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 246 PKQKINDKEVDVKKA 260
+ +++ K +D K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 46.5 bits (110), Expect = 1e-06
Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
E L+E+F ++GE++ + DP T RSRGF F+ F D ++K
Sbjct: 15 EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 57
>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 = 56.1 bits (135), Expect = 4e-10
Identities = 27/69 (39%), Positives = 42/69 (60%), Gaps = 5/69 (7%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK 174
+L EHFS++G +E + +D TG+ RGF F+ F++ +S +KA+V H IN +
Sbjct: 15 DLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKF-----HPINGHR 69
Query: 175 IEAKKAKAK 183
+E KKA K
Sbjct: 70 VEVKKAVPK 78
Score = 53.4 bits (128), Expect = 4e-09
Identities = 27/80 (33%), Positives = 44/80 (55%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVGGL ++ + ++ HF+QFG + + E+ DK +++ F F+ F++
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 246 PKQKINDKEVDVKKATPKPE 265
IN V+VKKA PK E
Sbjct: 61 KFHPINGHRVEVKKAVPKEE 80
Score = 49.1 bits (117), Expect = 1e-07
Identities = 21/54 (38%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV 653
G+ + E +L EHFS++G +E + +D TG+ RGF F+ F++ +S +KA+V
Sbjct: 6 GLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV 59
Score = 27.2 bits (60), Expect = 8.1
Identities = 16/53 (30%), Positives = 25/53 (47%)
Query: 447 ETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPKPE 499
+ E+ DK +++ F F+ F++ IN V+VKKA PK E
Sbjct: 28 KAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKFHPINGHRVEVKKAVPKEE 80
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 56.1 bits (135), Expect = 5e-10
Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 7/79 (8%)
Query: 107 GIVHKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA 164
G + + TEE L+++F KYG+IE + + D +G+ RGFAF+ F D ++++K ++
Sbjct: 6 GGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDK-----IVV 60
Query: 165 EGNHVINNKKIEAKKAKAK 183
+ H IN E KKA +K
Sbjct: 61 QKYHTINGHNCEVKKALSK 79
Score = 53.5 bits (128), Expect = 4e-09
Identities = 23/78 (29%), Positives = 42/78 (53%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGG+ + ++ ++ +F ++G I E+ D+ +++ F F+TF+ V ++
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61
Query: 246 PKQKINDKEVDVKKATPK 263
IN +VKKA K
Sbjct: 62 KYHTINGHNCEVKKALSK 79
Score = 46.5 bits (110), Expect = 9e-07
Identities = 22/56 (39%), Positives = 38/56 (67%), Gaps = 2/56 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
G + + TEE L+++F KYG+IE + + D +G+ RGFAF+ F D ++++K V+
Sbjct: 6 GGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61
Score = 35.3 bits (81), Expect = 0.010
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 446 IET-EMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 497
IET E+ D+ +++ F F+TF+ V ++ IN +VKKA K
Sbjct: 27 IETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSK 79
>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 = 55.7 bits (135), Expect = 6e-10
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 111 KITEE-LKEHFSKYGEIENVTL--KSDPNTGRSR-GFAFIVFKDTESLEKASVEDVIAEG 166
K+ E+ L+ FSK+GE+E++ + K D GR GFAF+ FKD S E A +
Sbjct: 11 KLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA-----LQLN 65
Query: 167 NHVINNKKIE 176
+ +KI
Sbjct: 66 GTELGGRKIS 75
Score = 53.0 bits (128), Expect = 5e-09
Identities = 23/51 (45%), Positives = 32/51 (62%), Gaps = 4/51 (7%)
Query: 605 KITEE-LKEHFSKYGEIENVTL--KSDPNTGRSR-GFAFIVFKDTESLEKA 651
K+ E+ L+ FSK+GE+E++ + K D GR GFAF+ FKD S E A
Sbjct: 11 KLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Score = 40.3 bits (95), Expect = 1e-04
Identities = 15/75 (20%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP---YDKSKSQRKNFCFITFEHESVVIDL 242
+I+V L ++ +++++ F++FG + +P +K F F+TF+ S +
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 243 LKNPKQKINDKEVDV 257
L+ ++ +++ V
Sbjct: 62 LQLNGTELGGRKISV 76
>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 = 55.9 bits (134), Expect = 6e-10
Identities = 28/67 (41%), Positives = 43/67 (64%), Gaps = 5/67 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
+ L+++FSK+GEI + DP T RSRGF F+ F D ASV+ V+A+ +H +++K
Sbjct: 14 DSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFAD-----PASVDKVLAQPHHELDSK 68
Query: 174 KIEAKKA 180
I+ K A
Sbjct: 69 TIDPKVA 75
Score = 48.9 bits (116), Expect = 1e-07
Identities = 20/43 (46%), Positives = 29/43 (67%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
+ L+++FSK+GEI + DP T RSRGF F+ F D S++K
Sbjct: 14 DSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDK 56
Score = 48.5 bits (115), Expect = 2e-07
Identities = 23/75 (30%), Positives = 43/75 (57%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+F+GGLS + + ++ +F++FG I E + D + + + F F+TF + V +L
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 246 PKQKINDKEVDVKKA 260
P +++ K +D K A
Sbjct: 61 PHHELDSKTIDPKVA 75
Score = 28.5 bits (63), Expect = 2.1
Identities = 15/51 (29%), Positives = 26/51 (50%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKA 494
EI E + D + + + F F+TF + V +L P +++ K +D K A
Sbjct: 25 EIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQPHHELDSKTIDPKVA 75
>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 = 55.5 bits (134), Expect = 7e-10
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
S ++FVG L ++ ++E+K F +FGN++E + + NF F+ F+ V +L
Sbjct: 3 SHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKIL 62
Query: 244 KN-PKQKINDKEVDV 257
N P D ++V
Sbjct: 63 ANKPIYFRGDHRLNV 77
Score = 47.8 bits (114), Expect = 3e-07
Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 110 HKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA-SVEDVIAEGN 167
H ITE ELKE F ++G + V + S GR F F+VF D E+++K + + + G+
Sbjct: 13 HDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANKPIYFRGD 72
Query: 168 HVINNKKIEAKK 179
H +N +E KK
Sbjct: 73 HRLN---VEEKK 81
Score = 43.2 bits (102), Expect = 2e-05
Identities = 17/44 (38%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ELKE F ++G + V + S GR F F+VF D E+++K
Sbjct: 18 DELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61
>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 = 55.4 bits (134), Expect = 7e-10
Identities = 21/44 (47%), Positives = 28/44 (63%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EEL+EHF G I +T+ D TG+ +GFA+I F D S+E A
Sbjct: 14 EELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA 57
Score = 55.4 bits (134), Expect = 7e-10
Identities = 21/44 (47%), Positives = 28/44 (63%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL+EHF G I +T+ D TG+ +GFA+I F D S+E A
Sbjct: 14 EELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA 57
Score = 49.2 bits (118), Expect = 9e-08
Identities = 20/57 (35%), Positives = 27/57 (47%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
IFVG + EE++ HF G I + DK Q K F +I F +S V + L
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL 58
>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 = 55.6 bits (134), Expect = 8e-10
Identities = 25/65 (38%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E L+ +FS+YGE+ + + D T RSRGF F+ FKD V V+A G H ++ +
Sbjct: 14 ETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD-----PNCVGTVLAGGPHTLDGR 68
Query: 174 KIEAK 178
I+ K
Sbjct: 69 TIDPK 73
Score = 54.8 bits (132), Expect = 1e-09
Identities = 23/78 (29%), Positives = 46/78 (58%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVGGLS E E ++ +F+Q+G +++ + DK+ ++ + F F+ F+ + V +L
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 246 PKQKINDKEVDVKKATPK 263
++ + +D K TP+
Sbjct: 61 GPHTLDGRTIDPKPCTPR 78
Score = 49.0 bits (117), Expect = 1e-07
Identities = 18/37 (48%), Positives = 25/37 (67%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD 644
E L+ +FS+YGE+ + + D T RSRGF F+ FKD
Sbjct: 14 ETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50
Score = 29.0 bits (65), Expect = 1.5
Identities = 12/54 (22%), Positives = 29/54 (53%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 497
E+++ + DK+ ++ + F F+ F+ + V +L ++ + +D K TP+
Sbjct: 25 EVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHTLDGRTIDPKPCTPR 78
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 54.9 bits (133), Expect = 8e-10
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
E+L+E FS YG++E V L + + R RGFAF+ F E E A + V++
Sbjct: 12 EEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAA----LKKLNGLVLDG 65
Query: 173 KKIE 176
+ +
Sbjct: 66 RTLR 69
Score = 54.5 bits (132), Expect = 1e-09
Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE-HESVVIDLLKN 245
++V L P + +E+++ F+ +G + + +K + + F F+ F E L K
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRP--RGFAFVEFASPEDAEAALKKL 58
Query: 246 PKQKINDKEV 255
++ + +
Sbjct: 59 NGLVLDGRTL 68
Score = 49.1 bits (118), Expect = 9e-08
Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+L+E FS YG++E V L + + R RGFAF+ F E E A
Sbjct: 12 EEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAA 54
>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 = 54.2 bits (131), Expect = 2e-09
Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
++ELKE+FS++G++++ + D TG S+G+ F+ F + LE A + H++
Sbjct: 13 SKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ-----KHILEG 67
Query: 173 KKI 175
K+
Sbjct: 68 NKL 70
Score = 53.5 bits (129), Expect = 3e-09
Identities = 20/73 (27%), Positives = 39/73 (53%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVG L + +E+K +F+QFG + +P+DK K + F++F + + L+
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 246 PKQKINDKEVDVK 258
K + ++ V+
Sbjct: 61 QKHILEGNKLQVQ 73
Score = 51.9 bits (125), Expect = 1e-08
Identities = 17/49 (34%), Positives = 32/49 (65%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 655
++ELKE+FS++G++++ + D TG S+G+ F+ F + LE A +
Sbjct: 13 SKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61
Score = 33.0 bits (76), Expect = 0.043
Identities = 9/44 (20%), Positives = 21/44 (47%)
Query: 449 EMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVK 492
+P+DK K + F++F + + L+ K + ++ V+
Sbjct: 30 NVPFDKETGLSKGYGFVSFSSRDGLENALQKQKHILEGNKLQVQ 73
>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 = 54.2 bits (131), Expect = 2e-09
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+LK+ F ++GE+ + + +D TGRSRGF F+ + E A
Sbjct: 14 EDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57
Score = 54.2 bits (131), Expect = 2e-09
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+LK+ F ++GE+ + + +D TGRSRGF F+ + E A
Sbjct: 14 EDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57
Score = 43.4 bits (103), Expect = 1e-05
Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
++VG L + +E++K F QFG + + D+ + + F F+ E ++
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE- 59
Query: 246 PKQKINDKEVD-----VKKATP 262
K+N + V +A P
Sbjct: 60 ---KLNGTDFGGRTLTVNEARP 78
>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 = 54.1 bits (131), Expect = 2e-09
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+LKE F KYG+I + + D G+S+GF F+ F++ E+ +KA V +N K
Sbjct: 16 EKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKA----VEELNGKEVNGK 70
Query: 174 KIEAKKAKAK 183
K+ +A+ K
Sbjct: 71 KLYVGRAQKK 80
Score = 50.3 bits (121), Expect = 5e-08
Identities = 21/49 (42%), Positives = 34/49 (69%), Gaps = 2/49 (4%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDV 656
E+LKE F KYG+I + + D G+S+GF F+ F++ E+ +KA VE++
Sbjct: 16 EKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKA-VEEL 62
Score = 39.5 bits (93), Expect = 3e-04
Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 9/75 (12%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETE-MPYDKSKSQRKNFCFITFE-HESVVIDLLK 244
++V L +M DE++K F ++G I + M D+ KS K F F+ FE HE+ +
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKS--KGFGFVNFENHEAA-----Q 56
Query: 245 NPKQKINDKEVDVKK 259
+++N KEV+ KK
Sbjct: 57 KAVEELNGKEVNGKK 71
>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 = 54.1 bits (131), Expect = 2e-09
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA-SVEDVIAEGNHVINN 172
EELKE FS++GE++ + D TG S+G AF+ FK ES +K D + ++
Sbjct: 15 EELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDG 74
Query: 173 KKIEAKKA 180
+++ A
Sbjct: 75 RRLIVTLA 82
Score = 53.0 bits (128), Expect = 5e-09
Identities = 21/43 (48%), Positives = 29/43 (67%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
EELKE FS++GE++ + D TG S+G AF+ FK ES +K
Sbjct: 15 EELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQK 57
Score = 33.7 bits (78), Expect = 0.038
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNI 211
+F+ L + +EE+K F+QFG +
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEV 27
>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 = 53.7 bits (130), Expect = 3e-09
Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L+E F +G I V L D TG+SRGFAF+ F E E+A
Sbjct: 14 DDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERA 57
Score = 53.7 bits (130), Expect = 3e-09
Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L+E F +G I V L D TG+SRGFAF+ F E E+A
Sbjct: 14 DDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERA 57
Score = 39.1 bits (92), Expect = 4e-04
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 192 LSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
LS + +++++ F FG I + DK Q + F F+TF
Sbjct: 7 LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTRE 52
>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 = 53.5 bits (128), Expect = 4e-09
Identities = 26/76 (34%), Positives = 47/76 (61%), Gaps = 7/76 (9%)
Query: 107 GIVHKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA 164
G + + TEE L+++F +YG+IE + + +D +G+ RGFAF+ F D +S++K ++
Sbjct: 6 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK-----IVI 60
Query: 165 EGNHVINNKKIEAKKA 180
+ H +N E +KA
Sbjct: 61 QKYHTVNGHNCEVRKA 76
Score = 47.7 bits (113), Expect = 4e-07
Identities = 21/75 (28%), Positives = 41/75 (54%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
KIFVGG+ + ++ ++ +F Q+G I E+ D+ +++ F F+TF+ V ++
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61
Query: 246 PKQKINDKEVDVKKA 260
+N +V+KA
Sbjct: 62 KYHTVNGHNCEVRKA 76
Score = 46.9 bits (111), Expect = 6e-07
Identities = 21/56 (37%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
G + + TEE L+++F +YG+IE + + +D +G+ RGFAF+ F D +S++K ++
Sbjct: 6 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61
>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 = 53.1 bits (128), Expect = 4e-09
Identities = 23/48 (47%), Positives = 27/48 (56%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 161
EEL+E F +GEI V L D T RS+GFAF+ F E KA E
Sbjct: 14 EELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Score = 53.1 bits (128), Expect = 4e-09
Identities = 23/48 (47%), Positives = 27/48 (56%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 655
EEL+E F +GEI V L D T RS+GFAF+ F E KA E
Sbjct: 14 EELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Score = 44.6 bits (106), Expect = 4e-06
Identities = 17/49 (34%), Positives = 26/49 (53%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++FV L +EE++ F FG I E +P DK + K F F++F
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFM 49
>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 = 52.7 bits (127), Expect = 5e-09
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 603 VDKIT-----EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
VD +T ++L+ F KYGE+ +V + D T SRGFAF+ F D E A
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA 56
Score = 51.5 bits (124), Expect = 1e-08
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L+ F KYGE+ +V + D T SRGFAF+ F D E A
Sbjct: 13 DDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA 56
Score = 29.6 bits (67), Expect = 0.89
Identities = 9/45 (20%), Positives = 23/45 (51%)
Query: 189 VGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
V L+ ++++ F ++G + + +P D+ + + F F+ F
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRF 47
>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 = 52.9 bits (127), Expect = 5e-09
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
L+ HF++YG++ + DPNT RSRGF FI F + ++A + H I+
Sbjct: 16 DSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA-----MEAQPHSIDG 70
Query: 173 KKIEAKKAK 181
+IE K+AK
Sbjct: 71 NQIELKRAK 79
Score = 45.9 bits (109), Expect = 1e-06
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
L+ HF++YG++ + DPNT RSRGF FI F + ++A
Sbjct: 16 DSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60
Score = 44.8 bits (106), Expect = 4e-06
Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVGGL+ + D ++ HF ++G + E + D + + + F FITF + ++
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63
Query: 246 PKQKINDKEVDVKKA 260
I+ ++++K+A
Sbjct: 64 QPHSIDGNQIELKRA 78
>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 = 52.6 bits (127), Expect = 5e-09
Identities = 16/48 (33%), Positives = 30/48 (62%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++VGGL+ E+ ++ + A F FG+I + ++P D + + F F+ FE
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFE 48
Score = 47.6 bits (114), Expect = 4e-07
Identities = 15/47 (31%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE 646
G+ +++ E+ L F +G+I+++ + D T + RGFAF+ F++ E
Sbjct: 5 GLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51
Score = 45.3 bits (108), Expect = 3e-06
Identities = 15/47 (31%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE 152
G+ ++ E+ L F +G+I+++ + D T + RGFAF+ F++ E
Sbjct: 5 GLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51
Score = 29.1 bits (66), Expect = 1.4
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 7/40 (17%)
Query: 436 EVTEAV------PM-EIIETEMPYDKSKSQRKNFCFITFE 468
EV E V P +I + ++P D + + F F+ FE
Sbjct: 9 EVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFE 48
>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 = 52.6 bits (127), Expect = 6e-09
Identities = 21/44 (47%), Positives = 29/44 (65%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L+E FS+YG IE V + D TGRSRGF F+ F+ E ++A
Sbjct: 14 RDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEA 57
Score = 52.6 bits (127), Expect = 6e-09
Identities = 21/44 (47%), Positives = 29/44 (65%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L+E FS+YG IE V + D TGRSRGF F+ F+ E ++A
Sbjct: 14 RDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEA 57
Score = 39.5 bits (93), Expect = 3e-04
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 189 VGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQ 248
V GLS + +++ F+++G I + ++ YD+ + + F F+ FE ++ K K+
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES----VEDAKEAKE 59
Query: 249 KINDKEVD 256
++N E+D
Sbjct: 60 RLNGMEID 67
>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 = 52.2 bits (126), Expect = 8e-09
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
D E+L E FS+ G + + L +D +TG+ +G+ F F+D E+ A
Sbjct: 9 DATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASA 56
Score = 51.9 bits (125), Expect = 1e-08
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+L E FS+ G + + L +D +TG+ +G+ F F+D E+ A
Sbjct: 12 EEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASA 56
Score = 36.1 bits (84), Expect = 0.004
Identities = 12/59 (20%), Positives = 28/59 (47%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+FVG + + +E++ F++ G ++ + D+ + K + F FE ++N
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN 59
>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 = 52.0 bits (124), Expect = 1e-08
Identities = 24/79 (30%), Positives = 47/79 (59%), Gaps = 7/79 (8%)
Query: 107 GIVHKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA 164
G + + TEE L+++F +YG+I+ + + +D +G+ RGF F+ F D + ++K ++
Sbjct: 6 GGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDK-----IVL 60
Query: 165 EGNHVINNKKIEAKKAKAK 183
+ H IN E +KA ++
Sbjct: 61 QKYHTINGHNAEVRKALSR 79
Score = 47.4 bits (112), Expect = 5e-07
Identities = 20/78 (25%), Positives = 42/78 (53%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVGG+ + ++ ++ +F ++G I E+ D+ +++ F F+TF+ V ++
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61
Query: 246 PKQKINDKEVDVKKATPK 263
IN +V+KA +
Sbjct: 62 KYHTINGHNAEVRKALSR 79
Score = 44.3 bits (104), Expect = 6e-06
Identities = 18/52 (34%), Positives = 35/52 (67%), Gaps = 2/52 (3%)
Query: 601 GIVDKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
G + + TEE L+++F +YG+I+ + + +D +G+ RGF F+ F D + ++K
Sbjct: 6 GGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDK 57
Score = 28.5 bits (63), Expect = 2.7
Identities = 13/54 (24%), Positives = 26/54 (48%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVDVKKATPK 497
+I E+ D+ +++ F F+TF+ V ++ IN +V+KA +
Sbjct: 26 KIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSR 79
>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 = 50.6 bits (121), Expect = 4e-08
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
GK+F+GGLS + ++ ++ F+++G I E + D+ + + F F+TFE+ D K
Sbjct: 1 GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN----PDDAK 56
Query: 245 NPKQKINDKEVD 256
+ +N K VD
Sbjct: 57 DAMMAMNGKSVD 68
Score = 46.8 bits (111), Expect = 8e-07
Identities = 18/44 (40%), Positives = 28/44 (63%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ L++ FSKYG+I V + D T RSRGF F+ F++ + + A
Sbjct: 15 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDA 58
Score = 46.8 bits (111), Expect = 8e-07
Identities = 18/44 (40%), Positives = 28/44 (63%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ L++ FSKYG+I V + D T RSRGF F+ F++ + + A
Sbjct: 15 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDA 58
>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 = 50.9 bits (122), Expect = 4e-08
Identities = 24/62 (38%), Positives = 39/62 (62%), Gaps = 4/62 (6%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYD-KSKSQR--KNFCFITFEHESVVIDL 242
K+FVGGL P++ ++EI A F +FG ++ + P+ +SKS K + F+ F+ ES V L
Sbjct: 2 KVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 60
Query: 243 LK 244
+
Sbjct: 61 ID 62
>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 = 49.5 bits (119), Expect = 7e-08
Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 111 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
K+ E +L E FSK G++ +V + D N+ RS+G A++ F D ES+ A
Sbjct: 10 KVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57
Score = 49.5 bits (119), Expect = 7e-08
Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 605 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
K+ E +L E FSK G++ +V + D N+ RS+G A++ F D ES+ A
Sbjct: 10 KVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57
Score = 27.6 bits (62), Expect = 3.8
Identities = 11/54 (20%), Positives = 28/54 (51%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVI 240
+FV LS ++++ ++ F++ G + + + D++ + K ++ F E V
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVP 55
>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 = 55.1 bits (132), Expect = 9e-08
Identities = 37/147 (25%), Positives = 70/147 (47%), Gaps = 25/147 (17%)
Query: 109 VHKITEELKEH-----FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE----SLE---- 155
V I+ EL+E F +G I+++ + DP TG+ +GFAF+ ++ E +LE
Sbjct: 112 VGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNG 171
Query: 156 --------KASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQ 207
K + + +I+ + EAKK +I+V + P++ + +IK+ F
Sbjct: 172 QMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFN----RIYVASVHPDLSETDIKSVFEA 227
Query: 208 FGNIIETEMPYDKSKSQRKNFCFITFE 234
FG I++ ++ + K + FI +
Sbjct: 228 FGEIVKCQLARAPTGRGHKGYGFIEYN 254
Score = 42.7 bits (100), Expect = 5e-04
Identities = 19/85 (22%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 152 ESLEKASVEDVIAEGNHVINNKKIEAKKAKAKS--GKIFVGGLSPEMKDEEIKAHFAQFG 209
+S+++ ++ A + N++ + ++ +A + +++VG +S E++++ I+ F FG
Sbjct: 73 QSIKQVLLKQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFG 132
Query: 210 NIIETEMPYDKSKSQRKNFCFITFE 234
I M +D + + K F F+ +E
Sbjct: 133 PIKSINMSWDPATGKHKGFAFVEYE 157
Score = 39.3 bits (91), Expect = 0.006
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 599 HPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
HP + + ++K F +GEI L P +G+ FI + + +S +A
Sbjct: 213 HPDLSE---TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA 262
Score = 38.1 bits (88), Expect = 0.016
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++K F +GEI L P +G+ FI + + +S +A
Sbjct: 219 TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA 262
Score = 33.5 bits (76), Expect = 0.35
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 603 VDKITEELKEH-----FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
V I+ EL+E F +G I+++ + DP TG+ +GFAF+ ++ E+ + A
Sbjct: 112 VGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLA 165
>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 = 49.1 bits (118), Expect = 1e-07
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
EEL++HF G++E V + D TG +GF +++FK +S+ A + + +
Sbjct: 14 EELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA-----LKLNGIKLKGR 68
Query: 174 KI 175
KI
Sbjct: 69 KI 70
Score = 49.1 bits (118), Expect = 1e-07
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL++HF G++E V + D TG +GF +++FK +S+ A
Sbjct: 14 EELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA 57
Score = 32.5 bits (75), Expect = 0.084
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH-ESVVIDLLKN 245
+FVG L ++++EE++ HF G++ + D+ K F ++ F+ +SV + L N
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61
Query: 246 PKQKINDKEVDVK 258
K+ +++ VK
Sbjct: 62 -GIKLKGRKIRVK 73
>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 = 49.3 bits (117), Expect = 1e-07
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E L+ HF ++G + + + DPNT RSRGF F+ + E ++ A + H ++ +
Sbjct: 17 ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA-----MNARPHKVDGR 71
Query: 174 KIEAKKAKAK 183
+E K+A ++
Sbjct: 72 VVEPKRAVSR 81
Score = 47.4 bits (112), Expect = 5e-07
Identities = 22/78 (28%), Positives = 43/78 (55%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+F+GGLS E DE +++HF Q+G + + + D + + + F F+T+ V +
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63
Query: 246 PKQKINDKEVDVKKATPK 263
K++ + V+ K+A +
Sbjct: 64 RPHKVDGRVVEPKRAVSR 81
Score = 46.6 bits (110), Expect = 1e-06
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E L+ HF ++G + + + DPNT RSRGF F+ + E ++ A
Sbjct: 17 ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60
>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 = 49.2 bits (118), Expect = 1e-07
Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 11/67 (16%)
Query: 111 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV 169
K TE LK+ FS +G + VT+ P G+ +GFAF+ F EKA ++ V
Sbjct: 10 KCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKA-IKGV------- 60
Query: 170 INNKKIE 176
N KKI+
Sbjct: 61 -NGKKIK 66
Score = 48.8 bits (117), Expect = 1e-07
Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 605 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
K TE LK+ FS +G + VT+ P G+ +GFAF+ F EKA
Sbjct: 10 KCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKA 56
Score = 34.5 bits (80), Expect = 0.013
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
++ V L + + ++K F+ FG + E +P ++ F F+ F
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKK-GFAFVQFTS 49
>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 = 49.1 bits (118), Expect = 1e-07
Identities = 19/44 (43%), Positives = 29/44 (65%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+++ F +YG IE VT+ D +TG+S+G AF+ F E +KA
Sbjct: 14 EDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKA 57
Score = 49.1 bits (118), Expect = 1e-07
Identities = 19/44 (43%), Positives = 29/44 (65%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+++ F +YG IE VT+ D +TG+S+G AF+ F E +KA
Sbjct: 14 EDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKA 57
Score = 41.4 bits (98), Expect = 6e-05
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
K+FVG L +E+++A F ++GNI E + DK Q K F+ F
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFS 49
>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 = 49.2 bits (118), Expect = 2e-07
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L+ F +YG I+ + L D TG+ RG+AFI F+ ++ A
Sbjct: 17 KLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59
Score = 49.2 bits (118), Expect = 2e-07
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L+ F +YG I+ + L D TG+ RG+AFI F+ ++ A
Sbjct: 17 KLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59
Score = 37.6 bits (88), Expect = 0.002
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FV L+ + + +++ F ++G I + DK + + + FI FEHE + K
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63
Query: 247 K-QKINDKE--VDVKKA 260
+KI+ + VDV++
Sbjct: 64 DGKKIDGRRVLVDVERG 80
>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 = 48.3 bits (116), Expect = 2e-07
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 112 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ ++ LKE FS YG +++V L D RG+A++ F+ E EKA
Sbjct: 10 VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKA 56
Score = 48.3 bits (116), Expect = 2e-07
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ ++ LKE FS YG +++V L D RG+A++ F+ E EKA
Sbjct: 10 VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKA 56
Score = 31.8 bits (73), Expect = 0.13
Identities = 10/48 (20%), Positives = 27/48 (56%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+ VG L+ + + +K F+ +G + + ++P D+ + + + ++ FE
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFE 48
>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 = 48.5 bits (116), Expect = 2e-07
Identities = 25/53 (47%), Positives = 35/53 (66%), Gaps = 1/53 (1%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 158
GI + TE E++ +FS GEIE + L + P+TGR RG AFI FK E+ ++A
Sbjct: 5 GIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL 57
Score = 45.0 bits (107), Expect = 2e-06
Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
GI TE E++ +FS GEIE + L + P+TGR RG AFI FK E+ ++A
Sbjct: 5 GIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL 57
Score = 28.1 bits (63), Expect = 2.7
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETE-MPYDKSKSQRKNFC---FITFEHESV 238
++VGG+ ++EI+++F+ G I E + M + + F FITF+ E
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDT----GRFRGIAFITFKTEEA 52
>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 = 48.2 bits (115), Expect = 3e-07
Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
++L++ FSK+GE+ V + D +G+S+GFA+++F D E KA E
Sbjct: 17 DDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63
Score = 48.2 bits (115), Expect = 3e-07
Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
++L++ FSK+GE+ V + D +G+S+GFA+++F D E KA E
Sbjct: 17 DDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63
Score = 41.2 bits (97), Expect = 7e-05
Identities = 14/50 (28%), Positives = 29/50 (58%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
+G++FV L K+++++ F++FG + E + DK + K F ++ F
Sbjct: 2 TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF 51
>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 = 48.4 bits (116), Expect = 3e-07
Identities = 17/34 (50%), Positives = 25/34 (73%)
Query: 120 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
FS+YGEI ++ L D TG+S+GFAF+ ++D S
Sbjct: 30 FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS 63
Score = 48.4 bits (116), Expect = 3e-07
Identities = 17/34 (50%), Positives = 25/34 (73%)
Query: 614 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
FS+YGEI ++ L D TG+S+GFAF+ ++D S
Sbjct: 30 FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS 63
Score = 43.0 bits (102), Expect = 2e-05
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
S I++GGL E+ + +I F+Q+G I++ + DK + K F F+ +E
Sbjct: 9 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYE 59
>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 = 48.0 bits (115), Expect = 3e-07
Identities = 19/67 (28%), Positives = 39/67 (58%), Gaps = 8/67 (11%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE--GNHVIN 171
EL+++FS++G + + L TG+S+G+AF+ F+ E V ++AE N+++
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE------VAKIVAETMNNYLLF 67
Query: 172 NKKIEAK 178
+ ++ K
Sbjct: 68 ERLLKCK 74
Score = 42.9 bits (102), Expect = 1e-05
Identities = 14/39 (35%), Positives = 26/39 (66%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE 646
EL+++FS++G + + L TG+S+G+AF+ F+ E
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE 52
Score = 35.6 bits (83), Expect = 0.005
Identities = 13/52 (25%), Positives = 26/52 (50%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV 238
+++G L + E++ +F+QFG + + K + K + F+ FE V
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEV 53
>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 = 47.3 bits (113), Expect = 4e-07
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+L HF G +V L +D TG+S+G AF+ F E++ KA
Sbjct: 14 AEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA 58
Score = 47.3 bits (113), Expect = 4e-07
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+L HF G +V L +D TG+S+G AF+ F E++ KA
Sbjct: 14 AEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA 58
Score = 39.6 bits (93), Expect = 2e-04
Identities = 16/58 (27%), Positives = 25/58 (43%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
+FVG L + E++ AHF G + DK + K F+ F+ + LK
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60
>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 = 47.8 bits (113), Expect = 4e-07
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
+ L+EHF K+G + + + DP T RSRGF F+ + E ++ A ++ H ++ +
Sbjct: 17 DSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA-----MSARPHKVDGR 71
Query: 174 KIEAKKAKAK 183
+E K+A ++
Sbjct: 72 VVEPKRAVSR 81
Score = 44.7 bits (105), Expect = 5e-06
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ L+EHF K+G + + + DP T RSRGF F+ + E ++ A
Sbjct: 17 DSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60
Score = 41.6 bits (97), Expect = 6e-05
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH-ESVVIDLLK 244
K+F+GGLS E D+ ++ HF ++G + + + D + + F F+T+ E V +
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63
Query: 245 NPKQKINDKEVDVKKATPK 263
P K++ + V+ K+A +
Sbjct: 64 RP-HKVDGRVVEPKRAVSR 81
>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 = 46.7 bits (111), Expect = 7e-07
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 4/65 (6%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
