RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14686
(306 letters)
>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 = 155 bits (395), Expect = 2e-48
Identities = 55/78 (70%), Positives = 63/78 (80%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLFIGGL Y T DDSLK +F QWGEI D VVMKDP TKRSRGFGF+T++ + VD AM+
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 105 RPHEIDGRVVETKRAVPR 122
RPH++DGR VE KRAVPR
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
Score = 30.0 bits (68), Expect = 0.32
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
YF Q+G I ++ + T RGF F+ F VD
Sbjct: 19 YFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDA 56
>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 = 122 bits (307), Expect = 3e-35
Identities = 54/80 (67%), Positives = 65/80 (81%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
LRKLFIGGL + T D+SL++ FEQWG + D VVM+DP TKRSRGFGF+TYS + VD AM
Sbjct: 2 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61
Query: 103 SNRPHEIDGRVVETKRAVPR 122
+ RPH++DGRVVE KRAV R
Sbjct: 62 NARPHKVDGRVVEPKRAVSR 81
Score = 27.0 bits (59), Expect = 3.7
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVD 177
+F Q+GT+ ++ + T RGF F+ + + VD
Sbjct: 21 SHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVD 58
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 117 bits (295), Expect = 1e-33
Identities = 55/80 (68%), Positives = 64/80 (80%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
LRKLFIGGL + T DDSL+ FE+WG + D VVM+DP TKRSRGFGF+TYS + VD AM
Sbjct: 2 LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61
Query: 103 SNRPHEIDGRVVETKRAVPR 122
S RPH++DGRVVE KRAV R
Sbjct: 62 SARPHKVDGRVVEPKRAVSR 81
>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 = 117 bits (294), Expect = 2e-33
Identities = 50/80 (62%), Positives = 63/80 (78%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
RKLFIGGL + T ++SL+ ++EQWG++ D VVM+DP +KRSRGFGF+T+S VD AM
Sbjct: 2 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61
Query: 103 SNRPHEIDGRVVETKRAVPR 122
+ RPH IDGRVVE KRAV R
Sbjct: 62 AARPHTIDGRVVEPKRAVAR 81
>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 = 113 bits (285), Expect = 5e-32
Identities = 36/72 (50%), Positives = 57/72 (79%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LFIGGL + T ++SL+ +F ++GE+VD V+MKDP+T RSRGFGF+T+++ VD+ ++ +
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 106 PHEIDGRVVETK 117
PH +DGR ++ K
Sbjct: 61 PHVLDGREIDPK 72
Score = 51.4 bits (124), Expect = 6e-09
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVL---EVD 190
+YF +YG + ++ + TG RGF F+ F D VDK++ K VL E+D
Sbjct: 17 EYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGREID 70
>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 = 104 bits (261), Expect = 2e-28
Identities = 42/78 (53%), Positives = 56/78 (71%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L KLF+GGL+ +T+D L+ F ++G++ + VVM DP TKRSRGFGFIT+S + DEAM
Sbjct: 2 LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
Query: 103 SNRPHEIDGRVVETKRAV 120
+PH IDG +E KRA
Sbjct: 62 EAQPHSIDGNQIELKRAK 79
Score = 29.4 bits (66), Expect = 0.58
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+F +YG + ++ + T RGF FI F
Sbjct: 21 RHFTRYGKLTECVVMVDPNTKRSRGFGFITF 51
>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 = 101 bits (252), Expect = 4e-27
Identities = 35/78 (44%), Positives = 52/78 (66%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLF+GGL + T ++L+ +F Q+GE+VD V+MKD T RSRGFGF+ + + V ++
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 105 RPHEIDGRVVETKRAVPR 122
PH +DGR ++ K PR
Sbjct: 61 GPHTLDGRTIDPKPCTPR 78
Score = 36.7 bits (85), Expect = 0.001
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
YF QYG + ++ +K T RGF F++F D
Sbjct: 19 YFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50
>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 = 100 bits (250), Expect = 5e-27
Identities = 39/77 (50%), Positives = 57/77 (74%), Gaps = 1/77 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+FIGGL++ T DDSL+ +F Q+GE+ D VM+D T RSRGFGF+T+ + K V+E M
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60
Query: 106 PHEIDGRVVETKRAVPR 122
H +DG++++ KRA+PR
Sbjct: 61 -HILDGKIIDPKRAIPR 76
Score = 41.8 bits (98), Expect = 2e-05
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+YFGQ+G + ++ + TG RGF F+ F V++++
Sbjct: 17 EYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVM 57
>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 = 98.7 bits (246), Expect = 2e-26
Identities = 35/75 (46%), Positives = 56/75 (74%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+FIGGL ++T + L+ +F ++GEI + +VM+DP TKRSRGFGF+T+S+ VD+ ++
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 106 PHEIDGRVVETKRAV 120
PHE+DG+ ++ K A
Sbjct: 61 PHELDGKKIDPKVAF 75
Score = 38.6 bits (90), Expect = 3e-04
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+YF ++G I+ ++ + T RGF F+ F D VDK++
Sbjct: 17 EYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVL 57
>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 = 89.3 bits (222), Expect = 1e-22
Identities = 34/78 (43%), Positives = 50/78 (64%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+K+F+GGL + L+ +F Q+G + +VVVM D KR RGFGFIT+ VD+ ++
Sbjct: 3 KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62
Query: 104 NRPHEIDGRVVETKRAVP 121
H+I+G+ VE KRA P
Sbjct: 63 EHFHDINGKKVEVKRAEP 80
Score = 43.1 bits (102), Expect = 7e-06
Identities = 17/41 (41%), Positives = 25/41 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
YF Q+GT+ V ++ + E RGF FI F+ D VD++V
Sbjct: 21 KYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61
>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 = 86.3 bits (213), Expect = 1e-21
Identities = 35/75 (46%), Positives = 57/75 (76%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+FIGGL ++T+ DSL+ +F ++GEI + +VM+DP TKRSRGFGF+T+++ VD+ ++
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 105 RPHEIDGRVVETKRA 119
HE+D + ++ K A
Sbjct: 61 PHHELDSKTIDPKVA 75
Score = 35.8 bits (82), Expect = 0.003
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
DYF ++G I ++ + T RGF F+ F D VDK++
Sbjct: 18 DYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58
>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 = 83.6 bits (207), Expect = 1e-20
Identities = 31/75 (41%), Positives = 46/75 (61%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL ++ K +F Q+G++VD +M+D T RSRGFGF+T+ V+ S
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 105 RPHEIDGRVVETKRA 119
E+ G+ VE KRA
Sbjct: 61 GMLELGGKQVEVKRA 75
Score = 42.0 bits (99), Expect = 2e-05
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKI 179
+YF Q+G + ++ + +TG RGF F+ FD V+++
Sbjct: 18 EYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERV 57
>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 = 82.6 bits (204), Expect = 2e-20
Identities = 32/74 (43%), Positives = 52/74 (70%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+F+GGL + T LK +F ++GE+VD + DPVT RSRGFGF+ + ++ V++ + +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 106 PHEIDGRVVETKRA 119
H++DGRV++ KRA
Sbjct: 61 EHKLDGRVIDPKRA 74
Score = 35.2 bits (81), Expect = 0.004
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+YF ++G + + + TG RGF F+ F D V+K++
Sbjct: 17 EYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVL 57
>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 = 80.8 bits (199), Expect = 1e-19
Identities = 33/75 (44%), Positives = 55/75 (73%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+FIGGL ++T + L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD+ ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 105 RPHEIDGRVVETKRA 119
HE+D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 31.5 bits (71), Expect = 0.086
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+YFGQ+G ++ ++ + T RGF F+ F D VDK++
Sbjct: 19 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>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 = 79.6 bits (197), Expect = 4e-19
Identities = 31/76 (40%), Positives = 51/76 (67%), Gaps = 1/76 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLF+ GL RT + L+A F ++G + +V++MKDP T SRGFGF+T+ + D A+ +
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62
Query: 105 -RPHEIDGRVVETKRA 119
E++GRV++ ++A
Sbjct: 63 LNGKELEGRVIKVEKA 78
Score = 43.4 bits (103), Expect = 6e-06
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F ++G +E V ++ + ETG RGF F+ F+
Sbjct: 20 ALFSKFGRVEEVLLMKDPETGESRGFGFVTFES 52
>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 = 79.3 bits (195), Expect = 5e-19
Identities = 30/75 (40%), Positives = 51/75 (68%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL + T+ LK +F ++GE+ D + DP T RSRGFGFI + ++ V++ +
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 105 RPHEIDGRVVETKRA 119
+ H +DGR+++ K+A
Sbjct: 61 KEHRLDGRLIDPKKA 75
Score = 37.7 bits (87), Expect = 6e-04
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
DYF ++G + + + TG RGF FI F D V+K++ K
Sbjct: 18 DYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61
>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 = 78.9 bits (194), Expect = 7e-19
Identities = 34/74 (45%), Positives = 53/74 (71%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+FIGGL + T LK +F ++GE+VD + DP+T RSRGFGF+ + ES+ VD+ M +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 106 PHEIDGRVVETKRA 119
H+++G+V++ KRA
Sbjct: 61 EHKLNGKVIDPKRA 74
Score = 34.6 bits (79), Expect = 0.006
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
DYF ++G + + + TG RGF F+ F + + VDK++ K
Sbjct: 17 DYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
>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 = 78.0 bits (193), Expect = 2e-18
Identities = 32/76 (42%), Positives = 47/76 (61%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
K+F+GGL Y T DDSL+ +F Q+GEI + VV+ D T +SRG+GF+T+ + + + A
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 104 NRPHEIDGRVVETKRA 119
+ IDGR A
Sbjct: 61 DPNPIIDGRKANVNLA 76
Score = 42.2 bits (100), Expect = 1e-05
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
YF Q+G IE ++T+++TG RG+ F+ F D +
Sbjct: 20 YFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKE 53
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 77.6 bits (192), Expect = 2e-18
Identities = 20/72 (27%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LF+G L T ++ L+ F ++G++ V +++D T +S+GF F+ + + ++A+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 105 -RPHEIDGRVVE 115
E+DGR ++
Sbjct: 61 LNGKELDGRPLK 72
Score = 52.6 bits (127), Expect = 2e-09
Identities = 17/41 (41%), Positives = 29/41 (70%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ F ++G +ESV +V +KETG +GFAF+EF+ + +K +
Sbjct: 18 ELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 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 = 77.7 bits (192), Expect = 2e-18
Identities = 32/44 (72%), Positives = 37/44 (84%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+YF QYG +ESV +VT+KETG KRGFAF+ FDDYD VDKIVL K
Sbjct: 18 EYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61
Score = 60.7 bits (148), Expect = 3e-12
Identities = 26/73 (35%), Positives = 43/73 (58%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLF+GGL ++ L+ +F Q+G + V ++ D T + RGF F+T+ + VD+ +
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 105 RPHEIDGRVVETK 117
+ H I+G VE K
Sbjct: 61 KYHTINGHRVEVK 73
>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 = 75.4 bits (185), Expect = 2e-17
Identities = 30/75 (40%), Positives = 52/75 (69%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+FIGGL + T+ L + ++GE++D + DPVT RSRGFGF+ + ++ VD+ +
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 105 RPHEIDGRVVETKRA 119
+ H++DG++++ KRA
Sbjct: 61 KEHKLDGKLIDPKRA 75
Score = 35.0 bits (80), Expect = 0.004
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 7/58 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVINGE 197
+Y ++G + + T+ TG RGF F+ F D VDK VLE+ + ++G+
Sbjct: 18 EYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDK-------VLELKEHKLDGK 68
>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 = 75.1 bits (185), Expect = 2e-17
Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L + GL ++T + LK +F +GE++ V V KDP T +S+GFGF+ +++ + + +S
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60
Query: 105 RPHEIDGRVVETKRAVPR 122
R H IDGR + K +
Sbjct: 61 R-HMIDGRWCDVKIPNSK 77
Score = 38.5 bits (90), Expect = 3e-04
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKI 179
DYF +G + V + + +TG +GF F+ F DY+ K+
Sbjct: 18 DYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein 3
(RBM3) and similar proteins. This subfamily corresponds
to the RRM domain of two structurally related
heterogenous nuclear ribonucleoproteins, CIRBP (also
termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL),
both of which belong to a highly conserved cold shock
proteins family. The cold shock proteins can be induced
after exposure to a moderate cold-shock and other
cellular stresses such as UV radiation and hypoxia.
CIRBP and RBM3 may function in posttranscriptional
regulation of gene expression by binding to different
transcripts, thus allowing the cell to response rapidly
to environmental signals. However, the kinetics and
degree of cold induction are different between CIRBP and
RBM3. Tissue distribution of their expression is
different. CIRBP and RBM3 may be differentially
regulated under physiological and stress conditions and
may play distinct roles in cold responses of cells.
CIRBP, also termed glycine-rich RNA-binding protein
CIRP, is localized in the nucleus and mediates the
cold-induced suppression of cell cycle progression.
CIRBP also binds DNA and possibly serves as a chaperone
that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore, RBM3
may be essential for cell proliferation and mitosis.
Both, CIRBP and RBM3, contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), that is
involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 74.9 bits (184), Expect = 3e-17
Identities = 34/76 (44%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLFIGGL + TN+ SL+ F ++G+I +VVV+KD T+RSRGFGF+T+ +AM
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 105 RPHE-IDGRVVETKRA 119
+ +DGR + +A
Sbjct: 62 MNGKSVDGRQIRVDQA 77
Score = 36.8 bits (85), Expect = 0.001
Identities = 17/40 (42%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 135 ALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+LEQ+ F +YG I V +V ++ET RGF F+ F++ D
Sbjct: 16 SLEQV--FSKYGQISEVVVVKDRETQRSRGFGFVTFENPD 53
>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 = 71.7 bits (176), Expect = 3e-16
Identities = 30/74 (40%), Positives = 48/74 (64%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL T +D +K +F Q+G++ D ++M D T R RGFGF+T+ +VD+
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 105 RPHEIDGRVVETKR 118
HEI+ ++VE K+
Sbjct: 61 HFHEINNKMVECKK 74
Score = 42.4 bits (100), Expect = 1e-05
Identities = 17/40 (42%), Positives = 26/40 (65%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
YF Q+G +E ++ +K+T RGF F+ F+ DVVDK+
Sbjct: 19 YFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVC 58
>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 = 71.2 bits (175), Expect = 5e-16
Identities = 26/75 (34%), Positives = 46/75 (61%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL T ++ ++ +F ++G IV++ + D T + RGF FIT+ + V + +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 105 RPHEIDGRVVETKRA 119
+ H I G+ VE K+A
Sbjct: 61 QFHVIGGKKVEVKKA 75
Score = 53.1 bits (128), Expect = 2e-09
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
+YFG++G I + + +K+T +RGF FI FD + V KI LE VI G
Sbjct: 18 EYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI-------LETQFHVIGG 67
>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 = 71.1 bits (175), Expect = 5e-16
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L++G L Y ++ LK F Q+GE+ V+ D T RSRGFGF+ ++ + A+
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 105 -RPHEIDGRVVETKRAVP 121
+ GR + A P
Sbjct: 61 LNGTDFGGRTLTVNEARP 78
Score = 52.2 bits (126), Expect = 4e-09
Identities = 15/41 (36%), Positives = 26/41 (63%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
D FGQ+G + S ++T++ETG RGF F+E + + + +
Sbjct: 18 DLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAI 58
>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 = 67.2 bits (165), Expect = 1e-14
Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+G L T ++ LK F ++G I + +++D T RS+GF F+ + + + ++A+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 106 P-HEIDGRVVE 115
E+ GR +
Sbjct: 60 NGKELGGRELR 70
Score = 49.1 bits (118), Expect = 4e-08
Identities = 18/41 (43%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
D F ++G IES+ +V + ETG +GFAF+EF+D + +K +
Sbjct: 17 DLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKAL 56
>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 = 64.7 bits (157), Expect = 2e-13
Identities = 30/76 (39%), Positives = 50/76 (65%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+K+F+GGL T + +K +FEQ+G++ D ++M D T R RGFGF+T+ +V++
Sbjct: 4 KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63
Query: 104 NRPHEIDGRVVETKRA 119
HEI+ ++VE K+A
Sbjct: 64 IHFHEINNKMVECKKA 79
Score = 38.9 bits (90), Expect = 2e-04
Identities = 16/39 (41%), Positives = 26/39 (66%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKI 179
YF Q+G +E ++ +K T RGF F+ F++ DVV+K+
Sbjct: 23 YFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61
>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 = 63.5 bits (154), Expect = 4e-13
Identities = 29/74 (39%), Positives = 48/74 (64%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL T + +K +FEQ+G++ D ++M D T R RGFGF+T+ +V++
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 105 RPHEIDGRVVETKR 118
HEI+ ++VE K+
Sbjct: 61 HFHEINNKMVECKK 74
Score = 37.7 bits (87), Expect = 5e-04
Identities = 14/39 (35%), Positives = 25/39 (64%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKI 179
YF Q+G ++ ++ +K T RGF F+ F+ D+V+K+
Sbjct: 19 YFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 68.0 bits (165), Expect = 4e-13
Identities = 23/85 (27%), Positives = 46/85 (54%), Gaps = 1/85 (1%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
E LF+G L Y ++ L+ F+++G + V +++D T +SRGF F+ + +
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESA 170
Query: 99 DEAMSNRPH-EIDGRVVETKRAVPR 122
++A+ E++GR + ++A P
Sbjct: 171 EKAIEELNGKELEGRPLRVQKAQPA 195
Score = 46.5 bits (109), Expect = 7e-06
Identities = 15/41 (36%), Positives = 28/41 (68%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ F ++G ++ V +V ++ETG RGFAF+EF+ + +K +
Sbjct: 134 ELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAI 174
>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 = 63.2 bits (154), Expect = 4e-13
Identities = 29/73 (39%), Positives = 45/73 (61%), Gaps = 5/73 (6%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY---SESKMVDEA 101
LF+G L + +D+ LKA FE++G +V V+ D T RSRGFG++ + ++K EA
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 102 MSNRPHEIDGRVV 114
M + E+DGR +
Sbjct: 61 MDGK--ELDGRPI 71
Score = 34.7 bits (80), Expect = 0.005
Identities = 12/39 (30%), Positives = 25/39 (64%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F ++GT+ ++T++ETG RGF +++F+ + K +
Sbjct: 20 FEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAI 58
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 65.1 bits (158), Expect = 5e-13
Identities = 33/75 (44%), Positives = 47/75 (62%), Gaps = 8/75 (10%)
Query: 42 SLR----KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
SLR KLFIGGL + T+D SL+ F +G++VD V+ D T RSRGFGF+ +++
Sbjct: 29 SLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGA 88
Query: 98 VDEAMSNRPHEIDGR 112
A+S E+DG+
Sbjct: 89 ATAAIS----EMDGK 99
Score = 37.3 bits (86), Expect = 0.003
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVINGEDH 199
D F +G + ++ ++ETG RGF F+ F+D + E+D + +NG
Sbjct: 53 DAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATA------AISEMDGKELNGRHI 106
Query: 200 RTH 202
R +
Sbjct: 107 RVN 109
>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 = 61.9 bits (150), Expect = 1e-12
Identities = 26/44 (59%), Positives = 35/44 (79%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
DYF QYG IE + ++T++ +G KRGFAF+ FDD+D VDKIV+ K
Sbjct: 19 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 62
Score = 56.1 bits (135), Expect = 2e-10
Identities = 24/77 (31%), Positives = 48/77 (62%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+T+ + VD+ +
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60
Query: 104 NRPHEIDGRVVETKRAV 120
+ H ++G E ++A+
Sbjct: 61 QKYHTVNGHNCEVRKAL 77
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 21/59 (35%), Positives = 38/59 (64%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L++G L + +D L+ FE +GEI V + +DP T RS+G+GFI +++++ +A+
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59
Score = 33.0 bits (76), Expect = 0.022
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G IE V + + ETG +G+ FI+F D
Sbjct: 19 FEPFGEIEFVQLQRDPETGRSKGYGFIQFAD 49
>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 = 61.6 bits (149), Expect = 2e-12
Identities = 24/44 (54%), Positives = 36/44 (81%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
DYF +YG I+++ ++T++++G KRGF F+ FDD+D VDKIVL K
Sbjct: 19 DYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQK 62
Score = 58.5 bits (141), Expect = 3e-11
Identities = 26/80 (32%), Positives = 51/80 (63%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+KLF+GG+ T + L+ +FE++G+I + ++ D + + RGFGF+T+ + VD+ +
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60
Query: 104 NRPHEIDGRVVETKRAVPRE 123
+ H I+G E ++A+ R+
Sbjct: 61 QKYHTINGHNAEVRKALSRQ 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 = 60.8 bits (147), Expect = 4e-12
Identities = 26/80 (32%), Positives = 51/80 (63%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+K+F+GG+ T + L+ +FE++G+I + VM+D + + RGF F+T+ + VD+ +
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 104 NRPHEIDGRVVETKRAVPRE 123
+ H I+G E K+A+ ++
Sbjct: 61 QKYHTINGHNCEVKKALSKQ 80
Score = 58.5 bits (141), Expect = 3e-11
Identities = 24/44 (54%), Positives = 36/44 (81%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
DYF +YG IE++ ++ ++++G KRGFAF+ FDD+D VDKIV+ K
Sbjct: 19 DYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQK 62
>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 = 59.6 bits (145), Expect = 7e-12
Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+G L T ++ L+ F ++GEI V +++D +S+GF F+ + + ++A+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59
Query: 106 PH-EIDGRVVE 115
E+DGR ++
Sbjct: 60 NGKELDGRKLK 70
Score = 43.1 bits (102), Expect = 6e-06
Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ F ++G IESV +V +K G +GFAF+EF+ + +K +