+ELK++FS++G ++NV + TG S+ + FI F + E A+ + N+++ K
Sbjct: 14 KELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAK----SMNNYLLMGK 69
Query: 174 KIEAK 178
++
Sbjct: 70 VLQVH 74
Score = 44.0 bits (104), Expect = 7e-06
Identities = 16/45 (35%), Positives = 28/45 (62%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
+ELK++FS++G ++NV + TG S+ + FI F + E A+
Sbjct: 14 KELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAA 58
Score = 37.1 bits (86), Expect = 0.002
Identities = 15/52 (28%), Positives = 27/52 (51%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV 238
I++G L ++E+K +F+QFG + + K K++ FI F + V
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEV 53
>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 = 47.3 bits (113), Expect = 7e-07
Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 3/64 (4%)
Query: 110 HKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE--DVIAEG 166
+ TEE L+E FS+YG+I + L D TG S+G+AF+ ++ +A + ++ +G
Sbjct: 13 LQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDG 72
Query: 167 NHVI 170
+ +
Sbjct: 73 SEIF 76
Score = 46.9 bits (112), Expect = 9e-07
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 607 TEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
TEE L+E FS+YG+I + L D TG S+G+AF+ ++ +A +
Sbjct: 16 TEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRD 64
Score = 38.0 bits (89), Expect = 0.002
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
+FVG LS + +E ++ F+++G+I + D K + F+ +EHE
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHER 56
>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 = 46.9 bits (112), Expect = 8e-07
Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 20/83 (24%)
Query: 111 KITE-ELKEHFSKYGEIENVT---LKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG 166
++TE L + FSKYG+I+ KS P G+ RG+ F+ F+ E EKA
Sbjct: 10 RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA--------- 60
Query: 167 NHVINNKKIEAKKAKAKSGKIFV 189
A K+ V
Sbjct: 61 -------LKSLNGKTALGKKLVV 76
Score = 46.1 bits (110), Expect = 1e-06
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 605 KITE-ELKEHFSKYGEIENVT---LKSDPNTGRSRGFAFIVFKDTESLEKA 651
++TE L + FSKYG+I+ KS P G+ RG+ F+ F+ E EKA
Sbjct: 10 RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Score = 37.6 bits (88), Expect = 0.001
Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKS---KSQRKNFCFITFEHE 236
++++G L + + + F+++G I + + + KS K Q + +CF+TFE +
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETK 54
>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 = 45.7 bits (109), Expect = 2e-06
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVG L+ +M +E+++ +F+QFG + + +P + F F+TF V L
Sbjct: 2 KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCGE 56
Query: 246 PKQKINDKEVDVKKAT 261
I V V A
Sbjct: 57 -DHIIKGVSVHVSNAE 71
Score = 45.3 bits (108), Expect = 2e-06
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV 169
E+L+++FS++GE+ +V + R FAF+ F D E + ED I +G V
Sbjct: 14 EEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCGEDHIIKGVSV 65
Score = 42.3 bits (100), Expect = 2e-05
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVED 655
E+L+++FS++GE+ +V + R FAF+ F D E + ED
Sbjct: 14 EEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCGED 57
>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 = 45.8 bits (109), Expect = 2e-06
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 604 DKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++TEE L E F + G +E V + DPN G+ + FAF+ FK S+ A
Sbjct: 11 ARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYA 58
Score = 45.0 bits (107), Expect = 3e-06
Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 111 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++TEE L E F + G +E V + DPN G+ + FAF+ FK S+ A
Sbjct: 12 RVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYA 58
Score = 40.4 bits (95), Expect = 1e-04
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV---IDLL 243
+FVG L + +E + F Q G + ++P D + K+F F+TF+HE V I LL
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDP-NGKPKSFAFVTFKHEVSVPYAIQLL 62
Query: 244 KN 245
Sbjct: 63 NG 64
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 45.6 bits (108), Expect = 2e-06
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 112 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ E L F K G IE V + DP T +GFA++ FKD ++EKA
Sbjct: 12 VEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57
Score = 45.6 bits (108), Expect = 2e-06
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 606 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ E L F K G IE V + DP T +GFA++ FKD ++EKA
Sbjct: 12 VEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57
Score = 27.5 bits (61), Expect = 5.8
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE-SVVIDLLKN 245
+FVG L E +E + F + G I + D + K F ++ F+ E +V LL N
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61
Query: 246 PKQK 249
K+
Sbjct: 62 EKKF 65
>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 = 45.3 bits (108), Expect = 2e-06
Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 113 TEELKEHFSK-YGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
ELKEHFSK GEI +V L + G+SR AFI +K E +KA
Sbjct: 14 EAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKA 58
Score = 45.3 bits (108), Expect = 2e-06
Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 607 TEELKEHFSK-YGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
ELKEHFSK GEI +V L + G+SR AFI +K E +KA
Sbjct: 14 EAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKA 58
Score = 29.2 bits (66), Expect = 1.3
Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQF-GNIIETEMPYDKSKSQRKNFCFITFEHE 236
++ V L + + E+K HF++ G I + ++ + R+ FI ++ E
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRR-IAFIGYKTE 52
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 45.1 bits (107), Expect = 3e-06
Identities = 15/50 (30%), Positives = 29/50 (58%)
Query: 185 GKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+++VG +S E+ ++ I+ F+ FG I +M +D + K F F+ +E
Sbjct: 1 CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYE 50
Score = 37.4 bits (87), Expect = 0.002
Identities = 12/40 (30%), Positives = 27/40 (67%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
+ +++ FS +G I+++ + DP T + +GFAF+ ++ E+
Sbjct: 15 DTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEA 54
Score = 37.4 bits (87), Expect = 0.002
Identities = 12/40 (30%), Positives = 27/40 (67%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
+ +++ FS +G I+++ + DP T + +GFAF+ ++ E+
Sbjct: 15 DTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEA 54
>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 = 45.5 bits (107), Expect = 3e-06
Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ + TEE L+ ++ ++G++ + + DP + RSRGF F+ F V+ +A
Sbjct: 9 GLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCM-----NEVDAAMAA 63
Query: 166 GNHVINNKKIEAKKAKAK 183
H I+ + +E K+A A+
Sbjct: 64 RPHTIDGRVVEPKRAVAR 81
Score = 41.6 bits (97), Expect = 6e-05
Identities = 20/78 (25%), Positives = 42/78 (53%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+F+GGLS E +E ++ ++ Q+G + + + D + + + F F+TF + V +
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63
Query: 246 PKQKINDKEVDVKKATPK 263
I+ + V+ K+A +
Sbjct: 64 RPHTIDGRVVEPKRAVAR 81
Score = 37.0 bits (85), Expect = 0.003
Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G+ + TEE L+ ++ ++G++ + + DP + RSRGF F+ F ++ A
Sbjct: 9 GLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA 60
>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 = 45.0 bits (107), Expect = 3e-06
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EEL+ F G IE+ + D TG+S G+ F+ + D +KA
Sbjct: 15 EELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA 58
Score = 45.0 bits (107), Expect = 3e-06
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL+ F G IE+ + D TG+S G+ F+ + D +KA
Sbjct: 15 EELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA 58
>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 = 45.0 bits (107), Expect = 3e-06
Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 16/75 (21%)
Query: 109 VHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH 168
+HKI FSKYG++ VT+ D T +S+G AFI+F D E K
Sbjct: 18 LHKI-------FSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV---------K 61
Query: 169 VINNKKIEAKKAKAK 183
+NNK++ + K
Sbjct: 62 ALNNKELFGRTLKCS 76
Score = 42.3 bits (100), Expect = 3e-05
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 614 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
FSKYG++ VT+ D T +S+G AFI+F D E K
Sbjct: 22 FSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC 59
>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 = 44.7 bits (106), Expect = 4e-06
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
IFVG LSPE+ E ++A FA FG I + + D + K + F++F
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSF 48
Score = 44.3 bits (105), Expect = 6e-06
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
TE L+ F+ +GEI + + D TG+S+G+ F+ F E E A
Sbjct: 13 TETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENA 57
Score = 44.3 bits (105), Expect = 6e-06
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
TE L+ F+ +GEI + + D TG+S+G+ F+ F E E A
Sbjct: 13 TETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENA 57
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 44.9 bits (107), Expect = 4e-06
Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 604 DKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
D I +E L+E FS +G I + + +D GRS+GF F+ F E KA E
Sbjct: 11 DSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTE 61
Score = 44.5 bits (106), Expect = 6e-06
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
E L+E FS +G I + + +D GRS+GF F+ F E KA E
Sbjct: 16 ERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTE 61
Score = 31.8 bits (73), Expect = 0.16
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETE-MPYDKSKSQRKNFCFITF 233
++V L + DE ++ F+ FG I + M +K +S K F F+ F
Sbjct: 3 NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRS--KGFGFVCF 49
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 44.9 bits (107), Expect = 5e-06
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 107 GIVHKITEE-LKEHFSKYG--EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS--VED 161
G+ TEE + + S I++V L D TG SRGFAF+ F SLE A+ ++
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEF---PSLEDATQWMDA 65
Query: 162 VIAEGNHVINNKKI 175
+ VI+ + +
Sbjct: 66 LNNLDPFVIDGRVV 79
Score = 39.5 bits (93), Expect = 4e-04
Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 601 GIVDKITEE-LKEHFSKYG--EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
G+ TEE + + S I++V L D TG SRGFAF+ F SLE A+
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEF---PSLEDAT 60
>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 = 44.5 bits (106), Expect = 5e-06
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 600 PGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
P V + + L+EHF GE+ +V + + G+SR F F+ FK E ++A
Sbjct: 9 PKYVTE--DRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQA 57
Score = 44.5 bits (106), Expect = 5e-06
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ L+EHF GE+ +V + + G+SR F F+ FK E ++A
Sbjct: 15 DRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQA 57
Score = 30.6 bits (70), Expect = 0.33
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETE-MPYDKSKSQRKNFCFITFEHE 236
+I V L + ++ ++ HF G + + + M KS+R F F+ F+ E
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRR--FGFVGFKSE 51
>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 = 48.9 bits (116), Expect = 5e-06
Identities = 45/191 (23%), Positives = 75/191 (39%), Gaps = 18/191 (9%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF-KDTESLEKASVEDVIAEGNHVINNK 173
EL F G I + D TG S G+AF+ F + +S + I + NK
Sbjct: 123 ELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGIT-----VRNK 177
Query: 174 KIEAKKAKA-----KSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF 228
+++ A+ K ++V L + D+++ F ++G I++ + DK +
Sbjct: 178 RLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGV 237
Query: 229 CFITF---EHESVVIDLLKNPKQKINDKEVDVKKA----TPKPEPFGVRGGRGGRGGRGG 281
F+ F E I L N + + + V+ A K + + G G G G
Sbjct: 238 AFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMGH 297
Query: 282 RGGRMAGGYGG 292
MAGG G
Sbjct: 298 GNMGMAGGSGM 308
Score = 38.5 bits (89), Expect = 0.010
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVIAEGNHVIN 171
++L F KYG+I + D TG RG AF+ F E ++A ++ +VI EG
Sbjct: 208 DQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPL 267
Query: 172 NKKIEAKKAKAKS 184
++ + KAK+
Sbjct: 268 TVRLAEEHGKAKA 280
Score = 34.6 bits (79), Expect = 0.14
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L F KYG+I + D TG RG AF+ F E ++A
Sbjct: 208 DQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEA 251
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 44.3 bits (104), Expect = 8e-06
Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L+E FSKYG I +V++ D + RSRGFAF+ F++ + ++A
Sbjct: 25 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67
Score = 44.3 bits (104), Expect = 8e-06
Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L+E FSKYG I +V++ D + RSRGFAF+ F++ + ++A
Sbjct: 25 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67
Score = 33.5 bits (76), Expect = 0.046
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 189 VGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQ 248
V GLS + +++ F+++G I + + YD+ + + F F+ FE+ +D K K+
Sbjct: 14 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN----VDDAKEAKE 69
Query: 249 KINDKEVDVKK 259
+ N E+D ++
Sbjct: 70 RANGMELDGRR 80
>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 = 43.6 bits (103), Expect = 8e-06
Identities = 20/66 (30%), Positives = 30/66 (45%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FVG LS E ++E++AHF + G I M + + K F F+ FE + LK
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60
Query: 247 KQKIND 252
Sbjct: 61 HLNGRA 66
Score = 41.3 bits (97), Expect = 6e-05
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL+ HF + G I V + + ++G+ +GFAF+ F++ E A
Sbjct: 13 DELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA 56
Score = 41.3 bits (97), Expect = 6e-05
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL+ HF + G I V + + ++G+ +GFAF+ F++ E A
Sbjct: 13 DELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA 56
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 43.8 bits (104), Expect = 9e-06
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 111 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
I E+ L++ F +G I +V LK + G+ R F F+ +K E +KA
Sbjct: 11 GIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKA 57
Score = 43.8 bits (104), Expect = 9e-06
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 605 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
I E+ L++ F +G I +V LK + G+ R F F+ +K E +KA
Sbjct: 11 GIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKA 57
Score = 37.7 bits (88), Expect = 0.001
Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
++ V L +K+++++ F FG I + ++ Y K RK F F+ ++ E
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRK-FGFVGYKTE 51
>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family. This family of
proteins includes several glycine rich proteins as well
as two nodulins 16 and 24. The family also contains
proteins that are induced in response to various
stresses.
Length = 91
Score = 44.4 bits (105), Expect = 9e-06
Identities = 21/35 (60%), Positives = 21/35 (60%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GG GG G GG GG GG G GG GGGYGG
Sbjct: 55 GGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYGG 89
Score = 42.4 bits (100), Expect = 3e-05
Identities = 23/51 (45%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 252 DKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
+ E + + + +G GG GG GG GG G G YGG GGYGGG GG
Sbjct: 30 NTEKSESENEVQDDKYG--GGGGGYGGGGGGGYGGGGYYGGGGGYGGGGGG 78
Score = 42.4 bits (100), Expect = 4e-05
Identities = 20/34 (58%), Positives = 20/34 (58%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G GG GG G GG GG GG G GG GGGYG
Sbjct: 55 GGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYG 88
Score = 40.5 bits (95), Expect = 2e-04
Identities = 22/50 (44%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 486 DKEVDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
+ E + + + +G GG GG GG GG G G YGG GGYGGG G
Sbjct: 30 NTEKSESENEVQDDKYG--GGGGGYGGGGGGGYGGGGYYGGGGGYGGGGG 77
Score = 30.1 bits (68), Expect = 0.94
Identities = 14/27 (51%), Positives = 14/27 (51%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYG 294
GG G GG GG G GGYGG G
Sbjct: 65 YYGGGGGYGGGGGGYPGGGGGGYGGGG 91
Score = 30.1 bits (68), Expect = 0.94
Identities = 14/27 (51%), Positives = 14/27 (51%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYG 528
GG G GG GG G GGYGG G
Sbjct: 65 YYGGGGGYGGGGGGYPGGGGGGYGGGG 91
>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 = 43.8 bits (104), Expect = 1e-05
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ + ++E+ +KE +G+++ L D TG S+G+AF + D SV D
Sbjct: 7 GLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDP------SVTDQAIA 60
Query: 166 G--NHVINNKKIEAKKA 180
G + +KK+ ++A
Sbjct: 61 GLNGMQLGDKKLTVQRA 77
Score = 38.4 bits (90), Expect = 7e-04
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV---VIDL 242
KIF+GGL + ++++K FG + + D + K + F + SV I
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 243 LKNPKQKINDKEVDVKKA 260
L ++ DK++ V++A
Sbjct: 62 LNG--MQLGDKKLTVQRA 77
Score = 37.2 bits (87), Expect = 0.002
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE 646
G+ + ++E+ +KE +G+++ L D TG S+G+AF + D
Sbjct: 7 GLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPS 53
>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 = 43.4 bits (103), Expect = 1e-05
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L + F+ +G + + + D NTG+S+ F F+ + + ES + A
Sbjct: 13 QDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA 56
Score = 43.4 bits (103), Expect = 1e-05
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L + F+ +G + + + D NTG+S+ F F+ + + ES + A
Sbjct: 13 QDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA 56
Score = 41.5 bits (98), Expect = 4e-05
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
+F+ L E D+++ FA FGN+I ++ DK+ Q K F F+++++
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDN 49
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 43.9 bits (104), Expect = 1e-05
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L+ F KYG I +V + D T R RGFA++ F+D E A
Sbjct: 15 DDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDA 58
Score = 43.9 bits (104), Expect = 1e-05
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L+ F KYG I +V + D T R RGFA++ F+D E A
Sbjct: 15 DDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDA 58
Score = 30.4 bits (69), Expect = 0.57
Identities = 9/48 (18%), Positives = 27/48 (56%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++V ++ + ++++ F ++G I++ +P D + + F ++ FE
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFE 50
>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 = 43.2 bits (102), Expect = 1e-05
Identities = 19/44 (43%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+E++ FS GEIE+ L D TG+S G+ F+ + D E EKA
Sbjct: 16 DEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59
Score = 43.2 bits (102), Expect = 1e-05
Identities = 19/44 (43%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+E++ FS GEIE+ L D TG+S G+ F+ + D E EKA
Sbjct: 16 DEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59
Score = 29.3 bits (66), Expect = 1.1
Identities = 11/46 (23%), Positives = 20/46 (43%)
Query: 192 LSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
L M +EI++ F+ G I ++ DK Q + F+ +
Sbjct: 9 LPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPE 54
>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 = 43.3 bits (102), Expect = 1e-05
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+L + FS I++ + +DP TG SRG+ F+ F E ++A + + NK
Sbjct: 14 EDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK---------LKNK 64
Query: 174 KIEAKKAK 181
K+ + +
Sbjct: 65 KLHGRILR 72
Score = 41.7 bits (98), Expect = 5e-05
Identities = 16/44 (36%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+L + FS I++ + +DP TG SRG+ F+ F E ++A
Sbjct: 14 EDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEA 57
Score = 29.0 bits (65), Expect = 1.5
Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE-HESVVIDLLKN 245
+FV L+ + E++ F+ I + D + + + F+TF E L K
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 246 PKQKINDKEVDVKKATPK 263
+K++ + + + A +
Sbjct: 62 KNKKLHGRILRLDIAERR 79
>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 = 42.7 bits (101), Expect = 2e-05
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 112 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+ + E F +YGEI +V L +DP++GR +GF ++ F E+ + A
Sbjct: 10 ADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAA 56
Score = 42.7 bits (101), Expect = 2e-05
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+ + E F +YGEI +V L +DP++GR +GF ++ F E+ + A
Sbjct: 10 ADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAA 56
Score = 31.6 bits (72), Expect = 0.19
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
+FVG LS + ++ I F ++G I +P D + K F ++ F
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEF 47
>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 = 42.9 bits (101), Expect = 2e-05
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EEL+ HF G + VT+ D +G +GFA+I F D ES+ A
Sbjct: 14 EELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTA 57
Score = 42.9 bits (101), Expect = 2e-05
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL+ HF G + VT+ D +G +GFA+I F D ES+ A
Sbjct: 14 EELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTA 57
Score = 28.6 bits (64), Expect = 1.8
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF-EHESV 238
++VG + EE++AHF G++ + DK K F +I F + ESV
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 54
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 43.0 bits (101), Expect = 2e-05
Identities = 19/43 (44%), Positives = 29/43 (67%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L+E FS+YG + V + D TGRSRGFAF+ F+ + ++A
Sbjct: 15 DLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEA 57
Score = 43.0 bits (101), Expect = 2e-05
Identities = 19/43 (44%), Positives = 29/43 (67%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L+E FS+YG + V + D TGRSRGFAF+ F+ + ++A
Sbjct: 15 DLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEA 57
Score = 29.9 bits (67), Expect = 0.77
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 189 VGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQ 248
V GLS + +++ F+++G + + YD+ + + F F+ FE ID K +
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFER----IDDSKEAME 59
Query: 249 KINDKEVDVKK 259
N E+D ++
Sbjct: 60 HANGMELDGRR 70
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 42.8 bits (101), Expect = 2e-05
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 3/55 (5%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF---EH 235
SG++F+ L+ +E+++ F+++G + E +P DK + K F F+T+ EH
Sbjct: 2 SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEH 56
Score = 36.6 bits (85), Expect = 0.003
Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
E+L++ FSKYG + V L D T + +GFAF+ + E KA E
Sbjct: 17 EDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63
Score = 36.6 bits (85), Expect = 0.003
Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
E+L++ FSKYG + V L D T + +GFAF+ + E KA E
Sbjct: 17 EDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63
>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 = 42.4 bits (100), Expect = 2e-05
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 194 PEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL-KNPKQKIND 252
+E++ +F QFG +++ +PY Q++ F F+TFE+ V +L K I
Sbjct: 9 SRFTEEDVSEYFGQFGPVLDVRIPY----QQKRMFGFVTFENAETVKRILSKGNPHFICG 64
Query: 253 KEVDVK 258
V VK
Sbjct: 65 SRVRVK 70
Score = 31.3 bits (71), Expect = 0.19
Identities = 17/66 (25%), Positives = 37/66 (56%), Gaps = 10/66 (15%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN-HVINN 172
E++ E+F ++G + +V + P + R F F+ F++ E +V+ ++++GN H I
Sbjct: 14 EDVSEYFGQFGPVLDVRI---PY-QQKRMFGFVTFENAE-----TVKRILSKGNPHFICG 64
Query: 173 KKIEAK 178
++ K
Sbjct: 65 SRVRVK 70
Score = 27.4 bits (61), Expect = 5.5
Identities = 11/41 (26%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESL 648
E++ E+F ++G + +V + P + R F F+ F++ E++
Sbjct: 14 EDVSEYFGQFGPVLDVRI---PY-QQKRMFGFVTFENAETV 50
>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 = 42.8 bits (101), Expect = 2e-05
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E LK F K+G + + +D TGRSRGF ++ F+ E +KA
Sbjct: 14 EWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKA 57
Score = 42.8 bits (101), Expect = 2e-05
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E LK F K+G + + +D TGRSRGF ++ F+ E +KA
Sbjct: 14 EWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKA 57
Score = 39.7 bits (93), Expect = 3e-04
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+FVG LS + DE +KA F +FG ++ + D+ + + F ++ FE K
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDA----KK 56
Query: 246 PKQKINDKEVD 256
+ ++ KE+D
Sbjct: 57 AIEAMDGKELD 67
>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 = 42.4 bits (100), Expect = 2e-05
Identities = 16/35 (45%), Positives = 26/35 (74%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 148
E+L+E F ++G+IE V++ D NTG S+GF ++ F
Sbjct: 15 EDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49
Score = 42.4 bits (100), Expect = 2e-05
Identities = 16/35 (45%), Positives = 26/35 (74%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 642
E+L+E F ++G+IE V++ D NTG S+GF ++ F
Sbjct: 15 EDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49
Score = 28.5 bits (64), Expect = 2.4
Identities = 10/39 (25%), Positives = 21/39 (53%)
Query: 195 EMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
+E+++ F +FG+I + DK+ + K F ++ F
Sbjct: 11 SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49
>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 = 42.2 bits (99), Expect = 2e-05
Identities = 17/60 (28%), Positives = 35/60 (58%), Gaps = 8/60 (13%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVG L PE ++EI++ F Q+G ++E ++ KN+ F+ + ++ + ++N
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53
>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 = 42.2 bits (100), Expect = 3e-05
Identities = 18/52 (34%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE-SLEK 156
G+ +TE +L+E FS++G + +V + + G RGFA+I + +E L+K
Sbjct: 6 GLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKK 57
Score = 40.2 bits (95), Expect = 1e-04
Identities = 14/48 (29%), Positives = 27/48 (56%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+FVGGLSP + + +++ F++FG + + E+ K + F +I
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49
Score = 39.1 bits (92), Expect = 4e-04
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTE-SLEK 650
+L+E FS++G + +V + + G RGFA+I + +E L+K
Sbjct: 14 SDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKK 57
>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 = 42.4 bits (99), Expect = 3e-05
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
+FVG LSPE+ ++IKA FA FG I + + D + + K + F++F
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50
Score = 32.4 bits (73), Expect = 0.093
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
T+++K F+ +G I + + D TG+S+G+ F+ F + E A
Sbjct: 15 TDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 59
Score = 32.4 bits (73), Expect = 0.093
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
T+++K F+ +G I + + D TG+S+G+ F+ F + E A
Sbjct: 15 TDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 59
>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 = 42.1 bits (100), Expect = 3e-05
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 12/56 (21%)
Query: 602 IVDKITEE------LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
V I E L EHFSK+G I N+ + +P + A + F +E +KA
Sbjct: 5 EVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKA 54
Score = 41.4 bits (98), Expect = 5e-05
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L EHFSK+G I N+ + +P + A + F +E +KA
Sbjct: 17 TKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKA 54
Score = 32.5 bits (75), Expect = 0.070
Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 186 KIFVGGLSPEM-KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
+ V + PE+ ++ HF++FG I+ ++ Y+ + F
Sbjct: 3 TLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYN------PESALVQFSTSE 49
>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 = 42.4 bits (99), Expect = 3e-05
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
+FVG LSPE+ E+IK+ FA FG I + + D + + K + F++F
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 50
Score = 34.3 bits (78), Expect = 0.020
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV 159
TE++K F+ +G+I + + D TG+S+G+ F+ F + E A V
Sbjct: 15 TEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61
Score = 34.3 bits (78), Expect = 0.020
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV 653
TE++K F+ +G+I + + D TG+S+G+ F+ F + E A V
Sbjct: 15 TEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61
>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 = 41.8 bits (99), Expect = 3e-05
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE-HES 237
++VG L + +EE++ F+ FG I E + D K + F+ F+ HE+
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEA 48
Score = 34.5 bits (80), Expect = 0.015
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 16/81 (19%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
+ H +TEE L+ FS +G IE V + D +G+AF+ F E+ A V
Sbjct: 7 NLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVA----- 55
Query: 166 GNHVINNKKIEAKKAKAKSGK 186
+N I + K GK
Sbjct: 56 ----VNGTSINGQTVKCSWGK 72
Score = 31.8 bits (73), Expect = 0.13
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
+ +TEE L+ FS +G IE V + D +G+AF+ F E+ A V
Sbjct: 7 NLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVA 55
>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 = 42.0 bits (99), Expect = 4e-05
Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 112 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
ITE +++E F K EI +V L +D TG +GF + F D ESL+ A
Sbjct: 11 ITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAA 56
Score = 42.0 bits (99), Expect = 4e-05
Identities = 21/47 (44%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 606 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
ITE +++E F K EI +V L +D TG +GF + F D ESL+ A
Sbjct: 11 ITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAA 56
>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 = 42.6 bits (100), Expect = 5e-05
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E L HFSK+G + D +TGR++G F+ FKD +
Sbjct: 16 ESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59
Score = 42.6 bits (100), Expect = 5e-05
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E L HFSK+G + D +TGR++G F+ FKD +
Sbjct: 16 ESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59
Score = 37.2 bits (86), Expect = 0.004
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FV L + +E + HF++FG++ DKS + K F+ F+ + LKN
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63
Query: 247 K 247
Sbjct: 64 P 64
>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 = 41.8 bits (99), Expect = 5e-05
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 114 EELKEHFSKYGEIENVTL-----KSDPNTGRSRGFAFIVFKDTESLEKA 157
E LK+HF K G + +VT+ P S G+ F+ FK E+ +KA
Sbjct: 15 ETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKA 63
Score = 41.8 bits (99), Expect = 5e-05
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 608 EELKEHFSKYGEIENVTL-----KSDPNTGRSRGFAFIVFKDTESLEKA 651
E LK+HF K G + +VT+ P S G+ F+ FK E+ +KA
Sbjct: 15 ETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKA 63
>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 = 41.5 bits (98), Expect = 5e-05
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK 220
+FVGGL P + ++E+++ F FG I+ ++P K
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGK 37
>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 = 41.5 bits (98), Expect = 6e-05
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EEL E FS++G+I V L N + FAFI F+ ++ +A
Sbjct: 18 EELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARA 59
Score = 41.5 bits (98), Expect = 6e-05
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL E FS++G+I V L N + FAFI F+ ++ +A
Sbjct: 18 EELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARA 59
Score = 40.4 bits (95), Expect = 2e-04
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
IFVG LSP++ EE+ F++ G I+ E+ K + F FI FE E
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKIL--EVNLIKRANHTNAFAFIKFEREQ 54
>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 = 40.6 bits (96), Expect = 6e-05
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 11/66 (16%)
Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN-HVINNKK 174
L + FS +G +E + L + GFAF+ F E+ EKA + N + +
Sbjct: 1 LYKLFSPFGNVEKIKL-----LKKKPGFAFVEFSTEEAAEKA-----VQYLNGVLFGGRP 50
Query: 175 IEAKKA 180
+ +
Sbjct: 51 LRVDYS 56
Score = 39.8 bits (94), Expect = 1e-04
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
L + FS +G +E + L + GFAF+ F E+ EKA
Sbjct: 1 LYKLFSPFGNVEKIKL-----LKKKPGFAFVEFSTEEAAEKA 37
Score = 35.6 bits (83), Expect = 0.005
Identities = 10/61 (16%), Positives = 22/61 (36%), Gaps = 6/61 (9%)
Query: 201 IKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN-PKQKINDKEVDVKK 259
+ F+ FGN+ + ++ K F F+ F E ++ + + V
Sbjct: 1 LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
Query: 260 A 260
+
Sbjct: 56 S 56
>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 = 41.1 bits (97), Expect = 6e-05
Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 7/52 (13%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G+ +++TE+ L++HF ++GEI ++T+ + AF+ F E+ EKA
Sbjct: 8 GLGERVTEKDLRDHFYQFGEIRSITVVP------RQQCAFVTFTTREAAEKA 53
Score = 39.6 bits (93), Expect = 3e-04
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 16/79 (20%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAE 165
G+ ++TE+ L++HF ++GEI ++T+ + AF+ F E+ EKA AE
Sbjct: 8 GLGERVTEKDLRDHFYQFGEIRSITVVP------RQQCAFVTFTTREAAEKA------AE 55
Query: 166 GNH---VINNKKIEAKKAK 181
+IN ++++ K +
Sbjct: 56 RLFNKLIINGRRLKLKWGR 74
Score = 36.9 bits (86), Expect = 0.002
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
++VGGL + +++++ HF QFG I + R+ F+TF
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITV------VPRQQCAFVTF 44
>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 = 45.8 bits (108), Expect = 7e-05
Identities = 40/144 (27%), Positives = 64/144 (44%), Gaps = 21/144 (14%)
Query: 105 HPGI-----VHKITEELKEH-----FSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESL 154
PG V KI +L E F K G I + L D + G++RG+AF+ F E
Sbjct: 54 QPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS-GQNRGYAFVTFCGKEEA 112
Query: 155 EKASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFG----N 210
++A V N+ I ++ + ++FVGG+ K EEI F++ +
Sbjct: 113 KEA----VKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVD 168
Query: 211 IIETEMPYDKSKSQRKNFCFITFE 234
+I DK K+ + F F+ +E
Sbjct: 169 VIVYHSAADKKKN--RGFAFVEYE 190
Score = 31.5 bits (71), Expect = 1.7
Identities = 56/257 (21%), Positives = 86/257 (33%), Gaps = 76/257 (29%)
Query: 111 KITEELKEHFSKYGE-IENVTLKSDP-NTGRSRGFAFIVFKDTESLEKAS---VEDVIAE 165
K EE+ E FSK E + +V + + ++RGFAF+ ++ + A + I
Sbjct: 150 KKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQL 209
Query: 166 GNHVIN----NKKIEAKKAKAKSGKI-FVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDK 220
HVI + E + KI +V L +E I+ F++F
Sbjct: 210 WGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEF----------KP 259
Query: 221 SKSQR----KNFCFITFEHESVVIDLLKNPKQK-INDKEVDVKKATPKPEPFGVRGGRGG 275
K +R +++ F+ FE + + K + E++V A P + VR RG
Sbjct: 260 GKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGT 319
Query: 276 RG--------------------------------------------------GRGGRGGR 285
G GRGG R
Sbjct: 320 GGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPIRGRGRGGAPSR 379
Query: 286 MAGGYGGYG-GYGGGYG 301
AGG G GY YG
Sbjct: 380 AAGGRGYPPYGYEAYYG 396
>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 = 41.0 bits (96), Expect = 8e-05
Identities = 21/53 (39%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV 239
+FVG L P++ +E I F Q G +I+ ++P DK K F F+ F+HE V
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKP-KQFAFVNFKHEVSV 55
Score = 29.1 bits (65), Expect = 1.4
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 111 KITEELK-EHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESL 154
K+TEEL E F + G + V + D G+ + FAF+ FK S+
Sbjct: 12 KVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSV 55
Score = 29.1 bits (65), Expect = 1.4
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 605 KITEELK-EHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESL 648
K+TEEL E F + G + V + D G+ + FAF+ FK S+
Sbjct: 12 KVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSV 55
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 44.7 bits (106), Expect = 8e-05
Identities = 20/35 (57%), Positives = 20/35 (57%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GGRGG G GG GGR GG GG G G G G
Sbjct: 5 GFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGR 39
Score = 44.0 bits (104), Expect = 1e-04
Identities = 20/41 (48%), Positives = 22/41 (53%)
Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLLF 310
GGRGG G G GR GG G GG GGG G ++ P F
Sbjct: 24 GGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGKVIVVPHRF 64
Score = 43.6 bits (103), Expect = 2e-04
Identities = 20/34 (58%), Positives = 20/34 (58%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G GGRGG G GG GGR GG GG G G G G
Sbjct: 5 GFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRG 38
Score = 43.2 bits (102), Expect = 3e-04
Identities = 21/35 (60%), Positives = 21/35 (60%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GGRGG G GGRGG G GG GG GG GG
Sbjct: 17 GGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGG 51
Score = 42.8 bits (101), Expect = 3e-04
Identities = 18/33 (54%), Positives = 18/33 (54%)
Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G G GGRGG G GG G GG GGG GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGG 33
Score = 42.8 bits (101), Expect = 4e-04
Identities = 17/36 (47%), Positives = 17/36 (47%)
Query: 267 FGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GGRGG G GG G GG GG GG G
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRG 36
Score = 42.0 bits (99), Expect = 5e-04
Identities = 22/35 (62%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G RGG G GGRGG GR G GG GG GGG GG
Sbjct: 20 GGRGGGGRGGGRGGGRGR--GRGGGGGGRGGGGGG 52
Score = 40.9 bits (96), Expect = 0.001
Identities = 21/34 (61%), Positives = 21/34 (61%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G RGG G GGRGG GR GG GG G GGG G
Sbjct: 20 GGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGG 53
Score = 40.9 bits (96), Expect = 0.001
Identities = 20/34 (58%), Positives = 20/34 (58%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G GGRGG G GGRGG G GG GG GG G
Sbjct: 17 GGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50
Score = 40.9 bits (96), Expect = 0.001
Identities = 17/32 (53%), Positives = 17/32 (53%)
Query: 504 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G G GGRGG G GG G GG GGG G
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRG 32
Score = 40.9 bits (96), Expect = 0.001
Identities = 16/35 (45%), Positives = 16/35 (45%)
Query: 501 FGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G GGRGG G GG G GG GG GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGR 35
Score = 40.9 bits (96), Expect = 0.002
Identities = 21/36 (58%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 268 GVRGGRGGRGGRGGRGG-RMAGGYGGYGGYGGGYGG 302
G GG GG G GGRGG R G G GG GGG GG
Sbjct: 13 GRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGG 48
Score = 38.6 bits (90), Expect = 0.007
Identities = 16/33 (48%), Positives = 16/33 (48%)
Query: 501 FGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 533
G RGG G G GRGG G GG GG G
Sbjct: 24 GGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
Score = 37.8 bits (88), Expect = 0.012
Identities = 20/40 (50%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 502 GVRGGRGG------RGGRGGRGGRMAGGYGGYGGYGGGYG 535
G RGG G RGG G GGR G G GG GGG G
Sbjct: 8 GGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRG 47
Score = 37.8 bits (88), Expect = 0.014
Identities = 18/36 (50%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 500 PFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G G GGRGG G G G GG GG GGG G
Sbjct: 17 GGGGGRGGGGRGGGRGGGRG-RGRGGGGGGRGGGGG 51
Score = 37.4 bits (87), Expect = 0.015
Identities = 14/27 (51%), Positives = 14/27 (51%)
Query: 266 PFGVRGGRGGRGGRGGRGGRMAGGYGG 292
G GRG GG GGRGG GG G
Sbjct: 30 GRGGGRGRGRGGGGGGRGGGGGGGPGK 56
Score = 37.4 bits (87), Expect = 0.015
Identities = 14/27 (51%), Positives = 14/27 (51%)
Query: 500 PFGVRGGRGGRGGRGGRGGRMAGGYGG 526
G GRG GG GGRGG GG G
Sbjct: 30 GRGGGRGRGRGGGGGGRGGGGGGGPGK 56
>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 = 41.0 bits (97), Expect = 8e-05
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 112 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+TE L E FS G + ++ + D T RS G+A++ F++ E+A
Sbjct: 11 VTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERA 57
Score = 41.0 bits (97), Expect = 8e-05
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 606 ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+TE L E FS G + ++ + D T RS G+A++ F++ E+A
Sbjct: 11 VTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERA 57
>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 = 41.1 bits (97), Expect = 9e-05
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+L+ FS++G+I++ + D TG S +AFI F+ E E+A
Sbjct: 18 EDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61
Score = 41.1 bits (97), Expect = 9e-05
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+L+ FS++G+I++ + D TG S +AFI F+ E E+A
Sbjct: 18 EDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61
Score = 36.1 bits (84), Expect = 0.005
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 11/66 (16%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE---------- 236
+FV L+P DE+++ F++FG I E+ DK + FI FE +
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65
Query: 237 -SVVID 241
+V+ID
Sbjct: 66 DNVLID 71
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 44.3 bits (105), Expect = 9e-05
Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 6/56 (10%)
Query: 597 VSHPGIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
VS+ + K TE ++KE FS G+IE V ++S+ RS+ A++ FKD + E A
Sbjct: 9 VSN--VSLKATERDIKEFFSFSGDIEYVEMQSE--NERSQ-IAYVTFKDPQGAETA 59
Score = 43.1 bits (102), Expect = 2e-04
Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 3/44 (6%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++KE FS G+IE V ++S+ RS+ A++ FKD + E A
Sbjct: 19 RDIKEFFSFSGDIEYVEMQSE--NERSQ-IAYVTFKDPQGAETA 59
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 40.6 bits (95), Expect = 1e-04
Identities = 19/44 (43%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EEL+ HFS G I VT+ D +G +G+A+I F +S+E A
Sbjct: 14 EELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAA 57
Score = 40.6 bits (95), Expect = 1e-04
Identities = 19/44 (43%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL+ HFS G I VT+ D +G +G+A+I F +S+E A
Sbjct: 14 EELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAA 57
Score = 28.7 bits (64), Expect = 1.9
Identities = 15/53 (28%), Positives = 24/53 (45%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV 239
++VG + EE++AHF+ G I + DK K + +I F V
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSV 54
>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 = 40.7 bits (96), Expect = 2e-04
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 18/73 (24%)
Query: 115 ELKEHFSKYGEIENVTLKSDP-----------------NTGRSRGFAFIVFKDTESLEKA 157
+LK+ F ++G IE+V +S P + + A++VFK+ ES EKA
Sbjct: 16 DLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYVVFKEEESAEKA 75
Query: 158 SVED-VIAEGNHV 169
+ EG+H+
Sbjct: 76 LKLNGTEFEGHHI 88
Score = 38.4 bits (90), Expect = 0.001
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 17/62 (27%)
Query: 609 ELKEHFSKYGEIENVTLKSDP-----------------NTGRSRGFAFIVFKDTESLEKA 651
+LK+ F ++G IE+V +S P + + A++VFK+ ES EKA
Sbjct: 16 DLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYVVFKEEESAEKA 75
Query: 652 SV 653
Sbjct: 76 LK 77
Score = 31.5 bits (72), Expect = 0.25
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNI 211
+FVG L K +++K F QFG I
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPI 27
>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 = 40.2 bits (95), Expect = 2e-04
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 12/64 (18%)
Query: 604 DKIT-EELKEH----FSKYGEI-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVED 655
+KI +ELK FS++G + + V K+ + RG AF+VFKD ES A +++
Sbjct: 9 EKIKKDELKRSLYALFSQFGPVLDIVASKTL----KMRGQAFVVFKDVESATNALRALQG 64
Query: 656 VYFY 659
FY
Sbjct: 65 FPFY 68
Score = 37.9 bits (89), Expect = 0.001
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 10/53 (18%)
Query: 111 KIT-EELKEH----FSKYGEI-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
KI +ELK FS++G + + V K+ + RG AF+VFKD ES A
Sbjct: 10 KIKKDELKRSLYALFSQFGPVLDIVASKTL----KMRGQAFVVFKDVESATNA 58
>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 = 40.5 bits (95), Expect = 2e-04
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 112 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEG-NHVI 170
+ + EHFSKYG + V + D R R +AF+ F + + + A +A+G ++
Sbjct: 19 LEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNA-----LAKGQGTIL 70
Query: 171 NNKKIEAKKAKA 182
+ + I ++AK
Sbjct: 71 DGRHIRCERAKV 82
Score = 35.5 bits (82), Expect = 0.009
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
D++ + EHFSKYG + V + D R R +AF+ F + + + A +
Sbjct: 17 DELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNALAK 64
>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 = 40.4 bits (95), Expect = 2e-04
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L+E F+ +GEI+++ + D T S+G A++ F S +A
Sbjct: 17 DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60
Score = 40.4 bits (95), Expect = 2e-04
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L+E F+ +GEI+++ + D T S+G A++ F S +A
Sbjct: 17 DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60
Score = 28.8 bits (65), Expect = 2.0
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 196 MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
+ +++++ FA FG I + + DK + K ++ F S
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKAS 55
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
or Set1 complex component, is encoded by SET1 from the
fission yeast S. pombe. It is essential for the H3
lysine-4 methylation. in vivo, and plays an important
role in telomere maintenance and DNA repair in an ATM
kinase Rad3-dependent pathway. spSet1p is the homology
counterpart of Saccharomyces cerevisiae Set1p (scSet1p).
However, it is more closely related to Set1 found in
mammalian. Moreover, unlike scSet1p, spSet1p is not
required for heterochromatin assembly in fission yeast.
spSet1p contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 86
Score = 40.4 bits (95), Expect = 2e-04
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
++++ HF +GEIE LK DP TG+S G + F+
Sbjct: 13 KQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPL 52
Score = 40.4 bits (95), Expect = 2e-04
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
++++ HF +GEIE LK DP TG+S G + F+
Sbjct: 13 KQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPL 52
Score = 35.0 bits (81), Expect = 0.012
Identities = 18/49 (36%), Positives = 25/49 (51%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
I + GLSP ++I+ HF FG I E+E+ D Q C +TF
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRG 49
>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 = 39.9 bits (93), Expect = 2e-04
Identities = 13/48 (27%), Positives = 28/48 (58%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
K+FVG + + ++E++ F + GN++E + DK ++ CF+ +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKY 48
Score = 31.1 bits (70), Expect = 0.27
Identities = 10/44 (22%), Positives = 23/44 (52%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+E++ F ++G + V + D TG +G F+ + + ++A
Sbjct: 14 QEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRA 57
Score = 31.1 bits (70), Expect = 0.27
Identities = 10/44 (22%), Positives = 23/44 (52%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+E++ F ++G + V + D TG +G F+ + + ++A
Sbjct: 14 QEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRA 57
>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 = 39.9 bits (94), Expect = 2e-04
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 158
+EEL + F KYG I + + + T RG AF+V++D + A
Sbjct: 16 SEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNAC 58
Score = 39.9 bits (94), Expect = 2e-04
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
+EEL + F KYG I + + + T RG AF+V++D + A
Sbjct: 16 SEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNAC 58
>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 = 39.3 bits (92), Expect = 3e-04
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 12/68 (17%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRG-FAFIVFKDTESLEKASVEDVIAEGNHVINN 172
E+L ++FS +G + NV + D +G +A + F E ++K V++E H +N
Sbjct: 17 EQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDK-----VLSEPQHTLNG 65
Query: 173 KKIEAKKA 180
++ +
Sbjct: 66 HRLRVRPR 73
Score = 35.8 bits (83), Expect = 0.005
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FV G +E++ +F+ FG ++ M DK + + + F+ + V +L P
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIM--DK---DKGVYAIVEFDSKEGVDKVLSEP 59
Query: 247 KQKINDKEVDVKKA 260
+ +N + V+
Sbjct: 60 QHTLNGHRLRVRPR 73
Score = 34.7 bits (80), Expect = 0.013
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRG-FAFIVFKDTESLEKA 651
E+L ++FS +G + NV + D +G +A + F E ++K
Sbjct: 17 EQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDKV 55
>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 = 39.7 bits (93), Expect = 3e-04
Identities = 23/53 (43%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV 239
+FVGGL +E I+ F Q G II M SK KNFC I F E V
Sbjct: 9 VFVGGLPENATEEIIREVFEQCGEIIAIRM----SK---KNFCHIRFAEEFAV 54
>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 = 39.2 bits (92), Expect = 3e-04
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L+E F + GE+ +V + D + GRS+GF + F E +KA
Sbjct: 14 DDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKA 56
Score = 39.2 bits (92), Expect = 3e-04
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L+E F + GE+ +V + D + GRS+GF + F E +KA
Sbjct: 14 DDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKA 56
Score = 34.2 bits (79), Expect = 0.021
Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FVG LS + ++++ F + G +++ + D K F + F E L+
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRS-KGFGHVEFATEEGAQKALEKS 60
Query: 247 KQKINDKEVDVKKATPK 263
+++ +E+ V AT +
Sbjct: 61 GEELLGREIRVDLATER 77
>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 = 38.7 bits (91), Expect = 4e-04
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 12/71 (16%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVG L EE++A F ++G + E ++ KN+ F+ E E D +K
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDV--------VKNYGFVHMEEEEDAEDAIKA 52
Query: 246 PKQKINDKEVD 256
+N E
Sbjct: 53 ----LNGYEFM 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 = 39.2 bits (92), Expect = 4e-04
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+I+V + P++ +++IK+ F FG I + D + K + FI +E
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYE 50
Score = 35.7 bits (83), Expect = 0.007
Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 109 VHKITEE--LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
VH E +K F +G+I++ +L DP TG+ +G+ FI +++ +S + A
Sbjct: 8 VHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDA 58
Score = 35.7 bits (83), Expect = 0.007
Identities = 14/44 (31%), Positives = 30/44 (68%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+++K F +G+I++ +L DP TG+ +G+ FI +++ +S + A
Sbjct: 15 DDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDA 58
>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 = 38.7 bits (91), Expect = 4e-04
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 12/63 (19%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+L+E FSKYG+I ++L +G+ F+ F + E A V E I +
Sbjct: 16 EDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAA----VAGENGREIAGQ 63
Query: 174 KIE 176
K++
Sbjct: 64 KLD 66
Score = 36.0 bits (84), Expect = 0.004
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 9/50 (18%)
Query: 603 VDKIT-EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
DK++ E+L+E FSKYG+I ++L +G+ F+ F + E A
Sbjct: 10 TDKVSKEDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAA 51
Score = 30.7 bits (70), Expect = 0.36
Identities = 12/52 (23%), Positives = 29/52 (55%), Gaps = 9/52 (17%)
Query: 186 KIFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
++FVG L+ + + E+++ F+++G I+ + K + F+ F++E
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNE 45
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 41.7 bits (98), Expect = 4e-04
Identities = 22/32 (68%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
GGRGG GG GG GG G GG GG GGGYGG
Sbjct: 109 GGRGGSGG-GGGGGDEGGYGGGGGGGGGGYGG 139
Score = 35.5 bits (82), Expect = 0.037
Identities = 17/33 (51%), Positives = 17/33 (51%)
Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
GG GG GG GG GG GG GGG GG
Sbjct: 128 GGGGGGGGGYGGESRSGGGGGRASGGGGGGAGG 160
Score = 35.5 bits (82), Expect = 0.038
Identities = 17/32 (53%), Positives = 17/32 (53%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GG GG GG GG G GG GGG GG
Sbjct: 126 YGGGGGGGGGGYGGESRSGGGGGRASGGGGGG 157
Score = 35.5 bits (82), Expect = 0.042
Identities = 19/35 (54%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGE 536
G RGG GG GG G GG GG GG GG GG
Sbjct: 109 GGRGGSGGGGGGGDEGG-YGGGGGGGGGGYGGESR 142
Score = 34.4 bits (79), Expect = 0.091
Identities = 17/32 (53%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 505 GGRGGRGGRGGRGGRM-AGGYGGYGGYGGGYG 535
G GG GG GG GG +GG GG GGG G
Sbjct: 126 YGGGGGGGGGGYGGESRSGGGGGRASGGGGGG 157
Score = 33.6 bits (77), Expect = 0.15
Identities = 17/35 (48%), Positives = 17/35 (48%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GG GG GG G R GG G G GGG G
Sbjct: 125 GYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAG 159
Score = 33.6 bits (77), Expect = 0.18
Identities = 15/32 (46%), Positives = 15/32 (46%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
GG GG G G GG GG G GG GG
Sbjct: 117 GGGGGDEGGYGGGGGGGGGGYGGESRSGGGGG 148
Score = 33.2 bits (76), Expect = 0.22
Identities = 16/32 (50%), Positives = 16/32 (50%)
Query: 504 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
GG GG GG GG GG GG GGG G
Sbjct: 128 GGGGGGGGGYGGESRSGGGGGRASGGGGGGAG 159
Score = 32.8 bits (75), Expect = 0.32
Identities = 17/32 (53%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 299
G GG GG GG GGR +GG GG G GG
Sbjct: 132 GGGGGYGGESRSGGGGGRASGG-GGGGAGGGA 162
Score = 32.8 bits (75), Expect = 0.32
Identities = 17/32 (53%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 533
G GG GG GG GGR +GG GG G GG
Sbjct: 132 GGGGGYGGESRSGGGGGRASGG-GGGGAGGGA 162
Score = 31.7 bits (72), Expect = 0.64
Identities = 19/35 (54%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGGY---GGYGGGYGG 302
GG G GG GG GG GGYGG GG GG G
Sbjct: 118 GGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASG 152
Score = 31.7 bits (72), Expect = 0.76
Identities = 17/48 (35%), Positives = 19/48 (39%), Gaps = 8/48 (16%)
Query: 499 EPFGVRGGRGGRGGRGGRGGRMAGGYGGYGG--------YGGGYGELD 538
G G G GG G GG GG GG GGG+ E+D
Sbjct: 130 GGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAPAGGGFDEMD 177
Score = 31.7 bits (72), Expect = 0.83
Identities = 14/31 (45%), Positives = 14/31 (45%)
Query: 505 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
GG GG G G GG GG G GG G
Sbjct: 117 GGGGGDEGGYGGGGGGGGGGYGGESRSGGGG 147
Score = 31.3 bits (71), Expect = 0.88
Identities = 15/35 (42%), Positives = 15/35 (42%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GG GG G R G G G GG G G G
Sbjct: 128 GGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGA 162
Score = 31.3 bits (71), Expect = 1.1
Identities = 17/39 (43%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 268 GVRGGRGGRGGRGGRGGR----MAGGYGGYGGYGGGYGG 302
G G G GG GG GG +GG GG GGG G
Sbjct: 120 GGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGA 158
Score = 30.9 bits (70), Expect = 1.5
Identities = 15/34 (44%), Positives = 15/34 (44%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G GG GG G R G G G GG G G G
Sbjct: 128 GGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGG 161
Score = 30.5 bits (69), Expect = 1.8
Identities = 18/31 (58%), Positives = 18/31 (58%)
Query: 505 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
GG G GG GG GG GGYGG GGG G
Sbjct: 118 GGGGDEGGYGGGGGGGGGGYGGESRSGGGGG 148
Score = 29.0 bits (65), Expect = 5.7
Identities = 12/31 (38%), Positives = 12/31 (38%)
Query: 265 EPFGVRGGRGGRGGRGGRGGRMAGGYGGYGG 295
G G G GG G GG GG GG
Sbjct: 130 GGGGGGGYGGESRSGGGGGRASGGGGGGAGG 160
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 40.0 bits (94), Expect = 4e-04
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
+K +FS +GEI + +DPNT G I + +
Sbjct: 18 IIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPG 56
Score = 40.0 bits (94), Expect = 4e-04
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
+K +FS +GEI + +DPNT G I + +
Sbjct: 18 IIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPG 56
Score = 28.1 bits (63), Expect = 5.5
Identities = 14/55 (25%), Positives = 21/55 (38%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVID 241
I V G P ++ IK +F+ FG I E D + + I + D
Sbjct: 5 IVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPD 59
>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 = 39.6 bits (92), Expect = 4e-04
Identities = 19/48 (39%), Positives = 28/48 (58%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
D +E+L+ F +YG I +V + D T R RGFA++ F+D E A
Sbjct: 11 DTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDA 58
Score = 39.2 bits (91), Expect = 5e-04
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+E+L+ F +YG I +V + D T R RGFA++ F+D E A
Sbjct: 14 SEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDA 58
Score = 36.1 bits (83), Expect = 0.005
Identities = 17/75 (22%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FV ++ + + E+++ F ++G I++ +P D + + F ++ FE D L N
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 247 KQK-INDKEVDVKKA 260
+K I ++++++ A
Sbjct: 63 DRKWICGRQIEIQFA 77
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 39.3 bits (91), Expect = 4e-04
Identities = 17/43 (39%), Positives = 28/43 (65%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L+E FS G++ +V + SD N+ RS+G A++ F D S+ A
Sbjct: 17 DLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLA 59
Score = 39.3 bits (91), Expect = 4e-04
Identities = 17/43 (39%), Positives = 28/43 (65%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L+E FS G++ +V + SD N+ RS+G A++ F D S+ A
Sbjct: 17 DLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLA 59
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 39.0 bits (91), Expect = 4e-04
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 187 IFVGGLSPE-MKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+FV G P ++E+I+ F FG ++ ++ RK F F+ FE L+
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEA 53
Query: 246 -PKQKINDKEVDVKKAT 261
+I+ + V+
Sbjct: 54 LHGSRIDGSVLTVEFVK 70
Score = 31.6 bits (72), Expect = 0.15
Identities = 11/45 (24%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E++++ F +G + ++ + FAF+ F+D+E KA
Sbjct: 14 EEDIEKLFEPFGPLVRCDIR--------KTFAFVEFEDSEDATKA 50
Score = 31.6 bits (72), Expect = 0.15
Identities = 11/45 (24%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E++++ F +G + ++ + FAF+ F+D+E KA
Sbjct: 14 EEDIEKLFEPFGPLVRCDIR--------KTFAFVEFEDSEDATKA 50
>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 = 38.8 bits (91), Expect = 4e-04
Identities = 18/45 (40%), Positives = 33/45 (73%), Gaps = 1/45 (2%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL++ FSK GEI +V L + G+S+G+A++ F++ ES+++A
Sbjct: 13 EDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA 56
Score = 38.8 bits (91), Expect = 4e-04
Identities = 18/45 (40%), Positives = 33/45 (73%), Gaps = 1/45 (2%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL++ FSK GEI +V L + G+S+G+A++ F++ ES+++A
Sbjct: 13 EDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA 56
Score = 32.6 bits (75), Expect = 0.062
Identities = 16/67 (23%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FV L + ++E++ F++ G I + + + K + K + ++ FE+E V + LK
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEALKLD 60
Query: 247 KQKINDK 253
++ I +
Sbjct: 61 RELIKGR 67
>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 = 39.0 bits (91), Expect = 5e-04
Identities = 20/80 (25%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+IFVGG+ + + +++ F+Q+G + E ++ D++ K + F+TFE + +L+
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRA-GVSKGYGFVTFETQEDAQKILQE 62
Query: 246 PKQKIN--DKEVDVKKATPK 263
++ DK++++ +A K
Sbjct: 63 AN-RLCFRDKKLNIGQAIRK 81
Score = 32.9 bits (75), Expect = 0.073
Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 156
GI K E +L++ FS+YG ++ V + +D G S+G+ F+ F+ E +K
Sbjct: 9 GIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQK 58
Score = 32.1 bits (73), Expect = 0.13
Identities = 18/51 (35%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
GI K E +L++ FS+YG ++ V + +D G S+G+ F+ F+ E +K
Sbjct: 9 GIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQK 58
>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 = 38.7 bits (90), Expect = 6e-04
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+LK+ F +YG++ T+ G+ GFAF+ K ++ E A
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIA 58
Score = 38.7 bits (90), Expect = 6e-04
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+LK+ F +YG++ T+ G+ GFAF+ K ++ E A
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIA 58
Score = 27.9 bits (62), Expect = 3.6
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 197 KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVD 256
K ++K F ++G + E +P + + F F+T + L+N N E+D
Sbjct: 14 KPVKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALEN----TNGLEID 68
Query: 257 VKK 259
+
Sbjct: 69 GRP 71
>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 = 6e-04
Identities = 20/44 (45%), Positives = 26/44 (59%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EELK F GEIE+ L D TG+S G+ F+ + D + EKA
Sbjct: 19 EELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62
Score = 38.9 bits (90), Expect = 6e-04
Identities = 20/44 (45%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EELK F GEIE+ L D TG+S G+ F+ + D + EKA
Sbjct: 19 EELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62
>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 = 38.6 bits (90), Expect = 6e-04
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
IFVG LSPE+ D + A F+ F + + + +D + + + F++F
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSF 48
Score = 37.1 bits (86), Expect = 0.002
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
L FS + + + D +GRSRG+ F+ F+ + E A
Sbjct: 14 ATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENA 57
Score = 37.1 bits (86), Expect = 0.002
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
L FS + + + D +GRSRG+ F+ F+ + E A
Sbjct: 14 ATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENA 57
>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 = 38.3 bits (90), Expect = 7e-04
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
++V P +I+ F Q+G I+ P + R+ FC++ F
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRR-FCYVQFTSPE 52
Score = 31.8 bits (73), Expect = 0.14
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 7/66 (10%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN-HVINN 172
++++ F +YGEI ++ S ++R F ++ F ES A +A N +
Sbjct: 15 SDIRDLFEQYGEILSIRFPSL-RFNKTRRFCYVQFTSPESAAAA-----VALLNGKLGEG 68
Query: 173 KKIEAK 178
K+ K
Sbjct: 69 YKLVVK 74
Score = 30.6 bits (70), Expect = 0.41
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++++ F +YGEI ++ S ++R F ++ F ES A
Sbjct: 15 SDIRDLFEQYGEILSIRFPSL-RFNKTRRFCYVQFTSPESAAAA 57
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 38.4 bits (90), Expect = 7e-04
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 594 NKMVSHPGIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
V G+ + +TE+ L HFS+YG + +V + R RG A + F E+ + A
Sbjct: 7 TNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVID------RQRGQALVFFDKVEAAQAA 59
Score = 36.5 bits (85), Expect = 0.004
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 100 NKMVSHPGIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
V G+ +TE+ L HFS+YG + +V + R RG A + F E+ + A
Sbjct: 7 TNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVID------RQRGQALVFFDKVEAAQAA 59
>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 = 38.5 bits (89), Expect = 7e-04
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+L+ F +YG I +V + D T R RGFA+I F+D E A
Sbjct: 15 EDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDA 58
Score = 38.5 bits (89), Expect = 7e-04
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+L+ F +YG I +V + D T R RGFA+I F+D E A
Sbjct: 15 EDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDA 58
Score = 31.1 bits (70), Expect = 0.36
Identities = 16/63 (25%), Positives = 32/63 (50%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FV ++ + E+++ F ++G I++ +P D + + F +I FE D L N
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 247 KQK 249
+K
Sbjct: 63 NRK 65
>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 = 38.3 bits (89), Expect = 7e-04
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
+F+ L E D E+ F FGN+I ++ D++ +Q K F F++F++
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDN 55
>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 = 38.5 bits (90), Expect = 7e-04
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 115 ELKEHFSKYGEIENVTLKSDPN-TGRSRGFAFIVFKDTESLEKA 157
EL+E FS +GE++ V L TG RGF F+ F + ++A
Sbjct: 16 ELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59
Score = 38.5 bits (90), Expect = 7e-04
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 609 ELKEHFSKYGEIENVTLKSDPN-TGRSRGFAFIVFKDTESLEKA 651
EL+E FS +GE++ V L TG RGF F+ F + ++A
Sbjct: 16 ELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 38.7 bits (91), Expect = 8e-04
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 603 VDKITEELKEHFSKYGEIENVTL---KSDPNTGRSRGFAFIVFKDTESLEKA 651
++I E++KE KYG++ +V + +++ G F+ F D E +KA
Sbjct: 21 YEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKA 72
Score = 38.3 bits (90), Expect = 0.001
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 112 ITEELKEHFSKYGEIENVTL---KSDPNTGRSRGFAFIVFKDTESLEKA 157
I E++KE KYG++ +V + +++ G F+ F D E +KA
Sbjct: 24 ILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKA 72
>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 = 38.3 bits (89), Expect = 8e-04
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 112 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVIAEG 166
+TE EL++ F YG I L D +TG RG AF+ + E + A S+ I G
Sbjct: 12 LTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPG 69
Score = 36.8 bits (85), Expect = 0.003
Identities = 18/47 (38%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 606 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+TE EL++ F YG I L D +TG RG AF+ + E + A
Sbjct: 12 LTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAA 58
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p 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. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal Rrp7 domain. .