Sbjct: 17 ELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKAL 56
>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 = 59.6 bits (145), Expect = 7e-12
Identities = 26/68 (38%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L + L YRT D L+ FE++GE+ DV + +D T+ SRGF F+ + + + ++AM
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Query: 106 P-HEIDGR 112
E+DGR
Sbjct: 61 DGKELDGR 68
Score = 27.6 bits (62), Expect = 1.7
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +YG + V + ++ T RGFAF+ F D
Sbjct: 17 RVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYD 49
>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 = 59.9 bits (145), Expect = 8e-12
Identities = 30/79 (37%), Positives = 43/79 (54%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLF+GGL + L F Q+G + V+ D T + RGFGF+ + D+A
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 105 RPHEIDGRVVETKRAVPRE 123
+ H I+G VE K+AVP+E
Sbjct: 61 KFHPINGHRVEVKKAVPKE 79
Score = 50.3 bits (120), Expect = 2e-08
Identities = 17/45 (37%), Positives = 29/45 (64%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
++F Q+G +E ++ +K+TG KRGF F+ F ++D DK + K
Sbjct: 17 TEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61
>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 = 58.8 bits (142), Expect = 2e-11
Identities = 25/79 (31%), Positives = 46/79 (58%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+ ++K+F+GGL+ ++ ++ +F ++GEI + + DP T + RGF FIT+ E V +
Sbjct: 2 DPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61
Query: 101 AMSNRPHEIDGRVVETKRA 119
+ + H + G E K A
Sbjct: 62 VLEKKFHNVSGSKCEIKVA 80
Score = 40.4 bits (94), Expect = 7e-05
Identities = 17/44 (38%), Positives = 29/44 (65%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+YFG++G IE++ + + +T +RGF FI F + D V K++ K
Sbjct: 23 EYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEKK 66
>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 = 57.3 bits (139), Expect = 7e-11
Identities = 21/59 (35%), Positives = 36/59 (61%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
++IGGL Y + + F Q+GEIVD+ +++D T +S+GF F+ Y + + A+ N
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDN 70
Score = 44.9 bits (107), Expect = 2e-06
Identities = 15/31 (48%), Positives = 23/31 (74%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F QYG I +N+V +K+TG +GFAF+ ++D
Sbjct: 30 FSQYGEIVDINLVRDKKTGKSKGFAFLAYED 60
>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 = 61.8 bits (150), Expect = 9e-11
Identities = 23/59 (38%), Positives = 38/59 (64%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
KL++G L + + L+ FE +G+I DV + +DP T RS+GFGFI + +++ EA+
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL 245
Score = 56.4 bits (136), Expect = 6e-09
Identities = 38/148 (25%), Positives = 64/148 (43%), Gaps = 19/148 (12%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +F+ L + + L FF + G++ DV +KD ++RS+G ++ + + + V +A++
Sbjct: 90 RTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA 149
Query: 104 -------NRPHEIDGRVVETKRAVPREVKVRRVTKVQIAL----------EQM--DYFGQ 144
RP + E RA + L EQ F
Sbjct: 150 LTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEP 209
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDD 172
+G IE V + + ETG +GF FI+F D
Sbjct: 210 FGDIEDVQLHRDPETGRSKGFGFIQFHD 237
Score = 31.8 bits (72), Expect = 0.41
Identities = 16/91 (17%), Positives = 32/91 (35%), Gaps = 15/91 (16%)
Query: 103 SNRPHEIDGRVVETKRAVPREVKV----------RRVTKVQIAL-----EQMDYFGQYGT 147
+ R R V +Q+AL + ++F + G
Sbjct: 56 NRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGK 115
Query: 148 IESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+ V + ++ + +G A++EF D + V K
Sbjct: 116 VRDVQCIKDRNSRRSKGVAYVEFYDVESVIK 146
>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 = 56.5 bits (137), Expect = 1e-10
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
L++GGL ++ L A F +G+I D+ + D T++ RGF F+ + E + A+ N
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 105 RPHEIDGRVV 114
E+ GR +
Sbjct: 61 NESELFGRTI 70
Score = 35.7 bits (83), Expect = 0.003
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G I+ + + + ET RGFAF+EF++
Sbjct: 19 FIPFGDIKDIQIPLDYETQKHRGFAFVEFEE 49
>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 = 56.5 bits (137), Expect = 1e-10
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
RK+F+G L ++ L+ +F Q+GE+ DV + K R F F+T+++ ++
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCG 55
Query: 104 NRPHEIDGRVVETKRA 119
H I G V A
Sbjct: 56 -EDHIIKGVSVHVSNA 70
Score = 34.9 bits (81), Expect = 0.005
Identities = 23/85 (27%), Positives = 33/85 (38%), Gaps = 24/85 (28%)
Query: 122 REVKVRRVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAK--RGFAFIEFDDYDVVDKI 179
R+V V R+T+ + YF Q+G + V + K R FAF+ F D +V +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI-------PKPFRAFAFVTFADPEVAQSL 53
Query: 180 VLDKVVVLEVDQEVINGEDHRTHGT 204
GEDH G
Sbjct: 54 C---------------GEDHIIKGV 63
>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 = 56.4 bits (137), Expect = 1e-10
Identities = 18/60 (30%), Positives = 36/60 (60%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLF+G L ++ ++A FE++G I +V +++D T +S+G F+ +S + +A+
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Score = 35.6 bits (83), Expect = 0.003
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +YG IE V ++ +K+TG +G AF++F
Sbjct: 18 ALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSS 50
>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 = 56.4 bits (137), Expect = 2e-10
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 50 GLDYRTNDDSLKAFFEQWG--EIVDVVVMKDPVTKRSRGFGFITYSE----SKMVDEAMS 103
GLD T ++ + I DV +++D +T SRGF F+ + ++ +D +
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68
Query: 104 NRPHEIDGRVV 114
P IDGRVV
Sbjct: 69 LDPFVIDGRVV 79
Score = 33.7 bits (78), Expect = 0.014
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 147 TIESVNMVTNKETGAKRGFAFIEFDD 172
I+ V ++ +K TG RGFAF+EF
Sbjct: 30 PIKDVRLIRDKLTGTSRGFAFVEFPS 55
>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 = 55.4 bits (134), Expect = 2e-10
Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+LF+ L + T ++ L+ FE +GEI +V + D TKRS+GF F+++ + +A S
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 105 RPHEI-DGRVV 114
I GR++
Sbjct: 61 LDGSIFQGRLL 71
Score = 37.3 bits (87), Expect = 8e-04
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
E + F +G I V++ +KET +GFAF+ F
Sbjct: 15 ELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMF 50
>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 = 61.0 bits (148), Expect = 2e-10
Identities = 42/155 (27%), Positives = 69/155 (44%), Gaps = 32/155 (20%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
L++ LD N+D L+ F ++GEI VMKD + RSRGF F+ + + + +A+
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239
Query: 105 RPHEID----GRVVETKRAVPR------------EVKVRRVTKVQ---IALEQMD----- 140
+I G+ + RA R E++ R K Q + ++ +D
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299
Query: 141 -----YFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F + G I S ++ + E G RGF F+ F
Sbjct: 300 EKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCF 333
Score = 51.7 bits (124), Expect = 2e-07
Identities = 35/148 (23%), Positives = 71/148 (47%), Gaps = 17/148 (11%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS---ESKMVDEAM 102
L++G LD + L F+ +G ++ V V +D VT+RS G+G++ + +++ E M
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 103 SNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQM----------DYFGQYGTIESVN 152
+ + + G+ + + R+ +RR I ++ + D F ++G I S
Sbjct: 63 NFKR--LGGKPIRIMWSQ-RDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCK 119
Query: 153 MVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ T+ E G RG+ F+ F+ + +
Sbjct: 120 VATD-ENGKSRGYGFVHFEKEESAKAAI 146
Score = 49.8 bits (119), Expect = 8e-07
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L++ LD D+ L+ F + GEI VM D SRGFGF+ +S + + A++
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVT-- 344
Query: 106 PHEIDGRVVETK 117
E+ GR++ K
Sbjct: 345 --EMHGRMLGGK 354
Score = 49.4 bits (118), Expect = 1e-06
Identities = 37/163 (22%), Positives = 73/163 (44%), Gaps = 32/163 (19%)
Query: 42 SLRK-----LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESK 96
SLR+ +F+ LD ++ +L F ++G I+ V D +SRG+GF+ + + +
Sbjct: 82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEE 140
Query: 97 MVDEAMSNRPHEIDGRVVETK-----RAVPREVKVRRVTKVQ----IALEQMD------- 140
A+ +++G ++ K R + + R ++ + ++ +D
Sbjct: 141 SAKAAIQ----KVNGMLLNDKEVYVGRFIKK--HEREAAPLKKFTNLYVKNLDPSVNEDK 194
Query: 141 ---YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F ++G I S V +G RGFAF+ F+ ++ K V
Sbjct: 195 LRELFAKFGEITSA-AVMKDGSGRSRGFAFVNFEKHEDAAKAV 236
>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 = 4e-10
Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM-SN 104
L++ L ++ L+ FF +G++ V ++++ R RGF F+ ++ + + A+
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58
Query: 105 RPHEIDGRVVE 115
+DGR +
Sbjct: 59 NGLVLDGRTLR 69
Score = 38.3 bits (90), Expect = 3e-04
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
++F YG +E V +V NK+ RGFAF+EF + +
Sbjct: 16 REFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEA 53
>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 = 55.3 bits (134), Expect = 4e-10
Identities = 26/85 (30%), Positives = 46/85 (54%), Gaps = 5/85 (5%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+ LF+ L+Y T + L+ FE++G I + +++D T + RG+ FI + + + A
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61
Query: 104 N-RPHEIDGR--VVETKRAVPREVK 125
+IDGR +V+ +R R VK
Sbjct: 62 YADGKKIDGRRVLVDVERG--RTVK 84
Score = 46.5 bits (111), Expect = 6e-07
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +YG I+ + +V +K+TG RG+AFIEF+