Length = 102
Score = 38.8 bits (91), Expect = 8e-04
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 16/61 (26%)
Query: 113 TEE-LKEHFSKYGEIENVTLKSDPNTGRS-------------RGF--AFIVFKDTESLEK 156
TEE LK FS+ G++E+V L+ P S +GF A++VFK SL +
Sbjct: 13 TEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVAYVVFKKPSSLSR 72
Query: 157 A 157
A
Sbjct: 73 A 73
Score = 38.8 bits (91), Expect = 8e-04
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 16/61 (26%)
Query: 607 TEE-LKEHFSKYGEIENVTLKSDPNTGRS-------------RGF--AFIVFKDTESLEK 650
TEE LK FS+ G++E+V L+ P S +GF A++VFK SL +
Sbjct: 13 TEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVAYVVFKKPSSLSR 72
Query: 651 A 651
A
Sbjct: 73 A 73
>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 = 38.3 bits (90), Expect = 9e-04
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 110 HKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
TEE + E FS+ G+I+ + + D T GF F+ + E E A
Sbjct: 8 FYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENA 56
Score = 37.9 bits (89), Expect = 0.001
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 607 TEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
TEE + E FS+ G+I+ + + D T GF F+ + E E A
Sbjct: 11 TEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENA 56
Score = 36.0 bits (84), Expect = 0.006
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
++VG LS +E+I F++ G+I M D+ FCF+ +
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYT 49
>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 = 38.0 bits (89), Expect = 0.001
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EL++ F KYG + +V + +P GFAF+ F+D E A
Sbjct: 14 RELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDA 52
Score = 38.0 bits (89), Expect = 0.001
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EL++ F KYG + +V + +P GFAF+ F+D E A
Sbjct: 14 RELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDA 52
Score = 28.4 bits (64), Expect = 2.3
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 11/53 (20%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKN---FCFITFEH 235
K++VG L P E++ F ++G + +S +N F F+ FE
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPL--------RSVWVARNPPGFAFVEFED 45
>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 = 38.0 bits (88), Expect = 0.001
Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 24/82 (29%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
+EL++ FS+YG I + D TG SRG FI F +K
Sbjct: 15 KELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRF-----------------------DK 51
Query: 174 KIEAKKA-KAKSGKIFVGGLSP 194
+IEA++A K +G+ G P
Sbjct: 52 RIEAEEAIKGLNGQKPEGASEP 73
Score = 37.6 bits (87), Expect = 0.002
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL++ FS+YG I + D TG SRG FI F E+A
Sbjct: 15 KELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEA 58
Score = 31.4 bits (71), Expect = 0.22
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++V GL M +E++ F+Q+G II + + D+ + FI F+
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFD 50
>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 = 37.6 bits (88), Expect = 0.001
Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 23/78 (29%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+L+E FS+ G I+ + D + + RGF ++ F A ED
Sbjct: 14 EQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF--------ALEED------------ 53
Query: 174 KIEAKKAKAKSGKIFVGG 191
AK+A + K GG
Sbjct: 54 ---AKRALEEKKKTKFGG 68
Score = 34.5 bits (80), Expect = 0.016
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+L+E FS+ G I+ + D + + RGF ++ F E ++A
Sbjct: 14 EQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRA 57
Score = 33.7 bits (78), Expect = 0.030
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
+FV L + DE+++ F++ G I + DK + + F ++TF
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF 48
>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 = 37.6 bits (88), Expect = 0.001
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 105 HPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
H + E+L+E F + GE++ V + D +GRS G A +VF+ E E+A
Sbjct: 9 HYDV---TEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERA 57
Score = 37.6 bits (88), Expect = 0.001
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 599 HPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
H + E+L+E F + GE++ V + D +GRS G A +VF+ E E+A
Sbjct: 9 HYDV---TEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERA 57
>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 = 37.3 bits (87), Expect = 0.001
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++FVG L ++ +EE K F+++G + E + + K F FI +
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLN------KEKGFGFIRLD 45
Score = 36.9 bits (86), Expect = 0.002
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
EE KE FSKYGE+ V L + +GF FI + EKA E
Sbjct: 16 EEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56
Score = 36.9 bits (86), Expect = 0.002
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
EE KE FSKYGE+ V L + +GF FI + EKA E
Sbjct: 16 EEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 38.0 bits (89), Expect = 0.001
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 593 KNKMVSHPGIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ V+ + D I E LK+ KYGE+E V + P T + G A +VF +S ++
Sbjct: 1 PPREVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRC 60
Score = 34.2 bits (79), Expect = 0.034
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
LK+ KYGE+E V + P T + G A +VF +S ++
Sbjct: 19 LKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRC 60
>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 = 37.7 bits (87), Expect = 0.002
Identities = 19/48 (39%), Positives = 28/48 (58%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
D +EL F K G I ++ L DP TG +RG+AF+ F E+ ++A
Sbjct: 12 DLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEA 59
Score = 36.5 bits (84), Expect = 0.003
Identities = 18/44 (40%), Positives = 27/44 (61%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL F K G I ++ L DP TG +RG+AF+ F E+ ++A
Sbjct: 16 DELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEA 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 = 37.3 bits (87), Expect = 0.002
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
++V GL M +E++A F+ +G II + + D + FI F+
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDK 51
Score = 36.5 bits (85), Expect = 0.003
Identities = 27/82 (32%), Positives = 35/82 (42%), Gaps = 24/82 (29%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
+EL+ FS YG I + D TG SRG FI F +K
Sbjct: 15 QELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF-----------------------DK 51
Query: 174 KIEAKKA-KAKSGKIFVGGLSP 194
+IEA++A KA +G I G P
Sbjct: 52 RIEAERAIKALNGTIPPGATEP 73
Score = 35.4 bits (82), Expect = 0.009
Identities = 18/44 (40%), Positives = 22/44 (50%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL+ FS YG I + D TG SRG FI F E+A
Sbjct: 15 QELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERA 58
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with wild
type of survival motor neuron (SMN) proteins directly,
further providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, and in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; it binds RNA
through its RRM domains. .
Length = 79
Score = 37.6 bits (87), Expect = 0.002
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
D +EL F K G I ++ L DP +G++RG+AFI F E+ ++A
Sbjct: 12 DLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59
Score = 36.9 bits (85), Expect = 0.003
Identities = 18/44 (40%), Positives = 28/44 (63%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL F K G I ++ L DP +G++RG+AFI F E+ ++A
Sbjct: 16 DELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 37.2 bits (87), Expect = 0.002
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ F++ GE+ +V + + TG+S G+ F+ F E+ E+A
Sbjct: 14 AYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQA 57
Score = 37.2 bits (87), Expect = 0.002
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ F++ GE+ +V + + TG+S G+ F+ F E+ E+A
Sbjct: 14 AYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQA 57
Score = 32.2 bits (74), Expect = 0.10
Identities = 11/48 (22%), Positives = 24/48 (50%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+++G L P M + I + FA+ G + ++ +K + + F+ F
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFA 49
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 36.8 bits (86), Expect = 0.002
Identities = 12/50 (24%), Positives = 25/50 (50%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
++VG L ++ +E + F Q G ++ +P D+ + + F+ F E
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSE 50
Score = 27.9 bits (63), Expect = 2.9
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ +K+TEE L E F + G + NV + D T +G+ F+ F E + A
Sbjct: 5 NLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYA 56
Score = 27.2 bits (61), Expect = 6.1
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 111 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
K+TEE L E F + G + NV + D T +G+ F+ F E + A
Sbjct: 9 KVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYA 56
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 36.5 bits (85), Expect = 0.003
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 108 IVHK-ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
+V K +T+E L F +E LK DP TG+S+GFA++ + + S
Sbjct: 6 VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPAS 53
Score = 35.8 bits (83), Expect = 0.006
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 602 IVDK-ITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
+V K +T+E L F +E LK DP TG+S+GFA++ + + S
Sbjct: 6 VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPAS 53
>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 = 36.5 bits (85), Expect = 0.003
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 16/68 (23%)
Query: 110 HKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH 168
+ +TEE LK+ FS +G I N++++ + N G F+ F+ ES ++A IAE
Sbjct: 12 YGLTEEILKKAFSPFGNIINISMEKEKNCG------FVTFEKMESADRA-----IAE--- 57
Query: 169 VINNKKIE 176
+N ++
Sbjct: 58 -LNGTTVQ 64
Score = 34.6 bits (80), Expect = 0.017
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 7/51 (13%)
Query: 605 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
+TEE LK+ FS +G I N++++ + N G F+ F+ ES ++A E
Sbjct: 13 GLTEEILKKAFSPFGNIINISMEKEKNCG------FVTFEKMESADRAIAE 57
Score = 28.8 bits (65), Expect = 1.7
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 10/44 (22%)
Query: 191 GLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
GL+ E+ +K F+ FGNII M + KN F+TFE
Sbjct: 13 GLTEEI----LKKAFSPFGNIINISM------EKEKNCGFVTFE 46
>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 = 36.4 bits (85), Expect = 0.003
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 14/71 (19%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN-HVIN 171
E+L+E FS+YGE+E V D +AF+ F++ + KA + E N +
Sbjct: 15 EEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKA-----MEEMNGKELE 61
Query: 172 NKKIEAKKAKA 182
IE AK
Sbjct: 62 GSPIEVSLAKP 72
Score = 36.1 bits (84), Expect = 0.004
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 9/51 (17%)
Query: 602 IVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ TEE L+E FS+YGE+E V D +AF+ F++ + KA
Sbjct: 9 LPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKA 51
>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 = 36.9 bits (85), Expect = 0.003
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 110 HKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV 159
H ++E EL+ F KYG IE V +K P G+ +AF+ F++ + +A V
Sbjct: 18 HNVSEVELRRAFDKYGIIEEVVIKR-PARGQGGAYAFLKFQNLDMAHRAKV 67
Score = 33.8 bits (77), Expect = 0.035
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 606 ITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASV 653
++E EL+ F KYG IE V +K P G+ +AF+ F++ + +A V
Sbjct: 20 VSEVELRRAFDKYGIIEEVVIKR-PARGQGGAYAFLKFQNLDMAHRAKV 67
>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 = 36.5 bits (85), Expect = 0.003
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 601 GIVDKITEE--LKEHFSKYGEI-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G +D +E L + FS +G I + + DP+TG S+GFAFI + E+ + A
Sbjct: 7 GNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60
Score = 36.1 bits (84), Expect = 0.005
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 116 LKEHFSKYGEI-ENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK 174
L + FS +G I + + DP+TG S+GFAFI + E+ + A + A + N+
Sbjct: 18 LYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA----IEAMNGQYLCNRP 73
Query: 175 I 175
I
Sbjct: 74 I 74
Score = 34.6 bits (80), Expect = 0.018
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIET-EMPYDKSKSQRKNFCFITF 233
+F+G L PE+ ++ + F+ FG I++T ++ D K F FI++
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY 51
>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 = 36.1 bits (84), Expect = 0.004
Identities = 17/37 (45%), Positives = 25/37 (67%), Gaps = 5/37 (13%)
Query: 114 EELKEHFSKYGEIENVTL--KSDPNTGRSRGFAFIVF 148
+EL+E FS +G++++V L K D G RGFAF+ F
Sbjct: 15 KELRELFSPFGQVKSVRLPKKFD---GSHRGFAFVEF 48
Score = 36.1 bits (84), Expect = 0.004
Identities = 17/37 (45%), Positives = 25/37 (67%), Gaps = 5/37 (13%)
Query: 608 EELKEHFSKYGEIENVTL--KSDPNTGRSRGFAFIVF 642
+EL+E FS +G++++V L K D G RGFAF+ F
Sbjct: 15 KELRELFSPFGQVKSVRLPKKFD---GSHRGFAFVEF 48
Score = 29.9 bits (68), Expect = 0.78
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
K+ V + E +E++ F+ FG + +P K + F F+ F
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLP-KKFDGSHRGFAFVEF 48
>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 = 36.2 bits (83), Expect = 0.004
Identities = 18/44 (40%), Positives = 25/44 (56%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EE + F GEIE+ L D TG+S G+ F+ + D + EKA
Sbjct: 17 EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Score = 36.2 bits (83), Expect = 0.004
Identities = 18/44 (40%), Positives = 25/44 (56%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EE + F GEIE+ L D TG+S G+ F+ + D + EKA
Sbjct: 17 EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
>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 = 35.7 bits (83), Expect = 0.005
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
LK+ F + G + +K+D + GRS+GF ++F+ E ++A
Sbjct: 15 LKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRA 55
Score = 35.7 bits (83), Expect = 0.005
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
LK+ F + G + +K+D + GRS+GF ++F+ E ++A
Sbjct: 15 LKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRA 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 = 36.0 bits (84), Expect = 0.005
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH-VINN 172
E L FSKY + + D TG+S+G+ F+ F D KA + E N + N
Sbjct: 21 EVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKA-----MKEMNGKYVGN 75
Query: 173 KKIEAKKA 180
+ I+ +K+
Sbjct: 76 RPIKLRKS 83
Score = 35.3 bits (82), Expect = 0.009
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E L FSKY + + D TG+S+G+ F+ F D KA
Sbjct: 21 EVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKA 64
Score = 34.9 bits (81), Expect = 0.016
Identities = 17/76 (22%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+IFVG L E+ DE + F+++ + + ++ DK + K + F++F + + +K
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67
Query: 246 PKQK-INDKEVDVKKA 260
K + ++ + ++K+
Sbjct: 68 MNGKYVGNRPIKLRKS 83
>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 = 0.005
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNF---CFITFEHESVVIDLL 243
++V G + ++I+ F +FG + M D K F F+ F+ E L
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDL----DKKFKGSVFVEFKTEEDAKKFL 57
Query: 244 KNPKQKINDKEVDVK 258
+ K K +KE+ V
Sbjct: 58 EKEKLKYKEKELTVM 72
Score = 31.8 bits (73), Expect = 0.13
Identities = 13/47 (27%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
D ++++E F K+G++ N+ ++ D + + +G F+ FK E +K
Sbjct: 10 DATLDDIQEFFEKFGKVNNIRMRRDLD-KKFKGSVFVEFKTEEDAKK 55
Score = 31.0 bits (71), Expect = 0.29
Identities = 12/43 (27%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 156
++++E F K+G++ N+ ++ D + + +G F+ FK E +K
Sbjct: 14 DDIQEFFEKFGKVNNIRMRRDLD-KKFKGSVFVEFKTEEDAKK 55
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable
RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 36.2 bits (83), Expect = 0.005
Identities = 15/43 (34%), Positives = 29/43 (67%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L++ FS G++ +V + SD N+ RS+G A++ F + +S+ A
Sbjct: 17 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 59
Score = 36.2 bits (83), Expect = 0.005
Identities = 15/43 (34%), Positives = 29/43 (67%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L++ FS G++ +V + SD N+ RS+G A++ F + +S+ A
Sbjct: 17 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 59
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 36.0 bits (84), Expect = 0.006
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
D+I E++ E SK+G +E++ + D N+ G ++ FK E+ +K
Sbjct: 22 DEIKEDVLEECSKFGPVEHIKV--DKNS--PEGVVYVKFKTVEAAQKCI 66
Score = 35.2 bits (82), Expect = 0.010
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 112 ITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 158
I E++ E SK+G +E++ + D N+ G ++ FK E+ +K
Sbjct: 24 IKEDVLEECSKFGPVEHIKV--DKNS--PEGVVYVKFKTVEAAQKCI 66
>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 = 35.7 bits (82), Expect = 0.006
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
S ++FVG L ++ E+K F Q+GN++E + S + NF F+ F+ V +L
Sbjct: 3 SHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQKIL 59
Query: 244 KN 245
N
Sbjct: 60 SN 61
Score = 34.1 bits (78), Expect = 0.029
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 600 PGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
P VDK ELKE F +YG + + + S G+ F F+VF D+E ++K
Sbjct: 12 PHDVDK--SELKEFFQQYGNVVELRINSG---GKLPNFGFVVFDDSEPVQK 57
Score = 32.2 bits (73), Expect = 0.11
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 156
ELKE F +YG + + + S G+ F F+VF D+E ++K
Sbjct: 19 ELKEFFQQYGNVVELRINSG---GKLPNFGFVVFDDSEPVQK 57
>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 = 35.6 bits (82), Expect = 0.007
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+FVG LS + + +++ FA FG+I E + D++ Q + F+TF ++ +K
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQCALNAIKA 61
Query: 246 PKQ 248
Sbjct: 62 MHH 64
Score = 35.2 bits (81), Expect = 0.011
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
+++ F+ +G IE T+ D N G+SRG AF+ F +
Sbjct: 16 NDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQC 54
Score = 35.2 bits (81), Expect = 0.011
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
+++ F+ +G IE T+ D N G+SRG AF+ F +
Sbjct: 16 NDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQC 54
>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of
uncharacterized plant proteins similar to fission yeast
Vip1. This subfamily corresponds to the Vip1-like,
uncharacterized proteins found in plants. Although their
biological roles remain unclear, these proteins show
high sequence similarity to the fission yeast Vip1. Like
Vip1 protein, members in this family contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 69
Score = 35.1 bits (81), Expect = 0.007
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ K TE ++ + FS G+IE V ++ G A++ FKD ++ E A
Sbjct: 5 NLSPKATERDIYDFFSFSGDIEYVEIQRS---GEQSQTAYVTFKDPQAQETA 53
Score = 34.7 bits (80), Expect = 0.013
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 111 KITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
K TE ++ + FS G+IE V ++ G A++ FKD ++ E A
Sbjct: 9 KATERDIYDFFSFSGDIEYVEIQRS---GEQSQTAYVTFKDPQAQETA 53
>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 = 35.5 bits (82), Expect = 0.007
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 5/46 (10%)
Query: 114 EELKEHFSKYGEIENVTL--KSDPNTGRSRGFAFIVFKDTESLEKA 157
E + EHF +YG +E+V + K + G + AF+ F D +S +KA
Sbjct: 14 ERISEHFKRYGRVESVKILPKRGSDGGVA---AFVDFVDIKSAQKA 56
Score = 35.5 bits (82), Expect = 0.007
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 5/46 (10%)
Query: 608 EELKEHFSKYGEIENVTL--KSDPNTGRSRGFAFIVFKDTESLEKA 651
E + EHF +YG +E+V + K + G + AF+ F D +S +KA
Sbjct: 14 ERISEHFKRYGRVESVKILPKRGSDGGVA---AFVDFVDIKSAQKA 56
Score = 29.7 bits (67), Expect = 0.83
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNI 211
++VG L +++E I HF ++G +
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRV 26
>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 = 35.6 bits (83), Expect = 0.008
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 17/76 (22%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK 174
L + FS +G I + + +D N G S+G+ F+ F+ E+ +A I + N ++ N K
Sbjct: 18 ALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRA-----IEKVNGMLLNDK 71
Query: 175 IEAKKAKAKSGKIFVG 190
K+FVG
Sbjct: 72 -----------KVFVG 76
Score = 34.1 bits (79), Expect = 0.027
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
L + FS +G I + + +D N G S+G+ F+ F+ E+ +A
Sbjct: 18 ALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRA 59
>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 = 35.5 bits (82), Expect = 0.008
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 197 KDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQKINDKEVD 256
+D +++ F QFG I++ E+ +++ S K F F+TF + ++K++ V+
Sbjct: 13 RDPDLRQMFGQFGPILDVEIIFNERGS--KGFGFVTFAN----SADADRAREKLHGTVVE 66
Query: 257 VKK 259
+K
Sbjct: 67 GRK 69
Score = 34.3 bits (79), Expect = 0.017
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 6/66 (9%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKK 174
+L++ F ++G I +V + N S+GF F+ F ++ ++A E + V+ +K
Sbjct: 16 DLRQMFGQFGPILDVEIIF--NERGSKGFGFVTFANSADADRAR-EKL---HGTVVEGRK 69
Query: 175 IEAKKA 180
IE A
Sbjct: 70 IEVNNA 75
Score = 32.4 bits (74), Expect = 0.098
Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L++ F ++G I +V + N S+GF F+ F ++ ++A
Sbjct: 16 DLRQMFGQFGPILDVEIIF--NERGSKGFGFVTFANSADADRA 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 = 35.4 bits (82), Expect = 0.008
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 6/65 (9%)
Query: 112 ITEELKEHFSKYGEIENVTLKSDP-NTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVI 170
+TEE + F + + +V L +P + GR RGF + F+D +SL +A ++ + +
Sbjct: 13 VTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQA-----LSLNDESL 67
Query: 171 NNKKI 175
N++I
Sbjct: 68 KNRRI 72
Score = 34.7 bits (80), Expect = 0.017
Identities = 17/47 (36%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 606 ITEELKEHFSKYGEIENVTLKSDP-NTGRSRGFAFIVFKDTESLEKA 651
+TEE + F + + +V L +P + GR RGF + F+D +SL +A
Sbjct: 13 VTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQA 59
>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 = 35.7 bits (83), Expect = 0.008
Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN 167
E++ + F+++GEI+N+ L D TG +G+A I + E+ ++A + I N
Sbjct: 21 EDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEY---ETKKEA--QAAIEGLN 69
Score = 34.5 bits (80), Expect = 0.022
Identities = 15/45 (33%), Positives = 29/45 (64%), Gaps = 3/45 (6%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
E++ + F+++GEI+N+ L D TG +G+A I + E+ ++A
Sbjct: 21 EDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEY---ETKKEAQ 62
Score = 33.0 bits (76), Expect = 0.079
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
IFV G+ E ++E++ FA+FG I + D+ K + I +E
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYET 57
>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 = 35.2 bits (82), Expect = 0.009
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL F K G I + L D + G +RG+AF+ + + E+ ++A
Sbjct: 16 DELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRA 58
Score = 35.2 bits (82), Expect = 0.009
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL F K G I + L D + G +RG+AF+ + + E+ ++A
Sbjct: 16 DELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRA 58
>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 = 35.5 bits (82), Expect = 0.010
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L+ F ++G+I +T+ D TG +G AF+ + ES KA
Sbjct: 20 KDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63
Score = 35.5 bits (82), Expect = 0.010
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L+ F ++G+I +T+ D TG +G AF+ + ES KA
Sbjct: 20 KDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63
Score = 33.9 bits (78), Expect = 0.032
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
K+FVG + +++++++ F QFG I E + DK K F+T+
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 54
>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 = 34.7 bits (80), Expect = 0.011
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 603 VDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
D E+++ F KYG I ++ LK P R G+AFI F+D E A
Sbjct: 9 GDIREREVEDLFYKYGPIVDIDLKLPP---RPPGYAFIEFEDARDAEDA 54
Score = 34.7 bits (80), Expect = 0.012
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+++ F KYG I ++ LK P R G+AFI F+D E A
Sbjct: 13 EREVEDLFYKYGPIVDIDLKLPP---RPPGYAFIEFEDARDAEDA 54
Score = 29.3 bits (66), Expect = 1.0
Identities = 12/50 (24%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
++VG L ++++ E++ F ++G I++ ++ K + + FI FE
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDA 48
>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 = 35.0 bits (80), Expect = 0.012
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGN 167
+++++ FS++G I N + D TG SRG AFI F +++ E+ I N
Sbjct: 15 KDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFD-----KRSEAEEAITSFN 63
Score = 34.6 bits (79), Expect = 0.019
Identities = 17/44 (38%), Positives = 26/44 (59%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+++++ FS++G I N + D TG SRG AFI F E+A
Sbjct: 15 KDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEA 58
Score = 31.9 bits (72), Expect = 0.20
Identities = 13/59 (22%), Positives = 31/59 (52%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+++ GL M ++++ F++FG II + + D++ + FI F+ S + + +
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61
>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 = 34.8 bits (80), Expect = 0.013
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 108 IVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
I ++ TEE LK+ FS+ G + + L D TG+ +G+ F +KD E+
Sbjct: 6 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQET 52
Score = 34.4 bits (79), Expect = 0.020
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
E+LK+ FS+ G + + L D TG+ +G+ F +KD E+
Sbjct: 13 EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQET 52
Score = 30.1 bits (68), Expect = 0.63
Identities = 13/59 (22%), Positives = 32/59 (54%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+FVG + E +E++K F++ G ++ + YD+ + K + F ++ + + ++N
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRN 59
>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 = 34.9 bits (80), Expect = 0.013
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLL 243
S ++FVG L ++ + E+K F FGN++E + + NF F+ F+ V +L
Sbjct: 5 SHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRIL 64
Score = 32.2 bits (73), Expect = 0.11
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 110 HKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 156
H I E ELKE F +G + + + + G+ F F+VF D+E +++
Sbjct: 15 HDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62
Score = 31.1 bits (70), Expect = 0.36
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
ELKE F +G + + + + G+ F F+VF D+E +++
Sbjct: 21 ELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62
>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 = 34.6 bits (80), Expect = 0.013
Identities = 22/52 (42%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
GI ++E+ LKE FS GE+ V L D S FAF+ F D ES A
Sbjct: 7 GIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAESALSA 56
Score = 34.6 bits (80), Expect = 0.014
Identities = 22/52 (42%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
GI ++E+ LKE FS GE+ V L D S FAF+ F D ES A
Sbjct: 7 GIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAESALSA 56
Score = 28.9 bits (65), Expect = 1.9
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
I VGG+ + ++++K F+ G + + D+ S R F F+ F
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR--FAFVEFAD 49
>gnl|CDD|234526 TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein.
Members of this protein family average 125 in length,
roughly half of which is the repetitive and extremely
Gly-rich C-terminal region. Virtually all members occur
in the Cyanobacteria, in a neighborhood that includes a
radical SAM/SPASM domain, often a marker of peptide
modification systems.
Length = 119
Score = 35.9 bits (83), Expect = 0.014
Identities = 19/42 (45%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 267 FGVRGGRG---GRGGRG---GRGGRMAGGYGGYGGYGGGYGG 302
+G GGRG G G G G GG GG+ GG+ GYGG
Sbjct: 73 WGNGGGRGWGNGGSGGGWVNGGGGWGNGGWVNGGGWRNGYGG 114
Score = 33.2 bits (76), Expect = 0.11
Identities = 18/41 (43%), Positives = 21/41 (51%), Gaps = 6/41 (14%)
Query: 501 FGVRGGRG---GRGGRG---GRGGRMAGGYGGYGGYGGGYG 535
+G GGRG G G G G GG GG+ GG+ GYG
Sbjct: 73 WGNGGGRGWGNGGSGGGWVNGGGGWGNGGWVNGGGWRNGYG 113
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 34.9 bits (81), Expect = 0.014
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 116 LKEHF-SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
L+E F ++Y + + DP TGRS+G+ F+ F D + ++A E
Sbjct: 18 LQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Score = 34.9 bits (81), Expect = 0.014
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 610 LKEHF-SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
L+E F ++Y + + DP TGRS+G+ F+ F D + ++A E
Sbjct: 18 LQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
>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 = 34.8 bits (80), Expect = 0.014
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKS--KSQRKNFCFITFEHESVVID 241
K+FVG + +++++ F Q+G + + + D+S Q K CF+TF ++
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALE 60
>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 = 34.6 bits (80), Expect = 0.015
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 9/69 (13%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+ +E S +G +E L +TG S+G+ F+ + S KA + ++ K
Sbjct: 14 EQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA---------KNQLDGK 64
Query: 174 KIEAKKAKA 182
+I +K +
Sbjct: 65 QIGGRKLQV 73
Score = 33.8 bits (78), Expect = 0.026
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+ +E S +G +E L +TG S+G+ F+ + S KA
Sbjct: 14 EQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57
>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 = 34.7 bits (80), Expect = 0.016
Identities = 20/45 (44%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 114 EELKEHF-SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++LK+ F K GE+ V L D G+SRG + FKD ES++KA
Sbjct: 14 QDLKDLFREKVGEVTYVELFKDEE-GKSRGCGVVEFKDKESVQKA 57
Score = 34.7 bits (80), Expect = 0.016
Identities = 20/45 (44%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 608 EELKEHF-SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++LK+ F K GE+ V L D G+SRG + FKD ES++KA
Sbjct: 14 QDLKDLFREKVGEVTYVELFKDEE-GKSRGCGVVEFKDKESVQKA 57
>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 = 34.9 bits (81), Expect = 0.016
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
L++ FS+ G+ L PN G+ RGFAF+ + E E+A
Sbjct: 17 VSILRKLFSQVGKPTFCQLAIAPN-GQPRGFAFVEYATAEDAEEA 60
Score = 34.9 bits (81), Expect = 0.016
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
L++ FS+ G+ L PN G+ RGFAF+ + E E+A
Sbjct: 17 VSILRKLFSQVGKPTFCQLAIAPN-GQPRGFAFVEYATAEDAEEA 60
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 34.5 bits (80), Expect = 0.016
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
EL+ F ++G I + DP R +A+I ++ E+
Sbjct: 13 AELEREFDRFGAIRRI--DYDPG----RNYAYIEYESIEA 46
Score = 34.5 bits (80), Expect = 0.016
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
EL+ F ++G I + DP R +A+I ++ E+
Sbjct: 13 AELEREFDRFGAIRRI--DYDPG----RNYAYIEYESIEA 46
Score = 28.7 bits (65), Expect = 1.8
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
++VGGL P E++ F +FG I + YD +N+ +I +E
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAI--RRIDYDPG----RNYAYIEYES 43
>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 = 34.1 bits (79), Expect = 0.019
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
+++ GL P DE+++ FG II T+ DK ++ K + F+ F+
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPE 53
Score = 31.8 bits (73), Expect = 0.13
Identities = 12/44 (27%), Positives = 23/44 (52%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+L++ +G+I + D T + +G+ F+ F E+ KA
Sbjct: 15 EDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKA 58
Score = 31.8 bits (73), Expect = 0.13
Identities = 12/44 (27%), Positives = 23/44 (52%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+L++ +G+I + D T + +G+ F+ F E+ KA
Sbjct: 15 EDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKA 58
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 34.3 bits (79), Expect = 0.019
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++++ F KYG I+ + LK+ R FAF+ F+D E A
Sbjct: 13 ERDIEDLFYKYGPIKAIDLKNRR---RGPPFAFVEFEDPRDAEDA 54
Score = 34.3 bits (79), Expect = 0.019
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++++ F KYG I+ + LK+ R FAF+ F+D E A
Sbjct: 13 ERDIEDLFYKYGPIKAIDLKNRR---RGPPFAFVEFEDPRDAEDA 54
Score = 30.8 bits (70), Expect = 0.31
Identities = 13/49 (26%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+I+VG L ++++ +I+ F ++G I ++ K++ + F F+ FE
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFE 46
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 34.2 bits (79), Expect = 0.019
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 8/51 (15%)
Query: 601 GIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G +D I ++L +++V L D T + +GF ++ F+D ESL++A
Sbjct: 16 GDLDAIFKDLS--------VKSVRLVRDKETDKFKGFCYVEFEDVESLKEA 58
Score = 33.5 bits (77), Expect = 0.038
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 125 EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+++V L D T + +GF ++ F+D ESL++A
Sbjct: 26 SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEA 58
>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM1 of the CPEB family of proteins
that bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins have been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bind to a protein such as maskin or
neuroguidin, which blocks translation initiation through
interfering with the assembly of eIF-4E and eIF-4G.
Although CPEB-1 is mainly located in cytoplasm, it can
shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to high sequence similarity, members in
this subfamily 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.
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 CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 112
Score = 35.3 bits (81), Expect = 0.021
Identities = 20/80 (25%), Positives = 30/80 (37%), Gaps = 22/80 (27%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNII------ETEMPYDKSKSQRKN------------ 227
K+FVGGL ++ + +I F +FG++ E D S
Sbjct: 2 KVFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDSDPSLCNEKSDGSINGDKGQ 61
Query: 228 ----FCFITFEHESVVIDLL 243
+ F+ FE E V LL
Sbjct: 62 HPKGYVFLLFEKERSVRSLL 81
>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 = 0.025
Identities = 19/65 (29%), Positives = 40/65 (61%), Gaps = 4/65 (6%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FVGG+ M + EI++ FA++G++ E ++ D++ K + F++F + +D+ K
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRT-GVSKGYGFVSFYDD---VDVQKIV 63
Query: 247 KQKIN 251
+ +IN
Sbjct: 64 ESQIN 68
Score = 32.1 bits (73), Expect = 0.12
Identities = 18/51 (35%), Positives = 32/51 (62%), Gaps = 2/51 (3%)
Query: 107 GIVHKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 156
GI ++ E E++ F+KYG ++ V + +D TG S+G+ F+ F D ++K
Sbjct: 12 GIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQK 61
Score = 32.1 bits (73), Expect = 0.14
Identities = 18/51 (35%), Positives = 32/51 (62%), Gaps = 2/51 (3%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
GI ++ E E++ F+KYG ++ V + +D TG S+G+ F+ F D ++K
Sbjct: 12 GIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQK 61
>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 = 33.7 bits (78), Expect = 0.030
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 10/69 (14%)
Query: 190 GGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQK 249
GGL + EE+ F ++G + + MP K +CF+++
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVMPPGKP------YCFVSYSSIEDAAAAY----DA 58
Query: 250 INDKEVDVK 258
+N KE+++
Sbjct: 59 LNGKELELP 67
Score = 31.8 bits (73), Expect = 0.14
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 593 KNKMVSHPGIVDKIT-EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++ +V++ G+ + ++ EEL F KYG +E++ + G+ + F+ + E A
Sbjct: 2 QHLVVANGGLGNGVSREELLRVFEKYGTVEDLVMP----PGKP--YCFVSYSSIEDAAAA 55
Score = 31.8 bits (73), Expect = 0.16
Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 99 KNKMVSHPGIVHKIT-EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++ +V++ G+ + ++ EEL F KYG +E++ + G+ + F+ + E A
Sbjct: 2 QHLVVANGGLGNGVSREELLRVFEKYGTVEDLVMP----PGKP--YCFVSYSSIEDAAAA 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 = 33.8 bits (78), Expect = 0.030
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL++ FSKYG++ +V + S + +G A + F ++ E A
Sbjct: 19 DELRKIFSKYGDVSDVVVSS-----KKKGSAIVEFASKKAAEAA 57
Score = 33.8 bits (78), Expect = 0.030
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL++ FSKYG++ +V + S + +G A + F ++ E A
Sbjct: 19 DELRKIFSKYGDVSDVVVSS-----KKKGSAIVEFASKKAAEAA 57
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM2 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 33.7 bits (77), Expect = 0.031
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G +TEE L+E F + ++E + L D +G+ + F+ F+ ++S A
Sbjct: 5 GFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAA 56
Score = 33.3 bits (76), Expect = 0.041
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
G +TEE L+E F + ++E + L D +G+ + F+ F+ ++S A
Sbjct: 5 GFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAA 56
Score = 31.0 bits (70), Expect = 0.25
Identities = 11/48 (22%), Positives = 23/48 (47%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
I+V G + + +E ++ F Q ++ +P D + +CF+ F
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFR 48
>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 = 33.9 bits (77), Expect = 0.036
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EE K F GEIE+ L D TG+S G+ F+ + D +KA
Sbjct: 18 EEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61
Score = 33.9 bits (77), Expect = 0.036
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EE K F GEIE+ L D TG+S G+ F+ + D +KA
Sbjct: 18 EEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 36.2 bits (84), Expect = 0.037
Identities = 17/36 (47%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 267 FGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G R G GG GG GG +G GG+ G GG GG
Sbjct: 231 LGRRRRSSGSGGSGGSGGGSSG--GGFSGGGGSSGG 264
Score = 35.4 bits (82), Expect = 0.066
Identities = 17/35 (48%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 501 FGVRGGRGGRGGRGGRGGRMAGG--YGGYGGYGGG 533
G R G GG GG GG +GG GG G GGG
Sbjct: 231 LGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGG 265
Score = 34.3 bits (79), Expect = 0.16
Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYGG-YGGG 299
G GG GG GG GG+ G GG GGG
Sbjct: 237 SSGSGGSGGSGGGSSG--GGFSGGGGSSGGG 265
Score = 33.1 bits (76), Expect = 0.33
Identities = 16/32 (50%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 301
GG GG GG GG GG G GG GG G
Sbjct: 240 SGGSGGSGGGSSGGGFSGGG-GSSGG-GGASG 269
Score = 33.1 bits (76), Expect = 0.33
Identities = 16/32 (50%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 504 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
GG GG GG GG GG G GG GG G
Sbjct: 240 SGGSGGSGGGSSGGGFSGGG-GSSGG-GGASG 269
Score = 32.3 bits (74), Expect = 0.70
Identities = 17/39 (43%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 495 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 533
P GV G R G GG GG GG G G GGG
Sbjct: 222 QPDRWLNGVLGRRRRSSGSGGSGGS-GGGSSGGGFSGGG 259
>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 = 33.5 bits (77), Expect = 0.038
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
EEL+ F +YG +E+V +K P G+ +AF+ F + + +A V
Sbjct: 17 EELRRAFERYGVVEDVDIKRPPR-GQGNAYAFVKFLNLDMAHRAKVA 62
Score = 33.5 bits (77), Expect = 0.038
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
EEL+ F +YG +E+V +K P G+ +AF+ F + + +A V
Sbjct: 17 EELRRAFERYGVVEDVDIKRPPR-GQGNAYAFVKFLNLDMAHRAKVA 62
Score = 28.1 bits (63), Expect = 2.9
Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+FVG L + +EE++ F ++G + + ++ + Q + F+ F
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIK-RPPRGQGNAYAFVKFL 51
>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 = 33.0 bits (76), Expect = 0.043
Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF-EHESVVIDLLKN 245
++VG L + ++ + F+Q G I ++ + + F+ + +H S L
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGND---PYAFVEYYDHRSAAAALQTM 57
Query: 246 PKQKINDKEVDV 257
+ I +E+ V
Sbjct: 58 NGRLILGQEIKV 69
>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 = 33.4 bits (77), Expect = 0.043
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
+FV ++ ++DEE++A F QFG+I Y K + F +++
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDI---RTLYTACKH--RGFIMVSY 45
Score = 30.7 bits (70), Expect = 0.34
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EEL+ F ++G+I + + RGF + + D + +A
Sbjct: 16 EELRALFEQFGDIRTLY-----TACKHRGFIMVSYYDIRAARRA 54
Score = 30.7 bits (70), Expect = 0.34
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL+ F ++G+I + + RGF + + D + +A
Sbjct: 16 EELRALFEQFGDIRTLY-----TACKHRGFIMVSYYDIRAARRA 54
>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 = 33.4 bits (76), Expect = 0.049
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
+F+ L E D ++ F FGN+I ++ DK + K F F+++++
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDN 55
>gnl|CDD|241167 cd12723, RRM1_CPEB1, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding
protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 100
Score = 33.9 bits (78), Expect = 0.050
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMP---YDKSKSQRKNFCFITFEHESVVI 240
S K+F+GG+ ++ + + F FG+ + E P + K + ++ FE E V
Sbjct: 2 SCKVFLGGVPWDITEAGLINTFKPFGS-VSVEWPGKDGKHPRHPPKGYVYLIFESEKSVK 60
Query: 241 DLLKN 245
LL+
Sbjct: 61 ALLQA 65
>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 = 33.4 bits (77), Expect = 0.050
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
I+VG + + E++ F FG I E + + + N+ F+T+ +
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHF---RDDGDNYGFVTYRYAC 52
Score = 31.5 bits (72), Expect = 0.22
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNH 168
EL++ F +GEIE +TL + G + + F+ ++ +A I GN
Sbjct: 17 SELRQRFQPFGEIEEITLHFRDD-GDN--YGFVTYRYACDAFRA-----IEHGND 63
Score = 28.4 bits (64), Expect = 2.7
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
I T EL++ F +GEIE +TL + G + + F+ ++ +A
Sbjct: 9 KIPIDTTRSELRQRFQPFGEIEEITLHFRDD-GDN--YGFVTYRYACDAFRA 57
>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 = 33.4 bits (77), Expect = 0.051
Identities = 12/51 (23%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRK---NFCFITFE 234
++VG L+P++ +E + F +FG + ++ + +++ +R+ N F+ F
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFM 54
Score = 28.4 bits (64), Expect = 3.1
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 110 HKITEE-LKEHFSKYGEIENVTL---KSDPNTGRSR--GF-AFIVFKDTESLEKASVEDV 162
K+TEE L + F ++G + +V + +++ R+R GF AF+ D E ++
Sbjct: 11 PKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER-ALDELDGK 69
Query: 163 IAEGN 167
G
Sbjct: 70 DVMGY 74
Score = 26.8 bits (60), Expect = 9.9
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 8/61 (13%)
Query: 605 KITEE-LKEHFSKYGEIENVTL---KSDPNTGRSR--GF-AFIVFKDTE-SLEKASVEDV 656
K+TEE L + F ++G + +V + +++ R+R GF AF+ D E +L++ +DV
Sbjct: 12 KVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERALDELDGKDV 71
Query: 657 Y 657
Sbjct: 72 M 72
>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa
MCM3-associated protein (Map80) and similar proteins.
This subfamily corresponds to the RRM of Map80, also
termed germinal center-associated nuclear protein
(GANP), involved in the nuclear localization pathway of
MCM3, a protein necessary for the initiation of DNA
replication and also involves in controls that ensure
DNA replication is initiated once per cell cycle. Map80
contains one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 73
Score = 33.1 bits (76), Expect = 0.053
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 6/44 (13%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ L+ HF K+G++ V + A + F D S A
Sbjct: 16 DWLERHFGKFGKVARV------YCNPRKKSAVVHFFDHASAALA 53
Score = 33.1 bits (76), Expect = 0.053
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 6/44 (13%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ L+ HF K+G++ V + A + F D S A
Sbjct: 16 DWLERHFGKFGKVARV------YCNPRKKSAVVHFFDHASAALA 53
>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 = 33.5 bits (76), Expect = 0.055
Identities = 14/58 (24%), Positives = 31/58 (53%)
Query: 178 KKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
+K + +F+ L E D+++ F FGN++ ++ DK + K F F+++++
Sbjct: 1 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 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 = 32.8 bits (75), Expect = 0.064
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 592 AKNKMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++N + + E+L+ FS+YGEIE+V N R + AF+ F + + KA
Sbjct: 3 SRNVYIGNIDDSLT-EEKLRNDFSQYGEIESV------NYLREKNCAFVNFTNISNAIKA 55
Score = 32.8 bits (75), Expect = 0.080
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E+L+ FS+YGEIE+V N R + AF+ F + + KA
Sbjct: 17 EEKLRNDFSQYGEIESV------NYLREKNCAFVNFTNISNAIKA 55
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 33.0 bits (76), Expect = 0.070
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH-ESVV--IDL 242
+FVG + + D+ I+ + G ++ + D S + K F F FE E + + L
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61
Query: 243 LKNPKQKINDKEVDVK 258
L ++ K++ VK
Sbjct: 62 LNG--LELGGKKLLVK 75
Score = 32.2 bits (74), Expect = 0.11
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 14/80 (17%)
Query: 109 VHKITEELKEHF-----SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVI 163
V I E + + F K G++ + DP+TG+ + F F F+D E +A +
Sbjct: 5 VGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRA-LR--- 60
Query: 164 AEGNHVINNKKIEAKKAKAK 183
++N ++ KK K
Sbjct: 61 -----LLNGLELGGKKLLVK 75
Score = 29.5 bits (67), Expect = 1.2
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 627 SDPNTGRSRGFAFIVFKDTESLEKA 651
DP+TG+ + F F F+D E +A
Sbjct: 34 KDPSTGKLKAFGFCEFEDPEGALRA 58
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 34.6 bits (80), Expect = 0.071
Identities = 19/33 (57%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
RGG GG GG GG GG G GG GG GGG
Sbjct: 122 RGG-GGGGGGGGFGGGGGGSGGGGGGGGGGGAP 153
Score = 34.2 bits (79), Expect = 0.11
Identities = 19/32 (59%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 504 RGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
RGG GG GG GG GG G GG GG GGG
Sbjct: 122 RGG-GGGGGGGGFGGGGGGSGGGGGGGGGGGA 152
Score = 33.1 bits (76), Expect = 0.28
Identities = 15/24 (62%), Positives = 16/24 (66%)
Query: 279 RGGRGGRMAGGYGGYGGYGGGYGG 302
R RGG GG GG+GG GGG GG
Sbjct: 119 RASRGGGGGGGGGGFGGGGGGSGG 142
Score = 32.7 bits (75), Expect = 0.33
Identities = 19/32 (59%), Positives = 19/32 (59%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
GG GG GG GG GG GG GG GG G GG
Sbjct: 125 GGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGG 156
Score = 32.3 bits (74), Expect = 0.44
Identities = 17/31 (54%), Positives = 17/31 (54%)
Query: 275 GRGGRGGRGGRMAGGYGGYGGYGGGYGGILY 305
GG GG GG GG GG GG GGG GG
Sbjct: 122 RGGGGGGGGGGFGGGGGGSGGGGGGGGGGGA 152
Score = 31.2 bits (71), Expect = 1.0
Identities = 19/48 (39%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 255 VDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
V +A+ G GG GG GG G GG GG GG GGG
Sbjct: 115 AKVTRASRGGGGGGGGGGFGGGGGGSGGGG--GGGGGGGAPGGGGAQA 160
Score = 31.2 bits (71), Expect = 1.1
Identities = 19/45 (42%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 489 VDVKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 533
V +A+ G GG GG GG G GG GG GG GGG
Sbjct: 115 AKVTRASRGGGGGGGGGGFGGGGGGSGGGG--GGGGGGGAPGGGG 157
Score = 30.8 bits (70), Expect = 1.5
Identities = 14/23 (60%), Positives = 15/23 (65%)
Query: 513 RGGRGGRMAGGYGGYGGYGGGYG 535
R RGG GG GG+GG GGG G
Sbjct: 119 RASRGGGGGGGGGGFGGGGGGSG 141
>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 = 32.4 bits (74), Expect = 0.077
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L+E F ++GEI ++ +K + +AFI + D S+ KA
Sbjct: 18 DLREAFERFGEIIDIDIKKQGG---NPAYAFIQYADIASVVKA 57
Score = 32.4 bits (74), Expect = 0.077
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L+E F ++GEI ++ +K + +AFI + D S+ KA
Sbjct: 18 DLREAFERFGEIIDIDIKKQGG---NPAYAFIQYADIASVVKA 57
Score = 29.3 bits (66), Expect = 0.95
Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
+F+G L +++ F +FG II+ ++ K + + FI + + V+ ++
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKAMR 59
>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 = 32.5 bits (74), Expect = 0.078
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L++ F KYG I ++ LK N FAF+ F+D E A
Sbjct: 14 KDLEDLFYKYGRIRDIELK---NRRGLVPFAFVRFEDPRDAEDA 54
Score = 32.5 bits (74), Expect = 0.078
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L++ F KYG I ++ LK N FAF+ F+D E A
Sbjct: 14 KDLEDLFYKYGRIRDIELK---NRRGLVPFAFVRFEDPRDAEDA 54
Score = 29.8 bits (67), Expect = 0.68
Identities = 13/49 (26%), Positives = 30/49 (61%), Gaps = 3/49 (6%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+I+VG L ++++++++ F ++G I + E+ K++ F F+ FE
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFE 46
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 32.8 bits (75), Expect = 0.080
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 108 IVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
I ++TEE L FS G++ + + DPN+ FAFI F D E A
Sbjct: 10 IDQQVTEEQLAALFSNCGQVVDCRVCGDPNS--VLRFAFIEFTDEEGARAA 58
Score = 32.4 bits (74), Expect = 0.095
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 602 IVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
I ++TEE L FS G++ + + DPN+ FAFI F D E A
Sbjct: 10 IDQQVTEEQLAALFSNCGQVVDCRVCGDPNS--VLRFAFIEFTDEEGARAA 58
>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 = 32.8 bits (74), Expect = 0.082
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL+ FS GE+E+ L D G S G+ F+ + + + E+A
Sbjct: 16 DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERA 59
Score = 32.8 bits (74), Expect = 0.082
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL+ FS GE+E+ L D G S G+ F+ + + + E+A
Sbjct: 16 DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERA 59
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 32.3 bits (73), Expect = 0.085
Identities = 13/60 (21%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+ VG +S ++E++A F ++G +IE ++ K++ F+ E ++ ++
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRG 53
>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 = 35.6 bits (82), Expect = 0.090
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVV---IDL 242
+I++G L + +++IK FG++ + D + K + F ++ SV I
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356
Query: 243 LKNPKQKINDKEVDVKKAT 261
L + D ++ V++A
Sbjct: 357 LNG--KDTGDNKLHVQRAC 373
Score = 34.5 bits (79), Expect = 0.17
Identities = 32/151 (21%), Positives = 54/151 (35%), Gaps = 40/151 (26%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA-------- 157
+ + E+ +KE +G+++ L D TG S+G+AF +KD + A
Sbjct: 302 NLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD 361
Query: 158 ------SVEDVIAEGNHV----INNKKIEAKKAKAKSGKIFVGGLSP------------- 194
V+ N N AKA S I G P
Sbjct: 362 TGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGD 421
Query: 195 EMKD--------EEIKAHFAQFGNIIETEMP 217
++ D E++K F+++G +I +P
Sbjct: 422 DLMDDEEYEEIYEDVKTEFSKYGPLINIVIP 452
Score = 32.9 bits (75), Expect = 0.55
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+++KE +G+++ L D TG S+G+AF +KD + A
Sbjct: 310 DQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVA 353
Score = 30.2 bits (68), Expect = 4.1
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 604 DKITEELKEHFSKYGEIENVTL---KSDPNTGRSRGFAFIVFKDTESLEKA 651
++I E++K FSKYG + N+ + D N+ G F+ + D S EKA
Sbjct: 430 EEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKA 480
>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 = 32.4 bits (74), Expect = 0.090
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 107 GIVHKITE-ELKEHF-SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ +TE +++E+F S+ G I+ V L + G+S G A I FK KA
Sbjct: 6 NLPKDVTEAQIREYFVSQIGPIKRVLLSYNEG-GKSTGIANITFKRAGDATKA 57
Score = 32.4 bits (74), Expect = 0.10
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 606 ITE-ELKEHF-SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+TE +++E+F S+ G I+ V L + G+S G A I FK KA
Sbjct: 11 VTEAQIREYFVSQIGPIKRVLLSYNEG-GKSTGIANITFKRAGDATKA 57
>gnl|CDD|240704 cd12258, RRM2_RBM26_like, RNA recognition motif 2 of vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM2 of RBM26, also
known as cutaneous T-cell lymphoma (CTCL) tumor antigen
se70-2, which represents a cutaneous lymphoma
(CL)-associated antigen. RBM26 contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
The RRMs may play some functional roles in RNA-binding
or protein-protein interactions.