Sbjct: 21 EFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEH 52
>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 = 54.8 bits (132), Expect = 5e-10
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
LF+ L + + L FF I VV+ DP T SRG+GF+T++ + EA++
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 105 RPHEIDGRVVETKRAVPR 122
+ ++ GR++ A R
Sbjct: 62 KNKKLHGRILRLDIAERR 79
Score = 34.8 bits (80), Expect = 0.007
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
D+F I+ +VT+ ETG RG+ F+ F +
Sbjct: 18 DFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLE 52
>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 = 53.5 bits (128), Expect = 1e-09
Identities = 26/75 (34%), Positives = 44/75 (58%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL T ++ +K +F +GEI ++ + D T RGF F+TY++ + V + + +
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 105 RPHEIDGRVVETKRA 119
R H+I E K A
Sbjct: 61 RYHQIGSGKCEIKVA 75
Score = 41.2 bits (96), Expect = 3e-05
Identities = 16/45 (35%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 137 EQM-DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
EQ+ +YFG +G IE++ + + +T +RGF F+ + D + V K++
Sbjct: 14 EQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLL 58
>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 = 53.7 bits (130), Expect = 1e-09
Identities = 24/78 (30%), Positives = 43/78 (55%), Gaps = 8/78 (10%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE----SKMVDEA 101
+++ L +D+ LK F ++G+I VMKD K S+GFGF+ + K V+E
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGK-SKGFGFVNFENHEAAQKAVEE- 61
Query: 102 MSNRPHEIDGRVVETKRA 119
++ + E++G+ + RA
Sbjct: 62 LNGK--EVNGKKLYVGRA 77
Score = 31.8 bits (73), Expect = 0.065
Identities = 13/41 (31%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ FG+YG I S ++ + + G +GF F+ F++++ K V
Sbjct: 20 ELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAV 59
>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 = 53.4 bits (129), Expect = 2e-09
Identities = 18/76 (23%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
++F+GG+ T ++ L+ FF ++G + DV ++ D S+G+GF+T+ + ++ ++
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62
Query: 105 RPHEIDGRVVETKRAV 120
G+ + A+
Sbjct: 63 GNLNFRGKKLNIGPAI 78
Score = 36.5 bits (85), Expect = 0.002
Identities = 11/48 (22%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVL 187
D+F ++G+++ V ++T++ G +G+ F+ F+ + +KI+ +
Sbjct: 21 DFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMGNLNF 67
>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 = 53.2 bits (128), Expect = 2e-09
Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 4/82 (4%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
P+S +LF+G L + +D LK FF+++G +++V + R FGF+ + + + V
Sbjct: 1 PDSH-QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQ 59
Query: 100 EAMSNRPHEIDGRV---VETKR 118
+ ++N+P G VE K+
Sbjct: 60 KILANKPIYFRGDHRLNVEEKK 81
Score = 33.1 bits (76), Expect = 0.023
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
++F ++G + V + + G F F+ FDD + V KI+ +K
Sbjct: 22 EFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65
>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 = 53.1 bits (128), Expect = 2e-09
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+G L + D L+ FF++ GE+VDV + +D RS+GFG + ++ + +A+
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEKS 60
Query: 106 PHEIDGRVVETKRAVPR 122
E+ GR + A R
Sbjct: 61 GEELLGREIRVDLATER 77
Score = 26.9 bits (60), Expect = 4.1
Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+F + G + V + + + G +GF +EF + K
Sbjct: 19 FFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQK 55
>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 = 53.0 bits (128), Expect = 2e-09
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE--A 101
R +FI L + ++ LK F Q+GE+ ++KD +T S+G F+ + + +
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 102 MSNRPHE----IDGRVVETKRA 119
++ + +DGR + A
Sbjct: 61 AADNAEDSGLSLDGRRLIVTLA 82
Score = 38.0 bits (89), Expect = 5e-04
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
F Q+G ++ +V +K TG +G AF++F + K
Sbjct: 20 LFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQK 57
>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 = 52.0 bits (125), Expect = 4e-09
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS-N 104
LF+G L + ++DS+ F ++GEI V + DP + R +GFG++ +S + A+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 105 RPHEIDGRVV 114
++ GR V
Sbjct: 61 GGTDLLGRPV 70
Score = 35.4 bits (82), Expect = 0.004
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
FG+YG I SV + T+ ++G +GF ++EF + +
Sbjct: 19 FGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57
>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 = 52.0 bits (125), Expect = 4e-09
Identities = 22/74 (29%), Positives = 45/74 (60%), Gaps = 5/74 (6%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY---SESKMVDEAM 102
+F+G L + ++L+A F +GEI D V+KD T +S+G+GF+++ +++ ++M
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 103 SNRPHEIDGRVVET 116
+ + + GR + T
Sbjct: 62 NGQ--WLGGRAIRT 73
Score = 27.3 bits (61), Expect = 2.1
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F +G I +V + +TG +G+ F+ F
Sbjct: 20 FAPFGEISDARVVKDMQTGKSKGYGFVSF 48
>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 = 51.8 bits (125), Expect = 6e-09
Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 9/89 (10%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
PE+ ++F+G L D+ L F ++ V++D T +S+G+GF+++S+
Sbjct: 3 PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62
Query: 100 EAMSNRPHEIDGRVVETKRAVPREVKVRR 128
+AM E++G+ V R +K+R+
Sbjct: 63 KAMK----EMNGKYVGN-----RPIKLRK 82
Score = 28.3 bits (64), Expect = 1.4
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +Y + + +V +K TG +G+ F+ F D
Sbjct: 27 FSKYPSFQKAKVVRDKRTGKSKGYGFVSFSD 57
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 51.1 bits (123), Expect = 8e-09
Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSR---GFGFITYSESKMVDE 100
R++++ LD++ ++D L+ F ++GE+ + + K K+ R GF F+T+ ++ +
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60
Query: 101 AMSNRPHEIDGRVVE 115
A+ E+ GR +
Sbjct: 61 ALQLNGTELGGRKIS 75
Score = 32.2 bits (74), Expect = 0.041
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 7/56 (12%)
Query: 122 REVKVRRV-TKVQI-ALEQMDYFGQYGTIESVNM-VTNKETGAK--RGFAFIEFDD 172
RE+ VR + K+ L + F ++G +ES+ + E + GFAF+ F D
Sbjct: 1 REIYVRNLDFKLDEDDLRGI--FSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKD 54
>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 = 50.3 bits (121), Expect = 2e-08
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+F+ LDY +D L+ F + GEI DV ++K+ +S+G+ ++ + + V EA+
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLD 60
Query: 106 PHEIDGR 112
I GR
Sbjct: 61 RELIKGR 67
Score = 32.6 bits (75), Expect = 0.028
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
F + G I V +V N + G +G+A++EF++ + V + L++D+E+I G
Sbjct: 17 RKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQE-------ALKLDRELIKG 66
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 50.3 bits (121), Expect = 2e-08
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+ L Y T D+ L+ FF + G I V+KD +K+ RGFG++T++ + A+ +
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 106 PH-EIDGRVVETKRAVPR 122
+ GR + + A +
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
Score = 29.9 bits (68), Expect = 0.31
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
++F + G I+ +V +K + RGF ++ F
Sbjct: 18 EFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF 48
>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 = 49.5 bits (119), Expect = 3e-08
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN-R 105
F+G + Y ++ L F + G +V ++ D T + +G+GF + + + A+ N
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 106 PHEIDGRV 113
+E +GR
Sbjct: 62 GYEFNGRA 69
Score = 42.6 bits (101), Expect = 8e-06
Identities = 14/39 (35%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 137 EQM-DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
EQ+ + F + G + S +VT+++TG +G+ F EF+D +
Sbjct: 13 EQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIE 51
>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 = 49.6 bits (119), Expect = 4e-08
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVV-VMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LFIG LD ++ L F +G I+ +M+DP T S+GF FI+Y + D A+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Score = 37.7 bits (88), Expect = 6e-04
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 140 DYFGQYGTI-ESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
D F +G I ++ ++ + +TG +GFAFI +D ++ D
Sbjct: 20 DTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDA 59
>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 = 48.9 bits (117), Expect = 6e-08
Identities = 19/67 (28%), Positives = 34/67 (50%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+G L Y T + L A F+ G V ++ D T +S+G F+ + ++ + +A+
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 106 PHEIDGR 112
+ GR
Sbjct: 63 HTLLKGR 69
Score = 38.9 bits (91), Expect = 2e-04
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+F G SV ++T+K+TG +G AF+EFD + + K
Sbjct: 19 AHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTK 57
>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 = 48.8 bits (116), Expect = 7e-08
Identities = 24/75 (32%), Positives = 41/75 (54%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+GGL T ++ ++ +F +GE+ + + D T + RGF FIT+ E + V + M
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 105 RPHEIDGRVVETKRA 119
+ H + E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
Score = 40.8 bits (95), Expect = 4e-05
Identities = 16/41 (39%), Positives = 27/41 (65%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+YFG +G +ES+ + + +T +RGF FI F + + V KI+