Length = 72
Score = 32.2 bits (74), Expect = 0.097
Identities = 14/26 (53%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNI 211
++ V G + E KDE + AHFAQFG I
Sbjct: 7 QLSVTGFTEEDKDE-LLAHFAQFGEI 31
Score = 28.4 bits (64), Expect = 2.0
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVYF 658
+EL HF+++GEIE+V + + I FK + E A+V F
Sbjct: 19 DELLAHFAQFGEIEDVEVDEEGLH------LVITFKTRKEAEIAAVRGRRF 63
Score = 27.6 bits (62), Expect = 4.0
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNT 137
+EL HF+++GEIE+V + +
Sbjct: 19 DELLAHFAQFGEIEDVEVDEEGLH 42
>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 = 32.2 bits (74), Expect = 0.11
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 599 HPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFK 643
+ +I E L+ HF ++G+IE++ S+G AF+ +K
Sbjct: 11 AGSALKQIEEILRRHFGEWGDIEDI------RVLPSKGIAFVRYK 49
Score = 30.3 bits (69), Expect = 0.49
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 105 HPGIVHKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFK 149
+ +I E L+ HF ++G+IE++ S+G AF+ +K
Sbjct: 11 AGSALKQIEEILRRHFGEWGDIEDI------RVLPSKGIAFVRYK 49
>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 = 32.0 bits (73), Expect = 0.14
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIE 213
K+FVG LS + +++++ F FG I E
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEE 30
Score = 31.3 bits (71), Expect = 0.29
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFK 149
++++ F +G IE T+ P+ G S+G AF+ F
Sbjct: 16 DDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFS 50
Score = 31.3 bits (71), Expect = 0.29
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFK 643
++++ F +G IE T+ P+ G S+G AF+ F
Sbjct: 16 DDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFS 50
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 32.1 bits (73), Expect = 0.14
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 121 SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
S++ ++ + +DP TG SRG+ F+ F D ++A +E
Sbjct: 24 SRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63
Score = 32.1 bits (73), Expect = 0.14
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 615 SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
S++ ++ + +DP TG SRG+ F+ F D ++A +E
Sbjct: 24 SRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63
>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 = 31.9 bits (73), Expect = 0.15
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 120 FSKYGEIENVTLKSDPNTGRSRGFAFI 146
FS +G + NV + D T + +G+ F+
Sbjct: 22 FSPFGAVTNVKVIRDLTTNKCKGYGFV 48
Score = 31.9 bits (73), Expect = 0.15
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 614 FSKYGEIENVTLKSDPNTGRSRGFAFI 640
FS +G + NV + D T + +G+ F+
Sbjct: 22 FSPFGAVTNVKVIRDLTTNKCKGYGFV 48
Score = 30.4 bits (69), Expect = 0.51
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFIT 232
IFV L P+ + + F+ FG + ++ D + ++ K + F+T
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVT 49
>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 = 31.2 bits (71), Expect = 0.17
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 603 VDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
D ++E FS YG ++ V + S FAF+ F+ ES +A
Sbjct: 9 PDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRA 49
Score = 31.2 bits (71), Expect = 0.19
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 12/64 (18%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
++E FS YG ++ V + S FAF+ F+ ES +A + V V+NN
Sbjct: 13 ESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRA-KDSV---HGKVLNN 60
Query: 173 KKIE 176
+
Sbjct: 61 NPLY 64
Score = 28.2 bits (63), Expect = 2.5
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+++V P+ + I+ F+ +G + E +M NF F+ FE
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFE 41
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 31.5 bits (72), Expect = 0.17
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 7/65 (10%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
E+LKE F ++GE+ V D G++ G ++ FK+ + ++A +E + N I
Sbjct: 16 EDLKEAFEEFGEVAWV----DFARGQTEG--YVRFKEENAAKEA-LEKLKEAKNLKIKGS 68
Query: 174 KIEAK 178
++ K
Sbjct: 69 EVTVK 73
>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 = 32.0 bits (73), Expect = 0.18
Identities = 12/53 (22%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 601 GIVDKITE-ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 652
G+ D + E +++++F ++G+ ++V + R++ F+ F+ E+ EK +
Sbjct: 9 GVEDDLPEYKIRDYFEQFGKSKSVIVNH-----RAK-CGFVRFETREAAEKFA 55
Score = 29.3 bits (66), Expect = 1.6
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 188 FVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
F+ G+ ++ + +I+ +F QFG + R F+ FE
Sbjct: 6 FLFGVEDDLPEYKIRDYFEQFGKSKSV------IVNHRAKCGFVRFETRE 49
Score = 28.9 bits (65), Expect = 1.9
Identities = 9/45 (20%), Positives = 26/45 (57%), Gaps = 6/45 (13%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKAS 158
+++++F ++G+ ++V + R++ F+ F+ E+ EK +
Sbjct: 17 YKIRDYFEQFGKSKSVIVNH-----RAK-CGFVRFETREAAEKFA 55
>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 = 31.7 bits (72), Expect = 0.18
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF--KDTESLEKASVEDVY 657
E++E FS YG +E++ + D +SRG AF+ + K+ ++ VY
Sbjct: 15 EVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKALNGVY 64
Score = 31.4 bits (71), Expect = 0.27
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 110 HKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+E++E FS YG +E++ + D +SRG AF+ + E + A
Sbjct: 10 QATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAA 56
Score = 30.2 bits (68), Expect = 0.69
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF---EHESVVIDL 242
K+FVG L+ + ++E++ F+ +G + + M D+ K Q + F+ + E I
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKA 59
Query: 243 L 243
L
Sbjct: 60 L 60
>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 = 31.6 bits (71), Expect = 0.21
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL++ FS+YG I + D TG SRG FI F E+A
Sbjct: 17 KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60
Score = 31.6 bits (71), Expect = 0.21
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL++ FS+YG I + D TG SRG FI F E+A
Sbjct: 17 KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 31.3 bits (71), Expect = 0.22
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 8/43 (18%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E++ F KYG ++ V +KS GFAF+ +D E A
Sbjct: 16 EIERLFGKYGRVDRVDMKS--------GFAFVYMEDERDAEDA 50
Score = 31.3 bits (71), Expect = 0.22
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 8/43 (18%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E++ F KYG ++ V +KS GFAF+ +D E A
Sbjct: 16 EIERLFGKYGRVDRVDMKS--------GFAFVYMEDERDAEDA 50
>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 = 31.6 bits (72), Expect = 0.22
Identities = 15/59 (25%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE-DVIAEGNHVI 170
EEL++ F K+G +++V L ++ + G+ +G A++ +++ S +A ++ D I
Sbjct: 16 KEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAVLKMDGTEIKEKTI 73
Score = 31.2 bits (71), Expect = 0.24
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
K+FV GL + EE++ F + G + + ++S K ++ +E+ES
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKP-KGLAYVEYENES 54
Score = 31.2 bits (71), Expect = 0.31
Identities = 13/45 (28%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EEL++ F K+G +++V L ++ + G+ +G A++ +++ S +A
Sbjct: 16 KEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQA 59
>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown].
Length = 334
Score = 34.1 bits (78), Expect = 0.23
Identities = 17/43 (39%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 266 PFGVRGGRGGRGGRGGRGGRMAGGYG-----GYGGYGGGYGGI 303
G G GG GG GG+G GG GGG+GGI
Sbjct: 64 YSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGGI 106
Score = 32.2 bits (73), Expect = 0.82
Identities = 15/45 (33%), Positives = 16/45 (35%)
Query: 261 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILY 305
P R G GG + GY G G GGGY G Y
Sbjct: 39 PPLSVAAAARSGGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGY 83
Score = 30.7 bits (69), Expect = 2.4
Identities = 16/43 (37%), Positives = 17/43 (39%), Gaps = 5/43 (11%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGG----YGGY-GGGYGGILYKPL 308
GG R G G GG G GGY GGG+G P
Sbjct: 54 GGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPG 96
Score = 29.9 bits (67), Expect = 4.5
Identities = 13/41 (31%), Positives = 14/41 (34%)
Query: 495 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
P R G GG + GY G G GGGY
Sbjct: 39 PPLSVAAAARSGGRIGGGSFRAPSGYSRGYSGGGPSGGGYS 79
Score = 29.9 bits (67), Expect = 4.9
Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 5/43 (11%)
Query: 500 PFGVRGGRGGRGGRGGRGGRMAGGYG-----GYGGYGGGYGEL 537
G G GG GG GG+G GG GGG+G +
Sbjct: 64 YSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGGI 106
Score = 29.5 bits (66), Expect = 5.5
Identities = 17/41 (41%), Positives = 17/41 (41%), Gaps = 2/41 (4%)
Query: 266 PFGVRGG--RGGRGGRGGRGGRMAGGYGGYGGYGGGYGGIL 304
G GG GG GG G GG GG GG GIL
Sbjct: 70 GGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGGIFGIL 110
>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 = 31.2 bits (71), Expect = 0.23
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 12/71 (16%)
Query: 107 GIVHKIT--EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIA 164
G + K E+LK F +YGEI+++ + RG A++ + + +A +
Sbjct: 8 GHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRA----LQK 57
Query: 165 EGNHVINNKKI 175
N + KKI
Sbjct: 58 LRNVKLAGKKI 68
Score = 30.8 bits (70), Expect = 0.33
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E+LK F +YGEI+++ + RG A++ + + +A
Sbjct: 17 EDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRA 54
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 80
Score = 31.3 bits (70), Expect = 0.24
Identities = 13/48 (27%), Positives = 27/48 (56%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+++ GL P D+++ +G I+ T+ DK+ +Q K + F+ F+
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFD 54
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 33.3 bits (76), Expect = 0.26
Identities = 16/32 (50%), Positives = 17/32 (53%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 299
G+ G GG GG G GG G GG GG GG
Sbjct: 35 GMGGPVGGGGGPGAGGGAPGGPVGGGGGGSGG 66
Score = 33.3 bits (76), Expect = 0.26
Identities = 16/32 (50%), Positives = 17/32 (53%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 533
G+ G GG GG G GG G GG GG GG
Sbjct: 35 GMGGPVGGGGGPGAGGGAPGGPVGGGGGGSGG 66
Score = 31.8 bits (72), Expect = 0.88
Identities = 18/32 (56%), Positives = 18/32 (56%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
GG GG G GG GG G G G GGGYGG
Sbjct: 191 GGGGGGMGGGGGGGMGEMGGMGPQGGGGGYGG 222
Score = 31.0 bits (70), Expect = 1.7
Identities = 17/31 (54%), Positives = 17/31 (54%)
Query: 505 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
GG GG G GG GG G G G GGGYG
Sbjct: 191 GGGGGGMGGGGGGGMGEMGGMGPQGGGGGYG 221
Score = 30.2 bits (68), Expect = 2.8
Identities = 17/41 (41%), Positives = 18/41 (43%)
Query: 496 PKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGE 536
P +G GG G GG GG G G G GG GG G
Sbjct: 185 PGGGGYGGGGGGMGGGGGGGMGEMGGMGPQGGGGGYGGMGA 225
Score = 29.9 bits (67), Expect = 3.9
Identities = 17/41 (41%), Positives = 18/41 (43%)
Query: 262 PKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
P +G GG G GG GG G G G GG GG G
Sbjct: 185 PGGGGYGGGGGGMGGGGGGGMGEMGGMGPQGGGGGYGGMGA 225
>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 = 31.3 bits (70), Expect = 0.28
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+EL++ FS+YG I + D TG SRG FI F E+A
Sbjct: 20 KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63
Score = 31.3 bits (70), Expect = 0.28
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+EL++ FS+YG I + D TG SRG FI F E+A
Sbjct: 20 KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily corresponds
to the RRM2 of La and LARP7. La is 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. LARP7
is an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
of 7SK RNA. It is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP), 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. LARP7 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.
Both La and LARP7 contain an N-terminal La motif (LAM),
followed by two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 31.1 bits (71), Expect = 0.28
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 8/65 (12%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN-N 172
E++K F+++GE++ V +TG +I FK E+ +KA E + +G ++
Sbjct: 16 EDIKAVFAQFGEVKYVDFTEGADTG------YIRFKTPEAAQKA-REAFVEKGEGLLGKE 68
Query: 173 KKIEA 177
K+ A
Sbjct: 69 IKLSA 73
Score = 28.8 bits (65), Expect = 1.7
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E++K F+++GE++ V +TG +I FK E+ +KA
Sbjct: 16 EDIKAVFAQFGEVKYVDFTEGADTG------YIRFKTPEAAQKA 53
>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 = 31.1 bits (70), Expect = 0.29
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+E+++ FS+YG I + D TG SRG FI F E+A
Sbjct: 16 KEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA 59
Score = 31.1 bits (70), Expect = 0.29
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+E+++ FS+YG I + D TG SRG FI F E+A
Sbjct: 16 KEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA 59
Score = 30.4 bits (68), Expect = 0.54
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++V GL M +E++ F+Q+G II + + D+ + FI F+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFD 51
>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 = 31.0 bits (70), Expect = 0.31
Identities = 25/59 (42%), Positives = 34/59 (57%), Gaps = 11/59 (18%)
Query: 608 EELKEH----FSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVYFY 659
EELK+ FS++G+I + V LK T + RG AF+VFKD S A S++ FY
Sbjct: 14 EELKKSLYAIFSQFGQILDIVALK----TLKMRGQAFVVFKDISSATNALRSMQGFPFY 68
Score = 30.3 bits (68), Expect = 0.52
Identities = 22/49 (44%), Positives = 29/49 (59%), Gaps = 9/49 (18%)
Query: 114 EELKEH----FSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EELK+ FS++G+I + V LK T + RG AF+VFKD S A
Sbjct: 14 EELKKSLYAIFSQFGQILDIVALK----TLKMRGQAFVVFKDISSATNA 58
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 30.9 bits (70), Expect = 0.31
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 9/62 (14%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFI---TFEHESVVIDLL 243
++VG + P ++ F FG I+E D+ F F+ T E ++ I L
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRG------FAFVKLDTHEQAAMAIVQL 56
Query: 244 KN 245
+
Sbjct: 57 QG 58
>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 = 31.0 bits (70), Expect = 0.31
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
EE +E YG IE L TG S+G+ F+ + +S KA +E
Sbjct: 14 EEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60
Score = 31.0 bits (70), Expect = 0.31
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
EE +E YG IE L TG S+G+ F+ + +S KA +E
Sbjct: 14 EEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60
>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 = 30.8 bits (70), Expect = 0.32
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+LK+ FSKYG++ + ++ + +R F F+ E K
Sbjct: 15 DLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKC 57
Score = 30.8 bits (70), Expect = 0.32
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+LK+ FSKYG++ + ++ + +R F F+ E K
Sbjct: 15 DLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKC 57
Score = 29.6 bits (67), Expect = 0.76
Identities = 11/47 (23%), Positives = 25/47 (53%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
++V GLS K ++K F+++G ++ ++ + + F F+T
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTM 48
>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 = 30.8 bits (69), Expect = 0.35
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 122 KYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAKK 179
K GE+ V L D G+SRG A + FK ES++KA VE + HV+N + ++ K+
Sbjct: 23 KVGEVTYVELLMD-AEGKSRGCAVVEFKMEESMKKA-VEVL---NKHVLNGRPLKVKE 75
Score = 28.5 bits (63), Expect = 2.5
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 616 KYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
K GE+ V L D G+SRG A + FK ES++KA
Sbjct: 23 KVGEVTYVELLMD-AEGKSRGCAVVEFKMEESMKKA 57
>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 = 30.6 bits (69), Expect = 0.35
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
KIFVG +S +E++ F +FG ++E + K++ F+ E E
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREE 45
>gnl|CDD|241166 cd12722, RRM_Nup53, RNA recognition motif in nucleoporin Nup53.
This subgroup corresponds to the RRM of nucleoporin
Nup53, also termed mitotic phosphoprotein 44 (MP-44), or
nuclear pore complex protein Nup53, required for normal
cell growth and nuclear morphology in vertebrate. It
tightly associates with the nuclear envelope membrane
and the nuclear lamina where it interacts with lamin B.
It may also interact with a group of nucleoporins
including Nup93, Nup155, and Nup205 and play a role in
the association of the mitotic checkpoint protein Mad1
with the nuclear pore complex (NPC). Nup35 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. This RRM lacks the conserved residues that
typically bind RNA in canonical RRM domains.
Length = 74
Score = 30.5 bits (69), Expect = 0.38
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 162 VIAEGN--HVINNKKIEAKKAKAKSGKIFVGGL 192
+ GN H+ K++AKKA +K+GKIF +
Sbjct: 33 MSNNGNWMHIQYQSKLQAKKALSKNGKIFGENI 65
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 33.1 bits (76), Expect = 0.38
Identities = 15/40 (37%), Positives = 16/40 (40%), Gaps = 7/40 (17%)
Query: 270 RGGR-GGRGGRG------GRGGRMAGGYGGYGGYGGGYGG 302
GGR GG R GG G YG GGG+G
Sbjct: 4 SGGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGF 43
Score = 32.7 bits (75), Expect = 0.55
Identities = 15/39 (38%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 504 RGGR-GGRGGRG------GRGGRMAGGYGGYGGYGGGYG 535
GGR GG R GG G YG GGG+G
Sbjct: 4 SGGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFG 42
Score = 31.1 bits (71), Expect = 1.8
Identities = 12/42 (28%), Positives = 15/42 (35%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKPLL 309
G GG R + GG G YG GG + L+
Sbjct: 6 GRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLI 47
Score = 30.4 bits (69), Expect = 3.0
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGG---YGGYGGGYGGILYKPLLF 310
R G GG G GG+G +G G GG L+ L+
Sbjct: 22 SPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGGGLFGLLIL 64
>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 = 30.9 bits (69), Expect = 0.38
Identities = 12/48 (25%), Positives = 27/48 (56%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
+++ GL P D+++ +G I+ T+ DK+ ++ K + F+ F+
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFD 57
>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 = 30.6 bits (69), Expect = 0.40
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
I++ LS M E+K F FG I E ++ KS+ + + FIT+ H L
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKV---LIKSRGEKYGFITYRHSEHAALSLGK 60
>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 = 30.5 bits (68), Expect = 0.41
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 184 SGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
+++ GL P D+++ +G I+ T+ DK+ ++ K + F+ F+ S
Sbjct: 1 KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS 54
Score = 29.0 bits (64), Expect = 1.7
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 599 HPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
HPG D ++L + YG+I + D T + +G+ F+ F + +KA
Sbjct: 10 HPGTTD---QDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 59
>gnl|CDD|111328 pfam02422, Keratin, Keratin. This family represents avian keratin
proteins, found in feathers, scale and claw.
Length = 98
Score = 31.0 bits (70), Expect = 0.43
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 278 GRGGRGGRMAGGYGGYGGYGGGYGG 302
G G +GGYGG GYGG Y G
Sbjct: 70 GYEGVPIS-SGGYGGLSGYGGRYLG 93
Score = 29.9 bits (67), Expect = 1.3
Identities = 14/30 (46%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYG 297
GV GG GG G GGR Y G GG
Sbjct: 73 GVPISSGGYGGLSGYGGR----YLGRGGPC 98
Score = 29.9 bits (67), Expect = 1.3
Identities = 14/30 (46%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYG 531
GV GG GG G GGR Y G GG
Sbjct: 73 GVPISSGGYGGLSGYGGR----YLGRGGPC 98
Score = 28.7 bits (64), Expect = 3.1
Identities = 12/24 (50%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 512 GRGGRGGRMAGGYGGYGGYGGGYG 535
G G +GGYGG GYGG Y
Sbjct: 70 GYEGVPIS-SGGYGGLSGYGGRYL 92
>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 = 30.3 bits (68), Expect = 0.43
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 14/65 (21%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNK 173
+ L+E F K +++ N GR +G+AF+ F S ED E + NN
Sbjct: 16 DSLQEVFEK-----ATSIRIPQNNGRPKGYAFVEF--------ESAEDA-KEALNSCNNT 61
Query: 174 KIEAK 178
+IE +
Sbjct: 62 EIEGR 66
Score = 29.5 bits (66), Expect = 0.91
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ L+E F K +++ N GR +G+AF+ F+ E ++A
Sbjct: 16 DSLQEVFEK-----ATSIRIPQNNGRPKGYAFVEFESAEDAKEA 54
>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 = 30.7 bits (69), Expect = 0.44
Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 6/66 (9%)
Query: 107 GIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLE--KASVEDVI 163
G+ TEE LKE F G I + +D +TG S+GF F+ F E + K ++ED
Sbjct: 7 GLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGE 63
Query: 164 AEGNHV 169
+GN V
Sbjct: 64 IDGNKV 69
Score = 29.9 bits (67), Expect = 0.78
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
+FV GLS + +E +K F I + D+ K F F+ F E K
Sbjct: 3 LFVKGLSEDTTEETLK---ESFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDA----KAA 55
Query: 247 KQKINDKEVDVKKAT 261
K+ + D E+D K T
Sbjct: 56 KEAMEDGEIDGNKVT 70
Score = 29.2 bits (65), Expect = 1.6
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 601 GIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
G+ + TEE LKE F G I + +D +TG S+GF F+ F E + A
Sbjct: 7 GLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAA 55
>gnl|CDD|240961 cd12517, RRM_RBM27, RNA recognition motif of vertebrate RNA-binding
protein 27 (RBM27). This subgroup corresponds to the
RRM of RBM27 which contains a single RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). Although the specific
function of the RRM in RBM27 remains unclear, it shows
high sequence similarity with RRM1of RBM26, which
functions as a cutaneous lymphoma (CL)-associated
antigen. .
Length = 76
Score = 30.4 bits (68), Expect = 0.45
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 14/72 (19%)
Query: 106 PGIVHKITEELKEHFSKYGEIEN--VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVI 163
P ++ IT+ L EHFSK+G I N V + DP A I + E +A I
Sbjct: 10 PQDLNNITQ-LNEHFSKFGTIVNIQVAFQGDPEA------ALIQYLTNEEARRA-----I 57
Query: 164 AEGNHVINNKKI 175
+ V+NN+ I
Sbjct: 58 SSTEAVLNNRFI 69
Score = 28.1 bits (62), Expect = 2.7
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 600 PGIVDKITEELKEHFSKYGEIEN--VTLKSDP 629
P ++ IT+ L EHFSK+G I N V + DP
Sbjct: 10 PQDLNNITQ-LNEHFSKFGTIVNIQVAFQGDP 40
>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein. This family of proteins
is greatly expanded in Trichomonas vaginalis. The
proteins are composed of several glycine rich motifs
interspersed through the sequence. Although many
proteins have been annotated by similarity in the family
these annotations given the biased composition of the
sequences these are unlikely to be functionally
relevant.
Length = 248
Score = 32.6 bits (75), Expect = 0.45
Identities = 16/34 (47%), Positives = 16/34 (47%)
Query: 267 FGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGY 300
FG G G GG GG G G Y G GG G Y
Sbjct: 163 FGYGGSGNGGGGGGGYFGGGGGHYAGGGGGGSSY 196
Score = 32.6 bits (75), Expect = 0.45
Identities = 16/34 (47%), Positives = 16/34 (47%)
Query: 501 FGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGY 534
FG G G GG GG G G Y G GG G Y
Sbjct: 163 FGYGGSGNGGGGGGGYFGGGGGHYAGGGGGGSSY 196
Score = 31.0 bits (71), Expect = 1.6
Identities = 16/31 (51%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 272 GRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GG G GG GG G +GG GG+ G GG
Sbjct: 164 GYGGSGNGGGGGG---GYFGGGGGHYAGGGG 191
Score = 30.2 bits (69), Expect = 2.5
Identities = 16/32 (50%), Positives = 16/32 (50%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 299
G G G G GG GG GG G Y G GGG
Sbjct: 161 GGFGYGGSGNGGGGGGGYFGGGGGHYAGGGGG 192
Score = 30.2 bits (69), Expect = 2.5
Identities = 16/32 (50%), Positives = 16/32 (50%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 533
G G G G GG GG GG G Y G GGG
Sbjct: 161 GGFGYGGSGNGGGGGGGYFGGGGGHYAGGGGG 192
Score = 29.9 bits (68), Expect = 3.4
Identities = 16/30 (53%), Positives = 17/30 (56%)
Query: 506 GRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
G GG G GG GG GG GG+ GGG G
Sbjct: 164 GYGGSGNGGGGGGGYFGGGGGHYAGGGGGG 193
Score = 29.1 bits (66), Expect = 7.6
Identities = 17/35 (48%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G GG GG G G G GG GGY GG GG
Sbjct: 152 GEGASSGGNGGFGYGGS--GNGGGGGGGYFGGGGG 184
>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 = 30.6 bits (69), Expect = 0.50
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
+++G + M E+K F+ FG I E + + +S+ N+ F+T+ +
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHF---RSEGDNYGFVTYRY 50
>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage
factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar
proteins. This subgroup corresponds to the RRM of
CFIm59. 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. The two separate genes,
CPSF6 and CPSF7, code for two isoforms of the large
subunit, CFIm68 and CFIm59. The family includes CFIm59,
also termed cleavage and polyadenylation specificity
factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59). CFIm59 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. The N-terminal
RRM of CFIm59 mediates the interaction with CFIm25. It
also serves to enhance RNA binding and facilitate RNA
looping. .
Length = 90
Score = 30.7 bits (69), Expect = 0.56
Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFG--NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLK 244
++VG S D+++ G +++E + +++ Q K + + E+ V LL+
Sbjct: 4 VYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 63
Query: 245 N-PKQKINDKEVDVKKAT 261
P + +N ++VDV+ AT
Sbjct: 64 LLPGKVLNGEKVDVRPAT 81
Score = 28.4 bits (63), Expect = 3.0
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 444 EIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN-PKQKINDKEVDVKKAT 495
+++E + +++ Q K + + E+ V LL+ P + +N ++VDV+ AT
Sbjct: 29 DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPAT 81
>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 = 30.5 bits (69), Expect = 0.58
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 9/68 (13%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCF-------ITFEHESV 238
+ V G P + + I+ HF+ FG IIE S +K F +T++
Sbjct: 3 SVIVFGFPPSLTNAVIE-HFSGFGEIIEDFEVPRSSSGLQKPPIFEGSNWVKLTYKEPLS 61
Query: 239 VID-LLKN 245
L +N
Sbjct: 62 AARALREN 69
>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 = 29.8 bits (67), Expect = 0.61
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
T +L+ HF YG++ NV ++ R FAF+ ++ E KA
Sbjct: 14 TRDLERHFEPYGKLVNVRIR--------RNFAFVQYETQEDATKA 50
Score = 29.8 bits (67), Expect = 0.61
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
T +L+ HF YG++ NV ++ R FAF+ ++ E KA
Sbjct: 14 TRDLERHFEPYGKLVNVRIR--------RNFAFVQYETQEDATKA 50
Score = 28.3 bits (63), Expect = 2.5
Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 10/76 (13%)
Query: 187 IFVGGLSP-EMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE-HESVVIDLLK 244
+FV P + +++ HF +G ++ + R+NF F+ +E E L
Sbjct: 2 LFVINFDPINTRTRDLERHFEPYGKLVNVRI--------RRNFAFVQYETQEDATKALES 53
Query: 245 NPKQKINDKEVDVKKA 260
K+ D+ + V+ A
Sbjct: 54 TNMSKVLDRVISVEYA 69
>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 = 30.1 bits (68), Expect = 0.62
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 178 KKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHE 236
+ + I V L ++ +E++ H A+ G I+ ++ +S K + F E
Sbjct: 1 RYCCPPTKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKV----FESNGKKQALVEFATE 55
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for growth.
Srp1p is closely related to the SR protein family found
in metazoa. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine hinge and a RS
domain in the middle, and a C-terminal domain. Some
family members also contain another RRM domain.
Length = 78
Score = 30.2 bits (68), Expect = 0.63
Identities = 10/48 (20%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++V G E + ++ F ++G ++ ++P ++ R F F+ +E
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRP-FAFVEYE 48
Score = 29.4 bits (66), Expect = 1.2
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+L F +YG + + P T +SR FAF+ ++ E A
Sbjct: 15 DLAYEFERYGRLVRCDIPP-PRTFQSRPFAFVEYESHRDAEDA 56
Score = 29.4 bits (66), Expect = 1.2
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+L F +YG + + P T +SR FAF+ ++ E A
Sbjct: 15 DLAYEFERYGRLVRCDIPP-PRTFQSRPFAFVEYESHRDAEDA 56
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 30.3 bits (69), Expect = 0.65
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L E FS+ GE++ V + D + +AF+ F + S+ A
Sbjct: 18 ADQLLEFFSQAGEVKYVRMAGDE--TQPTRYAFVEFAEQTSVINA 60
Score = 30.3 bits (69), Expect = 0.65
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L E FS+ GE++ V + D + +AF+ F + S+ A
Sbjct: 18 ADQLLEFFSQAGEVKYVRMAGDE--TQPTRYAFVEFAEQTSVINA 60
Score = 29.6 bits (67), Expect = 1.1
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNP 246
I+VG L P +++ F+Q G + M D++ Q + F+ F ++ VI+ LK
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDET--QPTRYAFVEFAEQTSVINALKLN 64
Query: 247 KQKINDKEVDVKKAT 261
+ + V +
Sbjct: 65 GAMFGGRPLKVNHSN 79
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 30.3 bits (69), Expect = 0.66
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 7/60 (11%)
Query: 596 MVSHPGIVDK-ITEELKEHFSKYGEIENV---TLKSDPNTGRSRGFAFIVFKDTESLEKA 651
MV+ PG +D+ + +E++E KYG++ NV + S R F+ F D + KA
Sbjct: 9 MVT-PGEIDEDLKDEIEEECEKYGKVLNVIVHEVASSEADDAVR--IFVEFSDADEAIKA 65
Score = 27.6 bits (62), Expect = 6.1
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 114 EELKEHFSKYGEIENV---TLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+E++E KYG++ NV + S R F+ F D + KA
Sbjct: 21 DEIEEECEKYGKVLNVIVHEVASSEADDAVR--IFVEFSDADEAIKA 65
>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 = 29.7 bits (67), Expect = 0.68
Identities = 15/50 (30%), Positives = 31/50 (62%), Gaps = 6/50 (12%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQR-KNFCFITFE 234
+I+VG L P+++ ++I+ F ++G I + ++ K++R F F+ FE
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDL-----KNRRGPPFAFVEFE 45
Score = 28.2 bits (63), Expect = 2.3
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 113 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
T+++++ F KYG I ++ LK+ R FAF+ F+D E A
Sbjct: 13 TKDIEDLFYKYGAIRDIDLKNR----RGPPFAFVEFEDPRDAEDA 53
Score = 28.2 bits (63), Expect = 2.3
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 607 TEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
T+++++ F KYG I ++ LK+ R FAF+ F+D E A
Sbjct: 13 TKDIEDLFYKYGAIRDIDLKNR----RGPPFAFVEFEDPRDAEDA 53
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 32.9 bits (75), Expect = 0.69
Identities = 19/44 (43%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 264 PEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILYKP 307
GG GG GG GG GG GG GG GG G + L+ P
Sbjct: 72 SASAISGGGGGGGGGFGGFGG--GGGGGGGGGGGWRFWLRLFAP 113
Score = 32.5 bits (74), Expect = 0.78
Identities = 17/37 (45%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 498 PEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGY 534
GG GG GG GG GG GG GG GG G +
Sbjct: 72 SASAISGGGGGGGGGFGGFGG--GGGGGGGGGGGWRF 106
Score = 32.1 bits (73), Expect = 1.0
Identities = 16/43 (37%), Positives = 17/43 (39%)
Query: 257 VKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 299
+ GG GG GG GG GG GG GG GG
Sbjct: 62 LVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGW 104
Score = 32.1 bits (73), Expect = 1.0
Identities = 16/43 (37%), Positives = 17/43 (39%)
Query: 491 VKKATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 533
+ GG GG GG GG GG GG GG GG
Sbjct: 62 LVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGW 104
Score = 31.0 bits (70), Expect = 2.9
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 260 ATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
+ V GG GG GG+GG+GG GGG GG
Sbjct: 59 SASLVANGAVALLSASAISGGGGGG--GGGFGGFGGGGGGGGG 99
Score = 29.1 bits (65), Expect = 9.7
Identities = 17/44 (38%), Positives = 19/44 (43%)
Query: 259 KATPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
A+ G GG GG GG+GG GG GGG GG
Sbjct: 59 SASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGG 102
>gnl|CDD|221210 pfam11759, KRTAP, Keratin-associated matrix. The major structural
proteins of mammalian hair are the hair keratin
intermediate filaments (KIFs) and the keratin-associated
proteins (KRTAPs). In the hair cortex, hair keratins are
embedded in an inter-filamentous matrix consisting of
KRTAPs which are essential for the formation of a rigid
and resistant hair shaft as a result of disulfide bonds
between cysteine residues. There are essentially three
groups of KRTAPs, viz: the high-sulfur (HS) and
ultra-high-sulfur (UHS) KRTAPs (cysteine content: 16-30
and >30 mol%, respectively) and the
high-glycine/tyrosine (HGT: 35-60 mol% glycine and
tyrosine) KRTAPs.
Length = 61
Score = 29.3 bits (66), Expect = 0.70
Identities = 17/35 (48%), Positives = 18/35 (51%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGGILY 305
GG GG G G G + G GG G G GYGG Y
Sbjct: 16 GGFGGLGCGYGCGCGLGYGSGGGYGCGSGYGGYGY 50
Score = 27.4 bits (61), Expect = 3.8
Identities = 17/32 (53%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 271 GGRG-GRGGRGGRGGRMAGGYGGYGGYGGGYG 301
GG G G GG GG G G G G GGGYG
Sbjct: 9 GGLGYGCGGFGGLGCGYGCGCGLGYGSGGGYG 40
Score = 27.4 bits (61), Expect = 3.8
Identities = 17/32 (53%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 505 GGRG-GRGGRGGRGGRMAGGYGGYGGYGGGYG 535
GG G G GG GG G G G G GGGYG
Sbjct: 9 GGLGYGCGGFGGLGCGYGCGCGLGYGSGGGYG 40
Score = 26.6 bits (59), Expect = 7.1
Identities = 20/38 (52%), Positives = 20/38 (52%), Gaps = 7/38 (18%)
Query: 505 GGRGGRG-GRG---GRGGRMAGGYG---GYGGYGGGYG 535
GG GG G G G G G GGYG GYGGYG G
Sbjct: 16 GGFGGLGCGYGCGCGLGYGSGGGYGCGSGYGGYGYGCC 53
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), an RNA-binding protein associated with the U1
snRNP, a small RNA-protein complex involved in pre-mRNA
splicing. U1A binds with high affinity and specificity
to stem-loop II (SLII) of U1 snRNA. It is predominantly
a nuclear protein and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large number
of non-snRNP proteins, including polypyrimidine tract
binding protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an important
role in virus replication. U1A contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and may
be free to bind other proteins. U1A also contains a
proline-rich region, and a nuclear localization signal
(NLS) in the central domain that is responsible for its
nuclear import. .
Length = 89
Score = 30.4 bits (68), Expect = 0.71
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA--SVEDVYFY 659
D++ + L FS++G+I ++ + + + RG AF++FK+ S A S++ FY
Sbjct: 18 DELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEVSSATNALRSMQGFPFY 72
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 32.4 bits (74), Expect = 0.73
Identities = 20/46 (43%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 508 GGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLWQFFDWISSSF 553
G G GG GG AGG+GG+ G GG G F+ I SSF
Sbjct: 69 GAAGANGGFGG-GAGGFGGFDGSGGFGG----------FEDIFSSF 103
Score = 31.2 bits (71), Expect = 1.9
Identities = 16/29 (55%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 274 GGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G G GG GG AGG+GG+ G GG+GG
Sbjct: 69 GAAGANGGFGG-GAGGFGGFDG-SGGFGG 95
>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 = 0.74
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 110 HKITEELKEHFSKYGE-IENVTLKSDPNTG-RSRGFAFIVFKD---TESLEKASVEDVIA 164
K EE+ E FSK E + +V + P+ ++RGFAF+ ++ + V I
Sbjct: 12 TKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMARRKLVPGRIL 71
Query: 165 EGNHVIN 171
H +
Sbjct: 72 LWGHEVA 78
Score = 28.0 bits (63), Expect = 3.8
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 604 DKITEELKEHFSKYGE-IENVTLKSDPNTG-RSRGFAFIVFKD 644
K EE+ E FSK E + +V + P+ ++RGFAF+ ++
Sbjct: 12 TKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYES 54
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 30.3 bits (69), Expect = 0.75
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 596 MVSHPGIVD-KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFA--FIVFKDTESLEKAS 652
MV PG VD + E+KE SKYG++ V + P F+ F+ ES KA
Sbjct: 10 MVG-PGEVDEDLEPEVKEECSKYGKVTKVLIFEIPGASPDDEAVRIFVEFERVESAIKAV 68
Query: 653 VE 654
V+
Sbjct: 69 VD 70
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM3 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 86
Score = 29.9 bits (68), Expect = 0.77
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 650
+ + + L EH K G + + L D + G+AFI F + E EK
Sbjct: 13 EMLLQLLDEHG-KGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEK 58
Score = 29.1 bits (66), Expect = 1.5
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 111 KITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEK 156
+ + L EH K G + + L D + G+AFI F + E EK
Sbjct: 14 MLLQLLDEHG-KGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEK 58
>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 = 29.5 bits (67), Expect = 0.78
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 188 FVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
V L PE+ +++ + FG + + KN F TF++E
Sbjct: 3 LVRHLPPELSEDDKEDLLKHFG-ASSVR--VMSRRGKLKNTAFATFDNEQ 49
>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 = 30.3 bits (69), Expect = 0.78
Identities = 15/89 (16%), Positives = 38/89 (42%), Gaps = 17/89 (19%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV-------- 238
++ G L ++ DE+++ F + E+ +++ ++N + +
Sbjct: 5 VYCGKLPKKVTDEDLREFFKDYN---PQEIWIFRTRKSKRNPLQLHRHFTAALVTLDTEE 61
Query: 239 ----VIDLLKNPKQKINDKEVDVKKATPK 263
+I+ LK +K+N K++ +K A
Sbjct: 62 TLDEIIESLK--SKKLNGKKISLKPAYLS 88
>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 = 29.6 bits (67), Expect = 0.79
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 114 EELKEHFSKYGEIENVTLK--SDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVIN 171
E+L+ ++ G ++ ++K G+S+GFA++ F + A+V++ + N
Sbjct: 13 EDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAA--AAAVKEKLE--GREFN 68
Query: 172 NKK 174
KK
Sbjct: 69 GKK 71
Score = 29.6 bits (67), Expect = 1.0
Identities = 10/42 (23%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 608 EELKEHFSKYGEIENVTLK--SDPNTGRSRGFAFIVFKDTES 647
E+L+ ++ G ++ ++K G+S+GFA++ F +
Sbjct: 13 EDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAA 54
>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar
proteins. This subgroup corresponds to the RRM of
PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect
modulator 6, a member of a family of transcription
coactivators that plays a central role in the regulation
of cellular energy metabolism. As an inducible
transcription coactivator, PGC-1alpha can interact with
a broad range of transcription factors involved in a
wide variety of biological responses, such as adaptive
thermogenesis, skeletal muscle fiber type switching,
glucose/fatty acid metabolism, and heart development.
PGC-1alpha stimulates mitochondrial biogenesis and
promotes oxidative metabolism. It participates in the
regulation of both carbohydrate and lipid metabolism and
plays a role in disorders such as obesity, diabetes, and
cardiomyopathy. PGC-1alpha is a multi-domain protein
containing an N-terminal activation domain region, a
central region involved in the interaction with at least
a nuclear receptor, and a C-terminal domain region. The
N-terminal domain region consists of three leucine-rich
motifs (L1, NR box 2 and 3), among which the two last
are required for interaction with nuclear receptors,
potential nuclear localization signals (NLS), and a
proline-rich region overlapping a putative repression
domain. The C-terminus of PGC-1alpha is composed of two
arginine/serine-rich regions (SR domains), a putative
dimerization domain, and an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). PGC-1alpha could interact
favorably with single-stranded RNA. .
Length = 91
Score = 30.3 bits (68), Expect = 0.79
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
I+VG + P+ E++ F FG I E + + ++ FIT+ + L+N
Sbjct: 5 IYVGKIRPDTTRTELRDRFEVFGEIEECTV---NLRDDGDSYGFITYRYTCDAFAALEN 60
>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 = 29.8 bits (67), Expect = 0.81
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
+ELKE F +I + K G S+G A+I FK EKA
Sbjct: 18 DELKEVFEDAVDIRLPSGK----DGSSKGIAYIEFKTEAEAEKA 57
Score = 29.8 bits (67), Expect = 0.81
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
+ELKE F +I + K G S+G A+I FK EKA
Sbjct: 18 DELKEVFEDAVDIRLPSGK----DGSSKGIAYIEFKTEAEAEKA 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 = 29.7 bits (67), Expect = 0.86
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHV-INN 172
EE + F G ++N + D TG S GF F+ ++ E ++A I N + + N
Sbjct: 15 EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRA-----IRTLNGLQLQN 69
Query: 173 KKIEAKKAKAKSG 185
K+I K A A+ G
Sbjct: 70 KRI--KVAYARPG 80
Score = 29.7 bits (67), Expect = 0.87
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EE + F G ++N + D TG S GF F+ ++ E ++A
Sbjct: 15 EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRA 58
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 29.3 bits (66), Expect = 0.92
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 4/48 (8%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++ G ++K F G + + M + FITFE
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRT----VQPHAFITFE 45
>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 = 29.9 bits (68), Expect = 0.95
Identities = 16/51 (31%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 603 VDKITEELKEHFSKYGEIENVTLKSDP--NTGRSRGFAFIVFKDTESLEKA 651
++K+ + L++ FSK+G + V + P TG+++G+AF+ F E ++A
Sbjct: 17 LEKLKKVLRKIFSKFGVGKIVGI-YMPVDETGKTKGYAFVEFATPEEAKEA 66
Score = 27.9 bits (63), Expect = 4.7
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 10/53 (18%)
Query: 107 GIVHKITEELKEHFSKYGEIENVTLKSDP--NTGRSRGFAFIVFKDTESLEKA 157
++ KI FSK+G + V + P TG+++G+AF+ F E ++A
Sbjct: 22 KVLRKI-------FSKFGVGKIVGI-YMPVDETGKTKGYAFVEFATPEEAKEA 66
>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 = 29.5 bits (67), Expect = 0.98
Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 6/51 (11%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHES 237
+F+ L E E ++ F QF E + R+ F+ FE E
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEE 49
>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM2 of CPEB family of proteins that
bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins has been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to the high sequence similarity, members
in this subfamily 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 CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 81
Score = 29.6 bits (67), Expect = 0.99
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 122 KYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINNKKIEAK 178
YG + V + +D G A + F + +S KA V +V E NK++ +
Sbjct: 24 LYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKA-VSEVFVELPFNDINKRVRIR 79
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein (hnRNP) H protein family.
This subfamily corresponds to the RRM2 of hnRNP H
protein family which 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). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation. hnRNP
H3 may be involved in the splicing arrest induced by
heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. .
Length = 77
Score = 29.3 bits (66), Expect = 1.1
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 114 EELKEHFSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EE+ + FS + N +TL D GRS G A++ F ES E+A
Sbjct: 15 EEIAQFFSGLEIVPNGITLPMDYR-GRSTGEAYVQFASQESAERA 58
Score = 29.3 bits (66), Expect = 1.1
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 608 EELKEHFSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EE+ + FS + N +TL D GRS G A++ F ES E+A
Sbjct: 15 EEIAQFFSGLEIVPNGITLPMDYR-GRSTGEAYVQFASQESAERA 58
>gnl|CDD|218059 pfam04391, DUF533, Protein of unknown function (DUF533). Some
family members may be secreted or integral membrane
proteins.
Length = 187
Score = 31.0 bits (71), Expect = 1.1
Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 13/84 (15%)
Query: 271 GGRGGRGG-----RGGRGGR-MAGGYGGYGGYGGGYGGILYKPLLFYELNELGISGRSLV 324
GG GG GG GG+ GR M G YGG GG+ YK ++ N+ +
Sbjct: 6 GGGGGLGGLLGALLGGKKGRKMGGKALKYGG-LAALGGLAYKAYQDWQQNQGTAAAGE-- 62
Query: 325 CRTGPMVQATPPLAEVDVTGVIMI 348
P P A+ + ++++
Sbjct: 63 ----PQPLDQLPPADEEQHSLLLL 82
>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 = 29.7 bits (66), Expect = 1.2
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
L + F +G + NV + D NT + +GF F+ + E A
Sbjct: 18 LWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMA 59
Score = 29.7 bits (66), Expect = 1.2
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
L + F +G + NV + D NT + +GF F+ + E A
Sbjct: 18 LWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMA 59
>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 = 29.2 bits (66), Expect = 1.3
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFG-NIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+++G L P M + IK FA G ++ ++ +K +CF+ F E+ L
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH- 60
Query: 246 PKQKINDK 253
K+N K
Sbjct: 61 ---KLNGK 65
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B). This
subgroup corresponds to the RRM of Setd1B, also termed
SET domain-containing protein 1B (Set1B), or lysine
N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits high
homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone H3
at Lys4. Set1B contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), an N- SET domain, and a
C-terminal catalytic SET domain followed by a post-SET
domain. .
Length = 93
Score = 29.6 bits (66), Expect = 1.3
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 595 KMVSHPGIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
K V+ + D I E L + KYGE+E V + +P + G A +VF + + A
Sbjct: 3 KQVTFAKLNDNIRENFLTDMCKKYGEVEEVEILYNPKNKKHLGIAKVVFATVKGAKDA 60
Score = 29.6 bits (66), Expect = 1.3
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 111 KITEELKEHF-----SKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
K+ + ++E+F KYGE+E V + +P + G A +VF + + A
Sbjct: 9 KLNDNIRENFLTDMCKKYGEVEEVEILYNPKNKKHLGIAKVVFATVKGAKDA 60
>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 = 29.4 bits (67), Expect = 1.3
Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 7/55 (12%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDP-------NTGRSRGFAFIVFKDTESLEKA 651
D EE E FSK G I+ P G +G A + ES+E A
Sbjct: 12 DITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKEESVELA 66
Score = 29.4 bits (67), Expect = 1.3
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 10/75 (13%)
Query: 114 EELKEHFSKYGEIENVTLKSDP-------NTGRSRGFAFIVFKDTESLEKASVEDVIAEG 166
EE E FSK G I+ P G +G A + ES+E A ++ + +G
Sbjct: 16 EEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKEESVELA-IQ--LLDG 72
Query: 167 NHVINNKKIEAKKAK 181
+ K++ ++AK
Sbjct: 73 TEIGRGYKMKVERAK 87
>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 = 29.2 bits (65), Expect = 1.3
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 111 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++ EE L E F + G + VT+ D G+ + F F+ FK +ES+ A
Sbjct: 12 RVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYA 58
Score = 29.2 bits (65), Expect = 1.3
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 605 KITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++ EE L E F + G + VT+ D G+ + F F+ FK +ES+ A
Sbjct: 12 RVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYA 58
Score = 29.2 bits (65), Expect = 1.4
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH-ESV 238
+FVG L +++E + F Q G + + + DK + + K+F F+ F+H ESV
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHSESV 55
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 31.7 bits (72), Expect = 1.4
Identities = 24/64 (37%), Positives = 26/64 (40%), Gaps = 7/64 (10%)
Query: 242 LLKN--PKQKINDKEVDVKKATPKPEPF-GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGG 298
LLK P+ I E D + K EP R RGG GGRG GGR G GG
Sbjct: 363 LLKKEIPRIAIPGYEPD---PSIKAEPIQNGRQQRGG-GGRGQGGGRGQQQGQPRRGEGG 418
Query: 299 GYGG 302
Sbjct: 419 AKSA 422
Score = 31.3 bits (71), Expect = 1.9
Identities = 24/61 (39%), Positives = 26/61 (42%), Gaps = 7/61 (11%)
Query: 476 LLKN--PKQKINDKEVDVKKATPKPEPF-GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGG 532
LLK P+ I E D + K EP R RGG GGRG GGR G GG
Sbjct: 363 LLKKEIPRIAIPGYEPD---PSIKAEPIQNGRQQRGG-GGRGQGGGRGQQQGQPRRGEGG 418
Query: 533 G 533
Sbjct: 419 A 419
>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 = 29.2 bits (65), Expect = 1.5
Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
+IF+G L ++ ++E+ + G I E M D + + R + F+TF ++ KN
Sbjct: 3 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNR-GYAFVTFSNKQEA----KN 57
Query: 246 PKQKINDKEV 255
+++N+ E+
Sbjct: 58 AIKQLNNYEI 67
>gnl|CDD|240960 cd12516, RRM1_RBM26, RNA recognition motif 1 of vertebrate
RNA-binding protein 26 (RBM26). This subgroup
corresponds to the RRM1 of RBM26, also known as
cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2,
which represents a cutaneous lymphoma (CL)-associated
antigen. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The RRMs may play some
functional roles in RNA-binding or protein-protein
interactions. .
Length = 76
Score = 28.8 bits (64), Expect = 1.6
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 13/64 (20%)
Query: 115 ELKEHFSKYGEIEN--VTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
+L EHFSK+G + N V K DP A I F E +KA I+ V+NN
Sbjct: 18 KLNEHFSKFGTLVNLQVAYKGDPEG------ALIQFATHEEAKKA-----ISSTEAVLNN 66
Query: 173 KKIE 176
+ I+
Sbjct: 67 RFIK 70
>gnl|CDD|191721 pfam07292, NID, Nmi/IFP 35 domain (NID). This family represents a
domain of approximately 90 residues that is tandemly
repeated within interferon-induced 35 kDa protein (IFP
35) and the homologous N-myc-interactor (Nmi). This
domain mediates Nmi-Nmi protein interactions and
subcellular localisation.
Length = 88
Score = 29.0 bits (65), Expect = 1.8
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 231 ITFEHESVVIDLLKNPKQKINDKEVDVK-KATPKPEPFGVR 270
ITFE E V ++L + + ++ ++ +A P P GVR
Sbjct: 3 ITFEKEEVAQNVLSMKEHHVQMEDCRLRVQAQPVPLNSGVR 43
Score = 29.0 bits (65), Expect = 1.8
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 465 ITFEHESVVIDLLKNPKQKINDKEVDVK-KATPKPEPFGVR 504
ITFE E V ++L + + ++ ++ +A P P GVR
Sbjct: 3 ITFEKEEVAQNVLSMKEHHVQMEDCRLRVQAQPVPLNSGVR 43
>gnl|CDD|222425 pfam13865, FoP_duplication, C-terminal duplication domain of Friend
of PRMT1. Fop, or Friend of Prmt1, proteins are
conserved from fungi and plants to vertebrates. There is
little that is actually conserved except for this
C-terminal LDXXLDAYM region where X is any amino acid).
The Fop proteins themselves are nuclear proteins
localised to regions with low levels of DAPI, with a
punctate/speckle-like distribution. Fop is a
chromatin-associated protein and it colocalises with
facultative heterochromatin. It is is critical for
oestrogen-dependent gene activation.
Length = 76
Score = 29.0 bits (65), Expect = 1.8
Identities = 16/32 (50%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 299
G RGG+ GRG R GR G GG G GG
Sbjct: 6 GSRGGKFRPRGRGARRGR-RRGRGGRKGKGGA 36
Score = 29.0 bits (65), Expect = 1.8
Identities = 16/32 (50%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 502 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGG 533
G RGG+ GRG R GR G GG G GG
Sbjct: 6 GSRGGKFRPRGRGARRGR-RRGRGGRKGKGGA 36
Score = 27.8 bits (62), Expect = 4.0
Identities = 11/19 (57%), Positives = 11/19 (57%)
Query: 267 FGVRGGRGGRGGRGGRGGR 285
F RG RG R GRGGR
Sbjct: 12 FRPRGRGARRGRRRGRGGR 30
Score = 27.8 bits (62), Expect = 4.0
Identities = 11/19 (57%), Positives = 11/19 (57%)
Query: 501 FGVRGGRGGRGGRGGRGGR 519
F RG RG R GRGGR
Sbjct: 12 FRPRGRGARRGRRRGRGGR 30
Score = 27.0 bits (60), Expect = 7.4
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
G +G RGG+ GRG R G G G GG
Sbjct: 3 GRKGSRGGKFRPRGRGAR--RGRRRGRGGRKGKGG 35
Score = 26.7 bits (59), Expect = 9.2
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 257 VKKATPKPEPFGVRGGR-GGRGGRGGRGG 284
+ +P G R GR GRGGR G+GG
Sbjct: 7 SRGGKFRPRGRGARRGRRRGRGGRKGKGG 35
Score = 26.7 bits (59), Expect = 9.2
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 491 VKKATPKPEPFGVRGGR-GGRGGRGGRGG 518
+ +P G R GR GRGGR G+GG
Sbjct: 7 SRGGKFRPRGRGARRGRRRGRGGRKGKGG 35
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 81
Score = 28.9 bits (65), Expect = 1.9
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 97 EAKNKMVSHPGIVHKITE-ELKEHFSKYG-EIENVTLKSDPNTGRSRGFAFIVFKDTESL 154
M+ G+ +TE +++ +G E ++V L TG SRGFAF+ F SL
Sbjct: 1 PNNTIMLR--GLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFM---SL 55
Query: 155 EKA 157
E+A
Sbjct: 56 EEA 58
Score = 28.9 bits (65), Expect = 2.1
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 591 EAKNKMVSHPGIVDKITE-ELKEHFSKYG-EIENVTLKSDPNTGRSRGFAFIVFKDTESL 648
M+ G+ +TE +++ +G E ++V L TG SRGFAF+ F SL
Sbjct: 1 PNNTIMLR--GLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFM---SL 55
Query: 649 EKA 651
E+A
Sbjct: 56 EEA 58
>gnl|CDD|234276 TIGR03601, B_an_ocin, probable heterocycle-containing bacteriocin,
BA_2677 family. Numerous bacteria encode systems for
producing bacteriocins by extensive modification of
ribosomally produced precursors. These proteins are
recognizable in part by proximity to the modification
proteins, and in part by small size, with leader
peptide-like N-terminal sequence followed by
low-complexity sequence rich in Cys, Gly, and/or Ser.
This protein family represents a probable member of the
class, though previously unrecognized because it is not
encoded adjacent to its modification proteins [Cellular
processes, Toxin production and resistance].
Length = 79
Score = 28.8 bits (64), Expect = 1.9
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 271 GGRGGRGGRGGR----GGRMAGGYGGYGGYG 297
GG GG G GGR GGR G +G +G +G
Sbjct: 43 GGCGGGGCCGGRCGGCGGRCGGCFGCFGCFG 73
Score = 28.8 bits (64), Expect = 1.9
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 505 GGRGGRGGRGGR----GGRMAGGYGGYGGYG 531
GG GG G GGR GGR G +G +G +G
Sbjct: 43 GGCGGGGCCGGRCGGCGGRCGGCFGCFGCFG 73
Score = 28.8 bits (64), Expect = 2.0
Identities = 15/36 (41%), Positives = 16/36 (44%)
Query: 508 GGRGGRGGRGGRMAGGYGGYGGYGGGYGELDYLQLW 543
GG GG G GGR G G GG G +G W
Sbjct: 43 GGCGGGGCCGGRCGGCGGRCGGCFGCFGCFGCFNCW 78
Score = 28.8 bits (64), Expect = 2.1
Identities = 14/28 (50%), Positives = 15/28 (53%)
Query: 274 GGRGGRGGRGGRMAGGYGGYGGYGGGYG 301
GG GG G GGR G G GG G +G
Sbjct: 43 GGCGGGGCCGGRCGGCGGRCGGCFGCFG 70
>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 = 29.1 bits (65), Expect = 2.0
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH 235
+F+G L + + +++ F +FG I E ++ + Q + F+ FE+
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIK-RPGRGQTSTYGFLKFEN 57
>gnl|CDD|147458 pfam05268, GP38, Phage tail fibre adhesin Gp38. This family
contains several Gp38 proteins from T-even-like phages.
Gp38, together with a second phage protein, gp57,
catalyzes the organisation of gp37 but is absent from
the phage particle. Gp37 is responsible for receptor
recognition.
Length = 261
Score = 30.9 bits (70), Expect = 2.1
Identities = 17/36 (47%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 268 GVRGGRGGR--GGRGGRGGRMAGGYGGYGGYGGGYG 301
GV GG GGR G G G M+GG GGG G
Sbjct: 171 GVCGGGGGRPFGAGGKSGSHMSGGNASLTAPGGGSG 206
Score = 30.9 bits (70), Expect = 2.1
Identities = 17/36 (47%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 502 GVRGGRGGR--GGRGGRGGRMAGGYGGYGGYGGGYG 535
GV GG GGR G G G M+GG GGG G
Sbjct: 171 GVCGGGGGRPFGAGGKSGSHMSGGNASLTAPGGGSG 206
Score = 29.4 bits (66), Expect = 5.0
Identities = 16/48 (33%), Positives = 16/48 (33%), Gaps = 11/48 (22%)
Query: 266 PFGVRGGRGGR-----------GGRGGRGGRMAGGYGGYGGYGGGYGG 302
PFG G G GG G G GG GG G GG
Sbjct: 180 PFGAGGKSGSHMSGGNASLTAPGGGSGTGSAYGGGNGGNVGAAGGRAW 227
Score = 29.4 bits (66), Expect = 6.3
Identities = 16/47 (34%), Positives = 16/47 (34%), Gaps = 11/47 (23%)
Query: 500 PFGVRGGRGGR-----------GGRGGRGGRMAGGYGGYGGYGGGYG 535
PFG G G GG G G GG GG G GG
Sbjct: 180 PFGAGGKSGSHMSGGNASLTAPGGGSGTGSAYGGGNGGNVGAAGGRA 226
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 85
Score = 28.9 bits (64), Expect = 2.1
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 595 KMVSHPGIVDKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 642
+M+ I +L+EH + E V L + ++G+SRGFAF+ F
Sbjct: 8 RMLPQNATETDIRGQLQEHGIQPRE---VRLMRNKSSGQSRGFAFVEF 52
>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 = 28.9 bits (64), Expect = 2.2
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITF 233
IFV LSPE + + F FG + ++ D + ++ K F F+T
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTM 50
>gnl|CDD|221759 pfam12764, Gly-rich_Ago1, Glycine-rich region of argonaut. This
domain is often found at the very N-terminal of
argonaut-like proteins.
Length = 102
Score = 29.2 bits (65), Expect = 2.3
Identities = 15/32 (46%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 271 GGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
GG GRG RGG G G GG G G G
Sbjct: 1 GGPPEYQGRG-RGGPPQQGGRGGGGGGRGGGS 31
>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 = 28.5 bits (63), Expect = 2.4
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKN 245
K+F+G +S + + +I+ F+ FG I E + R F+TF ++ +K
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSR-GCAFVTFTTRAMAQTAIKA 61
Query: 246 PKQ 248
Q
Sbjct: 62 MHQ 64
>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 = 28.4 bits (63), Expect = 2.4
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV 238
++FVG L ++ +E+ K F ++G E + D+ F FI E ++
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRG------FGFIRLESRTL 49
Score = 28.4 bits (63), Expect = 2.6
Identities = 18/51 (35%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 604 DKITEELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
D E+ K+ F KYGE V + R RGF FI + E A E
Sbjct: 12 DITEEDFKKLFEKYGEPSEVFIN------RDRGFGFIRLESRTLAEIAKAE 56
Score = 27.6 bits (61), Expect = 4.3
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
E+ K+ F KYGE V + R RGF FI + E A E
Sbjct: 16 EDFKKLFEKYGEPSEVFIN------RDRGFGFIRLESRTLAEIAKAE 56
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM2 of polypyrimidine tract-binding protein 1 (PTB or
hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2
or nPTB), regulator of differentiation 1 (Rod1),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), polypyrimidine tract-binding protein homolog
3 (PTBPH3), polypyrimidine tract-binding protein homolog
1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and
RRM3 of PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. Rod1 is a mammalian polypyrimidine tract
binding protein (PTB) homolog of a regulator of
differentiation in the fission yeast Schizosaccharomyces
pombe, where the nrd1 gene encodes an RNA binding
protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. .