Sbjct: 18 EYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>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 = 49.2 bits (118), Expect = 7e-08
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+G L +T +++L+ F ++G+I + +++D VT S+G+ F+ Y + A +
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65
Query: 106 PHE-IDGRVV 114
IDG +
Sbjct: 66 HKLVIDGSEI 75
Score = 37.6 bits (88), Expect = 8e-04
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 8/58 (13%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD-------YDVVDKIVLDKVVVLEVDQE 192
F +YG I + +V + TG +G+AF+E++ Y K+V+D + VD E
Sbjct: 24 FSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSEIF-VDFE 80
>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 = 48.4 bits (116), Expect = 8e-08
Identities = 26/67 (38%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 50 GLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS--NRPH 107
GL T + L+ F ++G I V V+ D T RSRGFGF+ + V++A R +
Sbjct: 6 GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES---VEDAKEAKERLN 62
Query: 108 --EIDGR 112
EIDGR
Sbjct: 63 GMEIDGR 69
Score = 38.8 bits (91), Expect = 2e-04
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F +YG IE V +V +++TG RGF F+ F+
Sbjct: 18 EVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES 50
>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 = 48.4 bits (116), Expect = 8e-08
Identities = 15/59 (25%), Positives = 34/59 (57%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
++++ + ++D +K+ FE +G+I + DP T + +G+GFI Y + +A++
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Score = 29.5 bits (67), Expect = 0.41
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
F +G I+S ++ + ETG +G+ FIE++
Sbjct: 21 FEAFGKIKSCSLAPDPETGKHKGYGFIEYE 50
>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 = 48.2 bits (115), Expect = 1e-07
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+LFI L Y ++ L+ F ++G + +V + D +TK+ +GF F+TY M+ E
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY----MIPEHAVK 59
Query: 105 RPHEIDGRV 113
E+DG V
Sbjct: 60 AFAELDGTV 68
Score = 31.6 bits (72), Expect = 0.084
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F +YG + V++ +K T +GFAF+ +
Sbjct: 23 FSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
>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 = 47.9 bits (115), Expect = 1e-07
Identities = 17/66 (25%), Positives = 34/66 (51%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNRP 106
F+G L + ++ L+ FE G++ V +++D T +GFG++ + V A+
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62
Query: 107 HEIDGR 112
++ GR
Sbjct: 63 IKLKGR 68
Score = 33.3 bits (77), Expect = 0.021
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
+F G +E+V +V +++TG +GF ++ F D V
Sbjct: 19 HFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVAL 56
>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 = 51.9 bits (124), Expect = 1e-07
Identities = 39/127 (30%), Positives = 58/127 (45%), Gaps = 16/127 (12%)
Query: 57 DDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVET 116
D L A F G I +M+D T S G+ F+ + A+ N ++G V
Sbjct: 121 DRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN----LNGITVRN 176
Query: 117 KR-----AVPREVKVRR----VTKV--QIALEQMD-YFGQYGTIESVNMVTNKETGAKRG 164
KR A P ++ VT + I +Q+D FG+YG I N++ +K TG RG
Sbjct: 177 KRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRG 236
Query: 165 FAFIEFD 171
AF+ F+
Sbjct: 237 VAFVRFN 243
Score = 43.1 bits (101), Expect = 1e-04
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 41 ESLR--KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
ES++ L++ L DD L F ++G+IV +++D +T RG F+ +++ +
Sbjct: 189 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEA 248
Query: 99 DEAMS 103
EA+S
Sbjct: 249 QEAIS 253
>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 = 47.6 bits (114), Expect = 2e-07
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L++ LD +D+ L+ F +G I VM D RS+GFGF+ +S + +A++
Sbjct: 3 NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVT- 60
Query: 105 RPHEIDGRVVETK 117
E++GR++ K
Sbjct: 61 ---EMNGRIIGGK 70
Score = 29.9 bits (68), Expect = 0.35
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
F +GTI S ++T+ E G +GF F+ F
Sbjct: 22 FSPFGTITSAKVMTD-EKGRSKGFGFVCFS 50
>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 = 47.4 bits (113), Expect = 2e-07
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
++L + + +R D L+ F Q+G I+DV ++ + + S+GFGF+T++ S D A
Sbjct: 1 KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN--ERGSKGFGFVTFANSADADRARE 58
Query: 104 N-RPHEIDGRVVETKRA 119
++GR +E A
Sbjct: 59 KLHGTVVEGRKIEVNNA 75
Score = 34.7 bits (80), Expect = 0.005
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
L QM FGQ+G I V ++ N E G+K GF F+ F + D+
Sbjct: 17 LRQM--FGQFGPILDVEIIFN-ERGSK-GFGFVTFANSADADR 55
>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 = 46.7 bits (111), Expect = 3e-07
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+F+G L D +L A F + D VM D + RSRG+GF+++ + + A++
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAIN 59
>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 = 47.6 bits (113), Expect = 3e-07
Identities = 16/61 (26%), Positives = 31/61 (50%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+ L Y ++SL F ++G + + + D T R++G GF+ + + + + N
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63
Query: 106 P 106
P
Sbjct: 64 P 64
>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 = 47.0 bits (112), Expect = 4e-07
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
KLF+G + + L+ FEQ+G+I ++ V+KD T +G F+TY
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 54
>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 = 46.4 bits (111), Expect = 4e-07
Identities = 17/42 (40%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLD 182
YF Q+GT+ + + +K+TG +G+AF+EF+ V KIV +
Sbjct: 19 YFSQFGTVTRLRLSRSKKTGKSKGYAFVEFES-PEVAKIVAE 59
Score = 39.9 bits (94), Expect = 8e-05
Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSES---KMVDEAM 102
++IG L + + L+ +F Q+G + + + + T +S+G+ F+ + K+V E M
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 103 SN 104
+N
Sbjct: 62 NN 63
>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 = 7e-07
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R LF+G LD R ++ L F Q G + V + KDP + + F F+T+ V A+
Sbjct: 2 RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQ 60
Score = 27.3 bits (61), Expect = 2.2
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVD 177
F Q G +E V + + G + FAF+ F V
Sbjct: 22 FLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVP 56
>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 = 45.8 bits (109), Expect = 7e-07
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+F+GGLD +D L++ F +GEIV V K P K G GF+ + + A+
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYV---KIPPGK---GCGFVQFVHRAAAEAAIQ 55
>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 = 45.8 bits (109), Expect = 7e-07
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+LF+ L Y +D L+ F ++GE+ +V V D + +S+GF ++ + + + +A
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK- 62
Query: 105 RPHEIDGRV 113
E+DG+V
Sbjct: 63 ---ELDGKV 68
Score = 37.0 bits (86), Expect = 0.001
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F ++G + V++ +K++G +GFA++ F D +
Sbjct: 23 FSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPE 55
>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 = 49.6 bits (118), Expect = 7e-07
Identities = 37/154 (24%), Positives = 70/154 (45%), Gaps = 20/154 (12%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
ES L + L + +++ F GEI +++D VT +S G+GF+ Y + ++
Sbjct: 1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60
Query: 101 AMSNRPHEIDGRVVETKR-----AVPREVKVRRV---------TKVQIALEQMDYFGQYG 146
A+++ ++G ++ K A P ++ T Q LE + F +G
Sbjct: 61 AVNS----LNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESI--FSPFG 114
Query: 147 TIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
I + ++++ TG +G FI FD D D+ +
Sbjct: 115 QIITSRILSDNVTGLSKGVGFIRFDKRDEADRAI 148
Score = 42.2 bits (99), Expect = 2e-04
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT---YSESKM 97
+F+ L T++ L F +G + +V +++D T + +G+GF++ Y E+ M
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAM 326
Score = 32.6 bits (74), Expect = 0.24
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
FG +G +++V ++ + T +G+ F+ +YD
Sbjct: 290 FGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYD 322
>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 = 45.7 bits (109), Expect = 8e-07
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LFI L D L F +G ++ V D T +S+ FGF++Y E+
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNP----ESAQAA 56
Query: 106 PHEIDGRVVETKR 118
++G V KR
Sbjct: 57 IKAMNGFQVGGKR 69
Score = 36.5 bits (85), Expect = 0.001
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
+ F +G + S + +K TG + F F+ +D
Sbjct: 14 DLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYD 48
>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 = 45.7 bits (108), Expect = 9e-07
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L++ GL L+ F Q+G I+ +++D +T SRG GFI + + +EA+
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Score = 38.0 bits (88), Expect = 4e-04
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 130 TKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
T Q LEQ+ F QYG I + ++ ++ TG RG FI FD
Sbjct: 11 TMTQKELEQL--FSQYGRIITSRILRDQLTGVSRGVGFIRFD 50
>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 = 45.3 bits (108), Expect = 1e-06
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
++ + L +D L+ FE GE+ DV VM+ +SR FGF+ + + +A+
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVK 59
>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 = 45.0 bits (107), Expect = 1e-06
Identities = 21/70 (30%), Positives = 39/70 (55%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLF+G L + LK +F Q+G++ V D T S+G+GF+++S ++ A+
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 105 RPHEIDGRVV 114
+ H ++G +
Sbjct: 61 QKHILEGNKL 70
Score = 43.4 bits (103), Expect = 5e-06
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 6/53 (11%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVV------DKIVLDKVVV 186
+YF Q+G ++S N+ +KETG +G+ F+ F D + K +L+ +
Sbjct: 18 EYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQKHILEGNKL 70
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+L + L ++ + LK F +G + +V + + P + +GF F+ ++ ++A+
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKG 59
Query: 105 -RPHEIDGRVV 114
+I GR V
Sbjct: 60 VNGKKIKGRPV 70
Score = 33.8 bits (78), Expect = 0.014
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F +G + V + G K+GFAF++F
Sbjct: 20 FSPFGFVWEVTIPRKP-DGKKKGFAFVQF 47
>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 = 45.4 bits (108), Expect = 1e-06
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L++ + T D L+ F ++G IVDV + D T+R RGF ++ + + + ++A+
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 106 PHE-IDGRVVE 115
GR +E
Sbjct: 63 DRTRFLGREIE 73
Score = 33.1 bits (76), Expect = 0.029
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
FG+YG I V + + T RGFA+++F+D
Sbjct: 21 FGKYGPIVDVYIPLDFYTRRPRGFAYVQFED 51
>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 = 44.9 bits (107), Expect = 2e-06
Identities = 11/33 (33%), Positives = 22/33 (66%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F YGT++ V++ ++E RG+A++EF+ +
Sbjct: 19 FSNYGTVKDVDLPIDREVNLPRGYAYVEFESPE 51
Score = 42.5 bits (101), Expect = 8e-06
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L +G L N D LK F +G + DV + D RG+ ++ + + ++A+ +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 106 PH-EIDGRVV 114
+IDG+ V
Sbjct: 61 DGGQIDGQEV 70
>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 = 44.8 bits (106), Expect = 2e-06
Identities = 18/48 (37%), Positives = 36/48 (75%), Gaps = 1/48 (2%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
++F+GG+D++TN++ L+ FF Q+G + +V ++ D S+G+GF+T+
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTF 50
Score = 32.5 bits (74), Expect = 0.042
Identities = 13/42 (30%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLD 182
+F QYGT++ V +V ++ G +G+ F+ F+ + KI+ +
Sbjct: 22 FFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQE 62
>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 = 44.9 bits (107), Expect = 2e-06
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVV-----MKDPVTKRSRGFGFITYSESKMVDE 100
LF+ L+++T +++LK FE+ G + V + K P S G+GF+ + + +
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 101 AMSNRPH-EIDGRVVETKR 118
A+ +DG +E K
Sbjct: 63 ALKRLQGTVLDGHALELKL 81
Score = 26.4 bits (59), Expect = 6.4
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 142 FGQYGTIESVNMVTNKETGAKR-----GFAFIEFDDYDVVDK 178
F + G + SV + K+ G+ F+EF + K
Sbjct: 21 FEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
>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 = 44.0 bits (104), Expect = 3e-06
Identities = 18/59 (30%), Positives = 31/59 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
LF+G L + T +D L+A F + G I V +M + + +GF F+ + E + A+
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKG 59
Score = 33.2 bits (76), Expect = 0.020
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+FG+ G I V M+T +++G +GFAF++F++ + + K
Sbjct: 18 HFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60
>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 = 44.2 bits (104), Expect = 3e-06
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
KLF+G + + ++ FE+ G +++V ++KD T +G F+ YS D A+
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
Score = 28.4 bits (63), Expect = 1.1
Identities = 10/40 (25%), Positives = 23/40 (57%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F ++G + V ++ +K TG ++G F+++ D D+ +
Sbjct: 19 MFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
>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 = 44.1 bits (104), Expect = 4e-06
Identities = 19/58 (32%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
KLF+G L+ + + ++ F +G + D+ +M+D + K+SRG F+ YS +M A+
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEMAQAAI 57
>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 = 43.9 bits (104), Expect = 4e-06
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 7/56 (12%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
+F G I V++ T++ETGA +GFA+IEF D V+K LE+D + G
Sbjct: 23 HFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK-------ALELDGSDLGG 71
Score = 33.1 bits (76), Expect = 0.026
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 45 KLFIGGLDYRTNDDSLKA----FFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+F+ G D +D ++ F GEI V + D T S+GF +I + V++
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60
Query: 101 AMSNRPHEIDGR 112
A+ ++ G
Sbjct: 61 ALELDGSDLGGG 72
>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 = 43.7 bits (104), Expect = 4e-06
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 55 TNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
++D L+ F +G I V + KD T +SRGF F+T+ + + A+
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59
Score = 39.4 bits (93), Expect = 1e-04
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 128 RVTKVQIALEQMDY---FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
RVT + ++ D F +G I V + +KETG RGFAF+ F
Sbjct: 3 RVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTF 48
>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 = 43.8 bits (103), Expect = 4e-06
Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 7/82 (8%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
P+S +LF+G L + + LK FF+Q+G +V++ + + FGF+ + +S+ V
Sbjct: 1 PDS-HQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSG---GKLPNFGFVVFDDSEPVQ 56
Query: 100 EAMSNRPHEIDGRV---VETKR 118
+ +SNRP G V VE K+
Sbjct: 57 KILSNRPIMFRGDVRLNVEEKK 78
Score = 30.3 bits (68), Expect = 0.28
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
E ++F QYG + + + G F F+ FDD + V KI+ ++ ++ D +N
Sbjct: 19 ELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQKILSNRPIMFRGDVR-LNV 74
Query: 197 EDHRT 201
E+ +T
Sbjct: 75 EEKKT 79
>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 = 43.7 bits (103), Expect = 4e-06
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+F+G L + ++ L F + G I V +++DP T +GF ++ + + V++A+
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALL-- 59
Query: 106 PHEIDGRVVETKRAVPREVKVRR 128
++ + PRE++V R
Sbjct: 60 ---LNEKKFPPML--PRELRVSR 77
Score = 39.5 bits (92), Expect = 1e-04
Identities = 16/41 (39%), Positives = 27/41 (65%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVL 181
FG+ G IE V +V + +T +GFA+++F D + V+K +L
Sbjct: 19 VFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALL 59
>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 = 43.9 bits (103), Expect = 4e-06
Identities = 27/95 (28%), Positives = 44/95 (46%), Gaps = 8/95 (8%)
Query: 29 NKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG 88
N+A D C L + GL T + L+ F ++G I DV ++ D ++RSRGF
Sbjct: 2 NRANPDPNCC-------LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 54
Query: 89 FITYSESKMVDEAMSN-RPHEIDGRVVETKRAVPR 122
F+ + EA E+DGR + ++ +
Sbjct: 55 FVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 89
Score = 31.2 bits (70), Expect = 0.14
Identities = 12/33 (36%), Positives = 23/33 (69%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F +YG I V++V ++++ RGFAF+ F++
Sbjct: 28 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60
>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 = 43.4 bits (103), Expect = 5e-06
Identities = 19/68 (27%), Positives = 35/68 (51%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNRP 106
F+G +DY T + L+ F+ G I + ++ D T + +GF +I + + V+ A+
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62
Query: 107 HEIDGRVV 114
E GR +
Sbjct: 63 SEFRGRQI 70
Score = 41.9 bits (99), Expect = 2e-05
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK-IVLD 182
E ++F GTI + ++ +K TG +GFA+IEF D V+ ++L+
Sbjct: 15 ELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61
>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 = 43.2 bits (102), Expect = 5e-06
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R LFIG L+ T L+ FE++GEI+D+ + K + + FI Y++ V +AM
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQG---GNPAYAFIQYADIASVVKAM- 58
Query: 104 NRPHEIDGRVVETKR 118
++DG + R
Sbjct: 59 ---RKMDGEYLGNNR 70
>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 = 47.2 bits (112), Expect = 6e-06
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
+S +++IG L +D +K E +G++ ++KD T S+G+ F Y + + D
Sbjct: 292 LDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTD 351
Query: 100 EAMS 103
A++
Sbjct: 352 VAIA 355
Score = 34.9 bits (80), Expect = 0.049
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 144 QYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVD 177
+G +++ N++ + TG +G+AF E+ D V D
Sbjct: 318 SFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTD 351
>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 = 43.2 bits (102), Expect = 6e-06
Identities = 13/35 (37%), Positives = 25/35 (71%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDV 175
YF Q+GT+++V + +K+TG + + FI+F + +V
Sbjct: 19 YFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEV 53
Score = 40.2 bits (94), Expect = 6e-05
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE---SKMVDEAM 102
++IG L + + LK +F Q+G + +V V + T S+ +GFI + + + ++M
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 103 SNRPHEIDGRVVETK 117
+N + + G+V++