Length = 85
Score = 28.7 bits (65), Expect = 2.5
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 9/58 (15%)
Query: 596 MVSHPGIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGF-AFIVFKDTESLEKA 651
+S+ + +T + L + FS YG +E + + ++ G A + F ES E A
Sbjct: 5 TISNL--LYPVTVDVLHQVFSPYGAVEKILIFE-----KNTGVQALVQFDSVESAENA 55
Score = 27.9 bits (63), Expect = 4.8
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 9/58 (15%)
Query: 102 MVSHPGIVHKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGF-AFIVFKDTESLEKA 157
+S+ ++ +T + L + FS YG +E + + ++ G A + F ES E A
Sbjct: 5 TISNL--LYPVTVDVLHQVFSPYGAVEKILIFE-----KNTGVQALVQFDSVESAENA 55
>gnl|CDD|237660 PRK14289, PRK14289, chaperone protein DnaJ; Provisional.
Length = 386
Score = 30.6 bits (69), Expect = 2.5
Identities = 17/46 (36%), Positives = 20/46 (43%), Gaps = 14/46 (30%)
Query: 271 GGRGGRGGRGGRGGRM--------------AGGYGGYGGYGGGYGG 302
GG G GG G G M GG+GG+GG+GGG
Sbjct: 76 GGAAGGGGFSGEGMSMEDIFSMFGDIFGGHGGGFGGFGGFGGGGSQ 121
Score = 30.2 bits (68), Expect = 3.3
Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 14/43 (32%)
Query: 505 GGRGGRGGRGGRGGRM--------------AGGYGGYGGYGGG 533
GG G GG G G M GG+GG+GG+GGG
Sbjct: 76 GGAAGGGGFSGEGMSMEDIFSMFGDIFGGHGGGFGGFGGFGGG 118
>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 = 28.3 bits (64), Expect = 2.6
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 114 EELKEHFSKYG-EIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVEDVIAEGNHVINN 172
E++++ FS + + + D + GR G A++ F E +A + N+ +
Sbjct: 14 EDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRALRKH-----NNKMGG 67
Query: 173 KKIE 176
+ IE
Sbjct: 68 RYIE 71
>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 = 28.2 bits (63), Expect = 2.6
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 148
EEL+E K+G I+ + + + + AF+ F
Sbjct: 18 EELREDLEKFGPIDQIKIVKE------KNIAFVHF 46
Score = 28.2 bits (63), Expect = 2.6
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 642
EEL+E K+G I+ + + + + AF+ F
Sbjct: 18 EELREDLEKFGPIDQIKIVKE------KNIAFVHF 46
>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 = 28.5 bits (63), Expect = 2.7
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++LKE FS+ G + +K + G+S+G + F ES EKA
Sbjct: 14 QKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKA 55
Score = 28.5 bits (63), Expect = 2.7
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++LKE FS+ G + +K + G+S+G + F ES EKA
Sbjct: 14 QKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKA 55
>gnl|CDD|240992 cd12548, RRM_Set1A, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1A (Set1A). This
subgroup corresponds to the RRM of Setd1A, also termed
SET domain-containing protein 1A (Set1A), or lysine
N-methyltransferase 2F, or Set1/Ash2 histone
methyltransferase complex subunit Set1, a ubiquitously
expressed vertebrates histone methyltransferase that
exhibits high homology to yeast Set1. Set1A is localized
to euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1A contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), an N- SET
domain, and a C-terminal catalytic SET domain followed
by a post-SET domain. In contrast to Set1B, Set1A
additionally contains an HCF-1 binding motif that
interacts with HCF-1 in vivo. .
Length = 95
Score = 28.8 bits (64), Expect = 2.8
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 595 KMVSHPGIVDKITEE-LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 647
K V+ + D + E L + K+GE+E V + P T + G A ++F T
Sbjct: 3 KEVTFARLNDNVREPFLADMCRKFGEVEEVEILLHPKTRKHLGLARVLFTSTRG 56
Score = 28.0 bits (62), Expect = 5.1
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTES 153
L + K+GE+E V + P T + G A ++F T
Sbjct: 19 LADMCRKFGEVEEVEILLHPKTRKHLGLARVLFTSTRG 56
>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 = 28.7 bits (65), Expect = 2.8
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 187 IFVGGLSPEMKDEEI---KAHFAQFGNII 212
++V GL P + DEE+ +F Q+G I
Sbjct: 8 VYVVGLPPRLADEEVLKKPEYFGQYGKIK 36
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 29.8 bits (67), Expect = 2.9
Identities = 14/30 (46%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 271 GGRGGRGGRGGRGGRMAGG-YGGYGGYGGG 299
GRG GG GG G GG +G G GG
Sbjct: 115 DGRGEGGGGGGGGDDGGGGDFGSSGPSRGG 144
Score = 29.8 bits (67), Expect = 2.9
Identities = 14/30 (46%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 505 GGRGGRGGRGGRGGRMAGG-YGGYGGYGGG 533
GRG GG GG G GG +G G GG
Sbjct: 115 DGRGEGGGGGGGGDDGGGGDFGSSGPSRGG 144
>gnl|CDD|164795 PHA00370, III, attachment protein.
Length = 297
Score = 30.3 bits (68), Expect = 3.0
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 505 GGRGGRGGRGGRGGRMAGGY--GGYGGYGGGYGELDYLQLWQFF-DWISSSFSENCLLED 561
G GG GG G GG GG G G G+ DY ++ D ++ +N L +D
Sbjct: 112 GDTGGSGGGGSDGGGSEGGSTGKSLTKEGVGAGDFDYPKMANANKDALTEDNDQNALQKD 171
Query: 562 SIGK 565
+ +
Sbjct: 172 ADEQ 175
>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 = 28.3 bits (64), Expect = 3.1
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 110 HKITEE-LKEHFSKYGEIENVTLKSDP------NTGRSRGFAFIVFKDTESLEKA 157
++TEE L F ++ +++ + + + GR +G AF+ F E KA
Sbjct: 11 KRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKA 63
Score = 27.9 bits (63), Expect = 3.7
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 608 EELKEHFSKYGEIENVTLKSDP------NTGRSRGFAFIVFKDTESLEKA 651
E+L F ++ +++ + + + GR +G AF+ F E KA
Sbjct: 16 EDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKA 63
>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional.
Length = 392
Score = 30.5 bits (69), Expect = 3.1
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 280 GGRGGRMAGGYGGYGGYGGGYGG 302
GG GGR G GG+GG+G G G
Sbjct: 81 GGFGGRRFDGGGGFGGFGTGGDG 103
Score = 29.7 bits (67), Expect = 5.9
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 514 GGRGGRMAGGYGGYGGYGGGYGELDY 539
GG GGR G GG+GG+G G ++
Sbjct: 81 GGFGGRRFDGGGGFGGFGTGGDGAEF 106
Score = 29.3 bits (66), Expect = 8.0
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 511 GGRGGRGGRMAGGYGGYGGYGGGYGELD 538
GG GGR GG+GG+G GG E +
Sbjct: 81 GGFGGRRFDGGGGFGGFGT-GGDGAEFN 107
Score = 28.9 bits (65), Expect = 10.0
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 277 GGRGGRGGRMAGGYGGYGGYGGGYG 301
GG GGR GG+GG+G G G
Sbjct: 81 GGFGGRRFDGGGGFGGFGTGGDGAE 105
>gnl|CDD|221518 pfam12301, CD99L2, CD99 antigen like protein 2. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 165 and 237 amino acids in length.
CD99L2 and CD99 are involved in trans-endothelial
migration of neutrophils in vitro and in the recruitment
of neutrophils into inflamed peritoneum.
Length = 154
Score = 29.4 bits (66), Expect = 3.1
Identities = 18/63 (28%), Positives = 22/63 (34%), Gaps = 12/63 (19%)
Query: 252 DKEVDVKKATPKPEPFGVRGGRGG------------RGGRGGRGGRMAGGYGGYGGYGGG 299
K P+P+P G GG G + +G GG GG GG GG
Sbjct: 44 GGAGPKPKPRPQPDPGNPGGDGGGFSDSDLADVAGDGGYKPDKGKGGGGGGGGGGGTDGG 103
Query: 300 YGG 302
G
Sbjct: 104 PEG 106
Score = 29.4 bits (66), Expect = 3.2
Identities = 17/63 (26%), Positives = 21/63 (33%), Gaps = 12/63 (19%)
Query: 486 DKEVDVKKATPKPEPFGVRGGRGG------------RGGRGGRGGRMAGGYGGYGGYGGG 533
K P+P+P G GG G + +G GG GG GG GG
Sbjct: 44 GGAGPKPKPRPQPDPGNPGGDGGGFSDSDLADVAGDGGYKPDKGKGGGGGGGGGGGTDGG 103
Query: 534 YGE 536
Sbjct: 104 PEG 106
>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 = 27.9 bits (62), Expect = 3.2
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++FVG L P++ +EE++ F ++G E + DK F FI E
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKG------FGFIRLE 45
Score = 26.8 bits (59), Expect = 7.6
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF--KDTESLEKASVEDVIAEGNHV 169
EE+++ F KYG+ + + D +GF FI + + KA ++++ G +
Sbjct: 16 EEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAELDNMPLRGKQL 67
>gnl|CDD|218967 pfam06273, eIF-4B, Plant specific eukaryotic initiation factor 4B.
This family consists of several plant specific
eukaryotic initiation factor 4B proteins.
Length = 496
Score = 30.4 bits (68), Expect = 3.3
Identities = 19/47 (40%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 258 KKATPKPEPFGVRGGRGGRGGR--GGRGGRMAGGYGGYGGYGGGYGG 302
KK+TP P R GR GG GG GG GG GG+ G
Sbjct: 164 KKSTPLPSFDQGRQGRYPSGGGAFGGGGGGGGGGERRSGGFRDSPGA 210
Score = 30.1 bits (67), Expect = 3.9
Identities = 20/49 (40%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 492 KKATPKPEPFGVRGGRGGRGGR--GGRGGRMAGGYGGYGGYGGGYGELD 538
KK+TP P R GR GG GG GG GG GG+ G D
Sbjct: 164 KKSTPLPSFDQGRQGRYPSGGGAFGGGGGGGGGGERRSGGFRDSPGADD 212
>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 = 28.1 bits (62), Expect = 3.4
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 116 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD 150
L + F +G + NV + D NT + +GF F+ +
Sbjct: 20 LWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTN 54
Score = 28.1 bits (62), Expect = 3.4
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 610 LKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKD 644
L + F +G + NV + D NT + +GF F+ +
Sbjct: 20 LWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTN 54
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its median
region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated in
protein shuttling and protein-protein interactions. .
Length = 77
Score = 28.1 bits (62), Expect = 3.5
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 115 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EL+ FS YG + V + +P GFAF+ F+D E A
Sbjct: 15 ELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDA 52
Score = 28.1 bits (62), Expect = 3.5
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 609 ELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EL+ FS YG + V + +P GFAF+ F+D E A
Sbjct: 15 ELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDA 52
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 30.1 bits (68), Expect = 3.7
Identities = 18/37 (48%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 265 EPFGVRGG-RGGRGGRGGRGGRMAGGYGGYGGYGGGY 300
GVRGG R R G GG GG GG GG G G
Sbjct: 179 SCGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPP 215
Score = 30.1 bits (68), Expect = 3.7
Identities = 18/37 (48%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 499 EPFGVRGG-RGGRGGRGGRGGRMAGGYGGYGGYGGGY 534
GVRGG R R G GG GG GG GG G G
Sbjct: 179 SCGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPP 215
Score = 28.9 bits (65), Expect = 7.5
Identities = 17/51 (33%), Positives = 18/51 (35%), Gaps = 10/51 (19%)
Query: 261 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGG----------YGGYGGGYG 301
+ P R G GG GG GG GG G G YG G G
Sbjct: 182 GVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAG 232
Score = 28.9 bits (65), Expect = 7.5
Identities = 17/51 (33%), Positives = 18/51 (35%), Gaps = 10/51 (19%)
Query: 495 TPKPEPFGVRGGRGGRGGRGGRGGRMAGGYGG----------YGGYGGGYG 535
+ P R G GG GG GG GG G G YG G G
Sbjct: 182 GVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAG 232
>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 = 28.0 bits (63), Expect = 3.7
Identities = 12/35 (34%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 148
+++KE F+++G ++ + D + GRS G A +VF
Sbjct: 15 DDIKELFAEFGALKKAAVHYDRS-GRSLGTADVVF 48
Score = 28.0 bits (63), Expect = 3.7
Identities = 12/35 (34%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVF 642
+++KE F+++G ++ + D + GRS G A +VF
Sbjct: 15 DDIKELFAEFGALKKAAVHYDRS-GRSLGTADVVF 48
>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 = 28.2 bits (63), Expect = 3.7
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNI 211
+FV L P ++++ HF G I
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGII 25
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 28.5 bits (64), Expect = 3.8
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
E++KE FS++GE++ V G R FK E+ +KA
Sbjct: 16 EDIKEAFSQHGEVKYVDFLEGDKEGYVR------FKTPEAAKKA 53
Score = 28.5 bits (64), Expect = 3.8
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
E++KE FS++GE++ V G R FK E+ +KA
Sbjct: 16 EDIKEAFSQHGEVKYVDFLEGDKEGYVR------FKTPEAAKKA 53
>gnl|CDD|220915 pfam10961, DUF2763, Protein of unknown function (DUF2763). This
eukaryotic family of proteins has no known function.
Length = 91
Score = 28.1 bits (63), Expect = 3.8
Identities = 11/40 (27%), Positives = 13/40 (32%)
Query: 263 KPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYGG 302
+ + G R G G GG G GGG G
Sbjct: 44 VTKRYRKNSSSGKRWDGGRGGPGPPGGGRRMGRIGGGGGP 83
Score = 27.4 bits (61), Expect = 8.7
Identities = 11/39 (28%), Positives = 13/39 (33%)
Query: 497 KPEPFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
+ + G R G G GG G GGG G
Sbjct: 44 VTKRYRKNSSSGKRWDGGRGGPGPPGGGRRMGRIGGGGG 82
>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 = 27.6 bits (61), Expect = 4.1
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESV 238
++FVG L ++ ++E K FA++G P + ++ K F FI E ++
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGE------PGEVFINKGKGFGFIKLESRAL 49
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 30.0 bits (67), Expect = 4.3
Identities = 16/56 (28%), Positives = 20/56 (35%), Gaps = 7/56 (12%)
Query: 252 DKEVDVKKATPKPE------PFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 301
V KK+ P + G + G+ G R G GG GG G GY
Sbjct: 485 GNNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGG-GGRGRGYN 539
Score = 30.0 bits (67), Expect = 4.3
Identities = 16/56 (28%), Positives = 20/56 (35%), Gaps = 7/56 (12%)
Query: 486 DKEVDVKKATPKPE------PFGVRGGRGGRGGRGGRGGRMAGGYGGYGGYGGGYG 535
V KK+ P + G + G+ G R G GG GG G GY
Sbjct: 485 GNNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGG-GGRGRGYN 539
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B") a unique protein that comprises the U2 snRNP.
It was initially identified as binding to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA. In addition, the
nuclear transport of U2B" is independent of U2 snRNA
binding. U2B" contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also contains a nuclear
localization signal (NLS) in the central domain.
However, nuclear import of U2B'' does not depend on this
NLS. The N-terminal RRM is sufficient to direct U2B" to
the nucleus. .
Length = 91
Score = 28.1 bits (62), Expect = 4.3
Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 10/54 (18%)
Query: 604 DKIT-EELKEH----FSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
DKI EELK FS++G + + V LK T + RG AF++FK+ S A
Sbjct: 11 DKIKKEELKRSLYALFSQFGHVVDIVALK----TMKMRGQAFVIFKELSSATNA 60
>gnl|CDD|220755 pfam10439, Bacteriocin_IIc, Bacteriocin class II with
double-glycine leader peptide. This is a family of
bacteriocidal bacteriocins secreted by Streptococcal
species in order to kill off closely-related competitor
Gram-positives. The sequence includes the peptide
precursor, this being cleaved off proteolytically at the
double-glycine. The family does not carry the YGNGVXC
motif characteristic of pediocin-like Bacteriocins,
Bacteriocin_II pfam01721. The producer bacteria are
protected from the effects of their own bacteriocins by
production of a specific immunity protein which is
co-transcribed with the genes encoding the bacteriocins,
eg family EntA_Immun pfam08951. The bacteriocins are
structurally more specific than their immunity-protein
counterparts. Typically, production of the bacteriocin
gene is from within an operon carrying up to 6 genes
including a typical two-component regulatory system (R
and H), a small peptide pheromone (C), and a dedicated
ABC transporter (A and -B) as well as an immunity
protein. The ABC transporter is thought to recognise the
N termini of both the pheromone and the bacteriocins and
to transport these peptides across the cytoplasmic
membrane, concurrent with cleavage at the conserved
double-glycine motif. Cleaved extracellular C can then
bind to the sensor kinase, H, resulting in activation of
R and up-regulation of the entire gene cluster via
binding to consensus sequences within each promoter. It
seems likely that this whole regulon is carried on a
transmissible plasmid which is passed between closely
related Firmicute species since many clinical isolates
from different Firmicutes can produce at least two
bacteriocins. and the same bacteriocins can be produced
by different species.
Length = 65
Score = 27.3 bits (61), Expect = 4.3
Identities = 14/37 (37%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 268 GVRGGRGGRGGRGGRGGRMAGGYGG--YGGYGGGYGG 302
G+ GG G GG GG G GG G GG
Sbjct: 28 GIGGGAAAGAVAGAAGGGPVGGLAGALVGGVVGAIGG 64
>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 = 28.1 bits (62), Expect = 4.4
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 120 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKD 150
F +G + NV + D NT + +GF F+ +
Sbjct: 24 FGPFGAVNNVKVIRDFNTNKCKGFGFVTMTN 54
Score = 28.1 bits (62), Expect = 4.4
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 614 FSKYGEIENVTLKSDPNTGRSRGFAFIVFKD 644
F +G + NV + D NT + +GF F+ +
Sbjct: 24 FGPFGAVNNVKVIRDFNTNKCKGFGFVTMTN 54
>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 = 27.7 bits (62), Expect = 4.6
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEH--ESV-VIDLL 243
IFV L ++ +++K F G ++ ++ DK R + FEH E+V I +
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSR-GMGVVQFEHPIEAVQAISMF 59
Query: 244 KNPKQKINDKEVDVK 258
Q + D+ + VK
Sbjct: 60 NG--QMLFDRPMRVK 72
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 27.2 bits (60), Expect = 4.9
Identities = 10/49 (20%), Positives = 28/49 (57%), Gaps = 8/49 (16%)
Query: 186 KIFVGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFE 234
++F+G L+P ++++++ F +G I + ++ ++ F F+ F+
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFD 41
Score = 27.2 bits (60), Expect = 5.0
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 160
++++ F YG I ++ LK RGF F+ F D + A E
Sbjct: 14 KDVERFFKGYGRIRDIDLK--------RGFGFVEFDDPRDADDAVYE 52
Score = 27.2 bits (60), Expect = 5.0
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKASVE 654
++++ F YG I ++ LK RGF F+ F D + A E
Sbjct: 14 KDVERFFKGYGRIRDIDLK--------RGFGFVEFDDPRDADDAVYE 52
>gnl|CDD|217975 pfam04228, Zn_peptidase, Putative neutral zinc metallopeptidase.
Members of this family have a predicted zinc binding
motif characteristic of neutral zinc metallopeptidases
(Prosite:PDOC00129).
Length = 292
Score = 29.7 bits (67), Expect = 5.2
Identities = 16/44 (36%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 270 RGGRGGRGGRGGRGGRMAGGYGGYG----GYGGGYGGILYKPLL 309
RG GG G GG G R+ GG G G Y G+ +L
Sbjct: 16 RGSSGGGGNGGGGGFRLGGGKTGLVVLILVLVGWYFGVDLSGIL 59
>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 = 27.7 bits (62), Expect = 5.4
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 187 IFVGGLSPEMKDEEIKAHFAQFGNI 211
I++ GL ++ ++ + F G I
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGII 25
>gnl|CDD|225826 COG3288, PntA, NAD/NADP transhydrogenase alpha subunit [Energy
production and conversion].
Length = 356
Score = 29.3 bits (66), Expect = 6.1
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 153 SLEKASVEDVIAEGNHVINNKKIEAKKAKAKSGKIFVGGLSPEMKDEEIKAHFAQFG 209
+ + D+I + A+ A K G V L+P DE + A A F
Sbjct: 58 AADAVWQADIILK-----VRAPSAAEIALLKEGATLVSFLNPYQNDELVFA-LAIFV 108
>gnl|CDD|183662 PRK12662, PRK12662, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 492
Score = 29.7 bits (67), Expect = 6.1
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 44 DYLQLWQYFDWVSSSFSENCLLEDSIGKPLTVSCSHHYYLFDQILRTHFF 93
D L LW+ ++ +F L IG P T +Y+ D ++++ +
Sbjct: 365 DCLNLWKSMPKITLAFVLLSL--SLIGMPPTSGFVAKWYILDAFIKSNAW 412
>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 = 27.3 bits (60), Expect = 6.2
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 122 KYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
K GE+ V L D G+SRG + FKD E ++KA
Sbjct: 23 KVGEVTYVELFKDAE-GKSRGCGVVEFKDEEFVKKA 57
Score = 27.3 bits (60), Expect = 6.2
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 616 KYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
K GE+ V L D G+SRG + FKD E ++KA
Sbjct: 23 KVGEVTYVELFKDAE-GKSRGCGVVEFKDEEFVKKA 57
>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 = 27.1 bits (60), Expect = 6.2
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 114 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
++L + F YGEI+ + + PN R FI F D S E A
Sbjct: 16 DDLHQIFGAYGEIKEI--RETPN---KRHHKFIEFYDVRSAEAA 54
Score = 27.1 bits (60), Expect = 6.2
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 608 EELKEHFSKYGEIENVTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
++L + F YGEI+ + + PN R FI F D S E A
Sbjct: 16 DDLHQIFGAYGEIKEI--RETPN---KRHHKFIEFYDVRSAEAA 54
>gnl|CDD|235799 PRK06419, rpl15p, 50S ribosomal protein L15P; Reviewed.
Length = 148
Score = 28.3 bits (64), Expect = 6.8
Identities = 15/42 (35%), Positives = 16/42 (38%), Gaps = 14/42 (33%)
Query: 268 GVRGGRGGRGGRGGRGGRMAG------------GYGGYGGYG 297
G G G RGGRG MAG G YG +G
Sbjct: 20 GTHKNHRGAGSRGGRG--MAGRHKHKWTWVVKYGPDWYGKHG 59
Score = 28.3 bits (64), Expect = 6.8
Identities = 15/42 (35%), Positives = 16/42 (38%), Gaps = 14/42 (33%)
Query: 502 GVRGGRGGRGGRGGRGGRMAG------------GYGGYGGYG 531
G G G RGGRG MAG G YG +G
Sbjct: 20 GTHKNHRGAGSRGGRG--MAGRHKHKWTWVVKYGPDWYGKHG 59
>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 29.3 bits (66), Expect = 6.9
Identities = 10/28 (35%), Positives = 10/28 (35%), Gaps = 1/28 (3%)
Query: 259 KATPKPE-PFGVRGGRGGRGGRGGRGGR 285
A FG RG G GRG G
Sbjct: 3 AARGGEGRGFGRRGRGGRGRGRGRGRGG 30
Score = 29.3 bits (66), Expect = 6.9
Identities = 10/28 (35%), Positives = 10/28 (35%), Gaps = 1/28 (3%)
Query: 493 KATPKPE-PFGVRGGRGGRGGRGGRGGR 519
A FG RG G GRG G
Sbjct: 3 AARGGEGRGFGRRGRGGRGRGRGRGRGG 30
>gnl|CDD|237665 PRK14295, PRK14295, chaperone protein DnaJ; Provisional.
Length = 389
Score = 29.4 bits (66), Expect = 7.1
Identities = 33/120 (27%), Positives = 52/120 (43%), Gaps = 19/120 (15%)
Query: 189 VGGLSPEMKDEEIKAHFAQFGNIIETEMPYDKSKSQRKNFCFITFEHESVVIDLLKNPKQ 248
V G+ + + EIK + + + +K++ + F+ S D+L + K+
Sbjct: 14 VLGVPKDATEAEIKKAYRKLAREYHPDANKGDAKAEER------FKEISEAYDVLSDEKK 67
Query: 249 KINDKEVDVKKATPKPEPFGVRGGRGGRGGRGGRG-----GRMAGGYGGYGGYGGGYGGI 303
+ KE D ++ FG G R G GG GG G G + GG GG GG GG+
Sbjct: 68 R---KEYDEARSL-----FGNGGFRPGPGGGGGGGFNFDLGDLFGGGAQGGGGAGGGGGL 119
>gnl|CDD|221517 pfam12300, DUF3628, Protein of unknown function (DUF3628). This
domain family is found in bacteria, and is typically
between 153 and 183 amino acids in length. The family is
found in association with pfam00270, pfam00271.
Length = 180
Score = 28.5 bits (63), Expect = 7.6
Identities = 14/26 (53%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 274 GGRGGRGGRGGRMAGGYGGYGGYGGG 299
GGR G G R GR G G G GGG
Sbjct: 58 GGRSGPGERSGRPVGK-GPRDGDGGG 82
Score = 28.5 bits (63), Expect = 7.6
Identities = 14/26 (53%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 508 GGRGGRGGRGGRMAGGYGGYGGYGGG 533
GGR G G R GR G G G GGG
Sbjct: 58 GGRSGPGERSGRPVGK-GPRDGDGGG 82
>gnl|CDD|241175 cd12731, RRM2_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM2 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 83
Score = 27.3 bits (60), Expect = 7.6
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 114 EELKEHFSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKA 157
EE+ + FS + N +TL D GRS G AF+ F E EKA
Sbjct: 16 EEIVQFFSGLEIVPNGITLPVDFQ-GRSTGEAFVQFASQEIAEKA 59
Score = 27.3 bits (60), Expect = 7.6
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 608 EELKEHFSKYGEIEN-VTLKSDPNTGRSRGFAFIVFKDTESLEKA 651
EE+ + FS + N +TL D GRS G AF+ F E EKA
Sbjct: 16 EEIVQFFSGLEIVPNGITLPVDFQ-GRSTGEAFVQFASQEIAEKA 59
>gnl|CDD|187738 cd09617, Peptidase_C12_UCH37_BAP1, Cysteine peptidase C12
containing ubiquitin carboxyl-terminal hydrolase (UCH)
families UCH37 (UCH-L5) and BAP1. This ubiquitin
C-terminal hydrolase (UCH) family includes UCH37 (also
known as UCH-L5) and BRCA1-associated protein-1 (BAP1).
They contain a UCH catalytic domain as well as an
additional C-terminal extension which plays a role in
protein-protein interactions. UCH37 is responsible for
ubiquitin (Ub) isopeptidase activity in the 19S
proteasome regulatory complex; it disassembles
Lys48-linked poly-ubiquitin from the distal end of the
chain. It is also associated with the human Ino80
chromatin-remodeling complex (hINO80) in the nucleus and
can be activated through transient association of hINO80
with hRpn13 that is bound to the 19S regulatory particle
or the proteasome. UCH37 possibly plays a role in
oncogenesis; it competes with Smad ubiquitination
regulatory factor 2 (Smurf2, ubiquitin ligase) in
binding concurrently to Smad7 in order to deubiquitinate
the activated type I transforming growth factor beta
(TGF-beta) receptor, thus rescuing it from proteasomal
degradation. BAP1 binds to the wild-type BRCA1 RING
finger domain, localized in the nucleus. In addition to
the UCH catalytic domain, BAP1 contains a UCH37-like
domain (ULD), binding domains for BRCA1 and BARD1, which
form a tumor suppressor heterodimeric complex, and a
binding domain for HCFC1, which interacts with
histone-modifying complexes during cell division. The
full-length human BRCA1 is a ubiquitin ligase. However,
BAP1 does not appear to function in the deubiquitination
of autoubiquitinated BRCA1. BAP1 exhibits tumor
suppressor activity in cancer cells, and gene mutations
have been reported in a small number of breast and lung
cancer samples. In metastasis of uveal melanoma, the
most common primary cancer of the eye, inactivating
somatic mutations have been identified in the gene
encoding BAP1 on chromosome 3p21.1. These mutations
include several that cause premature protein termination
as well as affect its UCH domain, thus implicating loss
of BAP1 and suggesting that the BAP1 pathway may be a
valuable therapeutic target.
Length = 219
Score = 28.7 bits (65), Expect = 8.9
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 9/57 (15%)
Query: 186 KIFVGGLSPEMKDEEI-------KAH--FAQFGNIIETEMPYDKSKSQRKNFCFITF 233
K F G PEMK E I K H FA+ + E K+ + F FI++
Sbjct: 107 KEFTKGFDPEMKGEAIGNSEEIRKVHNSFARPEPFLLDEKLNKKATKEEDAFHFISY 163
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 0.136 0.406
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,748,478
Number of extensions: 3509073
Number of successful extensions: 6616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5856
Number of HSP's successfully gapped: 1002
Length of query: 661
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 558
Effective length of database: 6,369,140
Effective search space: 3553980120
Effective search space used: 3553980120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 62 (27.6 bits)