Sbjct: 62 NN--YLLMGKVLQVH 74
>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 = 43.0 bits (102), Expect = 7e-06
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
K+FIGGL ++D +K E +G++ ++KD T S+G+ F Y + + D+A
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQA 58
Score = 37.2 bits (87), Expect = 7e-04
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDDYDVVD 177
+G +++ N+V + TG +G+AF E+ D V D
Sbjct: 24 FGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTD 56
>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 = 43.0 bits (101), Expect = 8e-06
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
++F+G + +D L FE+ G I D+ +M DP++ ++RG+ FIT+ + EA+
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60
>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 = 46.6 bits (110), Expect = 9e-06
Identities = 18/77 (23%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 27 IINKAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRG 86
II+ E+++ ++++ + ++ +K+ FE +GEIV + + P + +G
Sbjct: 193 IIDMVQEEAK-----KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKG 247
Query: 87 FGFITYSESKMVDEAMS 103
+GFI Y+ + EA++
Sbjct: 248 YGFIEYNNLQSQSEAIA 264
Score = 43.5 bits (102), Expect = 8e-05
Identities = 31/151 (20%), Positives = 61/151 (40%), Gaps = 27/151 (17%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY---SESKMVDEA 101
++++G + + +D+++ F+ +G I + + DP T + +GF F+ Y +++ E
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 102 MS-----------NRP------HEIDGRVVETKRAVPREVKVRRVTKVQIALEQMD---Y 141
M+ RP I V E + R V V L + D
Sbjct: 169 MNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIY----VASVHPDLSETDIKSV 224
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G I + +G+ FIE+++
Sbjct: 225 FEAFGEIVKCQLARAPTGRGHKGYGFIEYNN 255
>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 = 42.3 bits (100), Expect = 1e-05
Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 10/83 (12%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE---SKMVDE 100
R LF+ ++ D+ L+A FEQ+G+I + K RGF ++Y + ++
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGDIRTLYT----ACK-HRGFIMVSYYDIRAARRAKR 56
Query: 101 AMSNRPHEIDGRVVETKRAVPRE 123
A+ E+ GR ++ ++P++
Sbjct: 57 ALQG--TELGGRKLDIHFSIPKD 77
Score = 27.6 bits (62), Expect = 2.1
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDV 175
E F Q+G I ++ RGF + + YD+
Sbjct: 17 ELRALFEQFGDIRTLYTACK-----HRGFIMVSY--YDI 48
>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 = 42.3 bits (99), Expect = 1e-05
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS- 103
++F+G + +D L FE+ G I D+ +M DP+T +RG+ F+T+ + EA+
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62
Query: 104 NRPHEI 109
HEI
Sbjct: 63 YNNHEI 68
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L + L + L++ FE G I +++D +T +S G+GF+ Y + +A++
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60
Query: 104 NRPHEIDGRVVETKR 118
++G + KR
Sbjct: 61 T----LNGFEIRNKR 71
Score = 39.3 bits (92), Expect = 2e-04
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 133 QIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
Q L + F G IES +V ++ TG G+ F+++ D
Sbjct: 14 QEELRSL--FEAIGPIESCKIVRDRITGQSLGYGFVDYVD 51
>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 = 1e-05
Identities = 18/47 (38%), Positives = 29/47 (61%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+G L D +KA F +G I D V+KD T +S+G+GF+++
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50
>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 = 42.3 bits (100), Expect = 2e-05
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA---M 102
LF+ L+ T D+ L+ F ++G+I V++D T S + FI + + +EA M
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65
Query: 103 SN 104
N
Sbjct: 66 DN 67
Score = 37.2 bits (87), Expect = 0.001
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F ++G I+S ++ +K+TG +AFIEF+
Sbjct: 24 FSRFGKIKSCEVIRDKKTGDSLQYAFIEFET 54
>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 = 42.1 bits (99), Expect = 2e-05
Identities = 17/62 (27%), Positives = 41/62 (66%), Gaps = 5/62 (8%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSES----KMVDEA 101
+F+GG+D R ++ +++FF ++G + +V ++ D T S+G+GF+++ + K+V+
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66
Query: 102 MS 103
++
Sbjct: 67 IN 68
Score = 33.3 bits (76), Expect = 0.021
Identities = 15/41 (36%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+F +YG+++ V ++T++ TG +G+ F+ F D V KIV
Sbjct: 24 SFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIV 63
>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 = 42.0 bits (98), Expect = 2e-05
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+F+G L + +K+ F +G+I D V+KD T +S+G+GF+++
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 50
>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 = 41.6 bits (98), Expect = 2e-05
Identities = 14/49 (28%), Positives = 29/49 (59%)
Query: 56 NDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
++ L+ F+++G+I V ++KD T S+GFG++ + + A+ N
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALEN 61
Score = 36.6 bits (85), Expect = 0.001
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+ F ++G IE V++V +K TG +GF +++F
Sbjct: 19 EKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49
>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 = 41.7 bits (98), Expect = 2e-05
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
+F+G + Y ++ LK F + G +V ++ D T + +G+GF Y + + AM N
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 105 RPHEIDGR 112
+E++GR
Sbjct: 61 NGYELNGR 68
Score = 34.4 bits (79), Expect = 0.008
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 137 EQM-DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
EQ+ D F + G + S +V ++ETG +G+ F E+ D
Sbjct: 13 EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKD 49
>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 = 42.0 bits (98), Expect = 2e-05
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
RKLFIG + + N++ ++ F +G+I + +++ P SRG F+T++ M A+
Sbjct: 2 RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 59
>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 = 41.8 bits (99), Expect = 2e-05
Identities = 12/47 (25%), Positives = 25/47 (53%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
L++G L + L F G ++ + V +D +T+RS G+ ++ +
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNF 48
Score = 26.0 bits (58), Expect = 9.2
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 10/43 (23%)
Query: 137 EQMDY--FGQYGTIESV----NMVTNKETGAKRGFAFIEFDDY 173
E M Y F G + S+ +++T + G+A++ F +
Sbjct: 13 EAMLYEIFSPAGPVLSIRVCRDLITRRS----LGYAYVNFQNP 51
>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 = 41.9 bits (98), Expect = 2e-05
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+ + T + L+ F ++G IVDV V D T+R RGF +I + + + ++A+ N
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 106 PHE-IDGRVVETKRA 119
+ + GR +E + A
Sbjct: 63 NRKWVCGRQIEIQFA 77
Score = 29.2 bits (65), Expect = 0.59
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
FG+YG I V + + T RGFA+I+F+D
Sbjct: 21 FGRYGPIVDVYVPLDFYTRRPRGFAYIQFED 51
>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 = 41.1 bits (97), Expect = 3e-05
Identities = 24/79 (30%), Positives = 46/79 (58%), Gaps = 9/79 (11%)
Query: 46 LFIGGLDYR-TNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY----SESKMVDE 100
+++ L + TN+D L F ++G++V V ++KD T++S+G FI + K V +
Sbjct: 4 VYVSNLPFSLTNND-LHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV-K 61
Query: 101 AMSNRPHEIDGRVVETKRA 119
A++N+ E+ GR ++ A
Sbjct: 62 ALNNK--ELFGRTLKCSIA 78
Score = 31.9 bits (73), Expect = 0.064
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F +YG + V +V +KET +G AFI F D +
Sbjct: 22 FSKYGKVVKVTIVKDKETRKSKGVAFILFLDRE 54
>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 = 40.8 bits (96), Expect = 4e-05
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 146 GTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVINGEDHR 200
I SV + T+KETG +GF ++F D + +D L++D V+ G R
Sbjct: 23 CEITSVRLATDKETGEFKGFGHVDFADEESLDA-------ALKLDGTVLCGRPIR 70
Score = 36.6 bits (85), Expect = 0.001
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 6/68 (8%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNRP 106
+IG L + +D ++ FF+ EI V + D T +GFG + +++ + +D A+
Sbjct: 3 YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL---- 57
Query: 107 HEIDGRVV 114
++DG V+
Sbjct: 58 -KLDGTVL 64
>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 = 40.6 bits (96), Expect = 6e-05
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 7/53 (13%)
Query: 46 LFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
L+I L+ + D LK A F Q+G ++D+V K T + RG F+ + +
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKD 51
Score = 27.9 bits (63), Expect = 1.6
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F Q+G + + +T RG AF+ F D
Sbjct: 23 LFSQFGPVLDIVA---SKTLKMRGQAFVVFKD 51
>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 = 40.7 bits (95), Expect = 6e-05
Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LF+ + T + L+ F ++G IVDV V D T+R RGF ++ + + + ++A+ N
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 106 PHE-IDGRVVETKRA 119
+ I GR +E + A
Sbjct: 63 DRKWICGRQIEIQFA 77
Score = 29.6 bits (66), Expect = 0.44
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
FG+YG I V + + T RGFA+++F+D
Sbjct: 21 FGRYGPIVDVYVPLDFYTRRPRGFAYVQFED 51
>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 = 39.9 bits (94), Expect = 7e-05
Identities = 14/56 (25%), Positives = 32/56 (57%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
F+ L + + L FF + G++ DV +++D ++RS+G ++ + + + V A+
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58
Score = 31.4 bits (72), Expect = 0.087
Identities = 9/37 (24%), Positives = 22/37 (59%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVV 176
++F + G + V ++ ++ + +G A++EF D + V
Sbjct: 18 EFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54
>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 = 40.2 bits (94), Expect = 7e-05
Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
RKLF+G L + N++ ++ F +G I + V++D + SRG F+T++
Sbjct: 2 RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQ-SRGCAFVTFA 50
>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 = 39.9 bits (94), Expect = 8e-05
Identities = 14/64 (21%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI---TYSESKMVDEAM 102
L++G L+ ++ + + F + GE+ V ++++ T +S G+GF+ T+ ++ +++
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61
Query: 103 SNRP 106
+ +P
Sbjct: 62 NGKP 65
Score = 37.6 bits (88), Expect = 7e-04
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKI 179
F + G + SV ++ NK+TG G+ F+EF ++ ++
Sbjct: 20 FAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQA 57
>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 = 39.5 bits (92), Expect = 1e-04
Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLF+G L + +++ FEQ+G++++ ++K+ +GF+ + DEA+ N
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRN 53
Query: 105 RPH 107
H
Sbjct: 54 LHH 56
>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 = 40.0 bits (93), Expect = 1e-04
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
P+S +LF+G L + ++ LK FF +G +V++ + V + FGF+ + +S+ V
Sbjct: 3 PDS-HQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQ 61
Query: 100 EAMSNRPHEIDGRV---VETKR 118
+ +P G V VE K+
Sbjct: 62 RILGAKPIMFRGEVRLNVEEKK 83
Score = 30.7 bits (69), Expect = 0.19
Identities = 13/51 (25%), Positives = 25/51 (49%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVL 187
E ++F +G + + + T G F F+ FDD + V +I+ K ++
Sbjct: 21 ELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILGAKPIMF 71
>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 = 39.9 bits (93), Expect = 1e-04
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L++ L + +D L+ FE +G IV +++D T RG F+ Y + + A+S
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
Score = 34.1 bits (78), Expect = 0.010
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
F YG I N++ +K TG RG AF+ +D
Sbjct: 21 FEAYGNIVQCNLLRDKSTGLPRGVAFVRYD 50
>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 = 39.6 bits (93), Expect = 1e-04
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+++GG+ Y + +D ++++F GEI ++ +M P T R RG FIT+ E + R
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFK-----TEEAAKR 55
Query: 106 PHEIDGRVVETKR 118
+DG + +
Sbjct: 56 ALALDGEDMGGRF 68
Score = 38.1 bits (89), Expect = 4e-04
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDV 175
YF G IE ++++T +TG RG AFI F +
Sbjct: 17 SYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEA 52
>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 = 39.6 bits (93), Expect = 1e-04
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQ-WGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM-- 102
+F+G L D L+ F + + V+ DPVT RS+G+GF+ + + D A+
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Query: 103 ------SNRPHEI 109
S+RP +
Sbjct: 64 MNGVYCSSRPMRV 76
Score = 26.1 bits (58), Expect = 7.4
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 143 GQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+Y ++ +V + TG +G+ F+ F D D
Sbjct: 24 ARYPSVRGAKVVMDPVTGRSKGYGFVRFGDED 55
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+++G L R L+ FE++G + V V ++P GF F+ + + + ++A+
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAV-- 53
Query: 105 RPHEIDGRVVETKR 118
+DGR + R
Sbjct: 54 --RALDGRRICGNR 65
Score = 33.4 bits (77), Expect = 0.017
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 9/54 (16%)
Query: 127 RRVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
R TK + LE D F +YG + SV + N GFAF+EF+D + V
Sbjct: 9 PRATKRE--LE--DEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDAV 53
>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 = 39.6 bits (92), Expect = 1e-04
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R LF+G L+ R ++ L F Q G + V + KD K + FGF+ + S+ V A++
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGK-PKSFGFVCFKHSESVPYAIA 60
>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 = 39.1 bits (91), Expect = 2e-04
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 10/73 (13%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+LF+G L ++ K FE++GE +V + +D RGFGFI + + A +
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA- 55
Query: 105 RPHEIDGRVVETK 117
E+DG +++ +
Sbjct: 56 ---ELDGTILKNR 65
>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 = 39.4 bits (91), Expect = 2e-04
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L++ GL L+ F Q+G I+ ++ D VT SRG GFI + + +EA+
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64
Score = 34.8 bits (79), Expect = 0.008
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 130 TKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
T Q LEQ+ F QYG I + ++ ++ TG RG FI FD
Sbjct: 16 TMTQKELEQL--FSQYGRIITSRILVDQVTGVSRGVGFIRFD 55
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 7/69 (10%)
Query: 58 DSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVETK 117
D L+ F +GEI D+ V+KD TK S+G ++ ++++ AM E++G+ +
Sbjct: 17 DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM----EEMNGKCLGGD 72
Query: 118 RAVPREVKV 126
+ +KV
Sbjct: 73 ---TKPLKV 78
Score = 34.2 bits (79), Expect = 0.009
Identities = 9/32 (28%), Positives = 20/32 (62%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
+ F +G I+ + +V +K+T +G A+++F
Sbjct: 21 EAFAPFGEIQDIWVVKDKQTKESKGVAYVKFA 52
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEI--VDVVVMKD-PVTKRSRGFGFITYSESKMVDEA 101
+L+IG LD R + L F ++G+I D + K P+ + RG+ F+T+ + ++A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 102 MSNRPHEIDGRVVETKRAVPR 122
+ ++G+ K+ V R
Sbjct: 61 L----KSLNGKTALGKKLVVR 77
Score = 34.2 bits (79), Expect = 0.012
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 127 RRVTKVQIALEQMDYFGQYGTIESVNMVTNK---ETGAKRGFAFIEF 170
R+T+ + + F +YG I+ + + +K G RG+ F+ F
Sbjct: 9 SRLTEFHL----LKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTF 51
>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 = 38.8 bits (90), Expect = 2e-04
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 50 GLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN-RPHE 108
GL T + L+ F ++G + V V+ D T RSRGF F+ + EAM + E
Sbjct: 6 GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGME 65
Query: 109 IDGRVVETKRAVPR 122
+DGR + ++ +
Sbjct: 66 LDGRRIRVDYSITK 79
Score = 35.7 bits (82), Expect = 0.003
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ F +YG + VN+V ++ TG RGFAF+ F+ D
Sbjct: 18 EVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERID 52
>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 = 38.4 bits (90), Expect = 3e-04
Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 15/83 (18%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+LF+G L ++ K F ++GE+ +V + K+ +GFGFI ++A +
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKA- 55
Query: 105 RPHEIDGRVVETKRAVPREVKVR 127
E+DG + + R+++VR
Sbjct: 56 ---ELDGIMRKG-----RQLRVR 70
>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 = 38.9 bits (90), Expect = 3e-04
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L++ GL L+ F Q+G I+ ++ D VT SRG GFI + + +EA+
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61
Score = 34.3 bits (78), Expect = 0.010
Identities = 18/42 (42%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 130 TKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
T Q LEQ+ F QYG I + ++ ++ TG RG FI FD
Sbjct: 13 TMTQKELEQL--FSQYGRIITSRILVDQVTGVSRGVGFIRFD 52
>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 = 38.8 bits (90), Expect = 3e-04
Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS---ESKMVDE 100
+ LF+ GL T +++LK F+ + ++ D T S+GFGF+ +S ++K E
Sbjct: 1 KTLFVKGLSEDTTEETLKESFDG---SIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57
Query: 101 AMSNRPHEIDGRVVETKRAVPR 122
AM + EIDG V A P+
Sbjct: 58 AMED--GEIDGNKVTLDFAKPK 77
Score = 29.2 bits (65), Expect = 0.62
Identities = 8/22 (36%), Positives = 17/22 (77%)
Query: 150 SVNMVTNKETGAKRGFAFIEFD 171
+ +VT+++TG+ +GF F++F
Sbjct: 26 AARIVTDRDTGSSKGFGFVDFS 47
>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 = 38.8 bits (90), Expect = 3e-04
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
L++ GL + ++ F Q+G I+ ++ D VT SRG GFI + + +EA+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60
Score = 33.8 bits (77), Expect = 0.013
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 130 TKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
T Q +EQ+ F QYG I + ++ ++ TG RG FI FD
Sbjct: 12 TMSQKEMEQL--FSQYGRIITSRILVDQVTGISRGVGFIRFD 51
>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 = 38.9 bits (90), Expect = 3e-04
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+S L + L + K+ F GEI +++D +T +S G+GF+ Y + D+
Sbjct: 1 DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60
Query: 101 AMSNRPHEIDGRVVETK 117
A++ ++G ++TK
Sbjct: 61 AINT----LNGLKLQTK 73
Score = 34.3 bits (78), Expect = 0.010
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
FG G IES +V +K TG G+ F+ + D + DK +
Sbjct: 24 FGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62
>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 = 38.4 bits (90), Expect = 3e-04
Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
L +G L D+ + +G + ++ T S+G+GF+ Y+ SK A+ +
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYA-SK--ASALKAK 58
Query: 106 PHEIDGRVVETKRA 119
+++DG+ + ++
Sbjct: 59 -NQLDGKQIGGRKL 71
Score = 30.7 bits (70), Expect = 0.16
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
+G +E +V ++ TG +G+ F+E+
Sbjct: 20 VSPFGAVERCFLVYSESTGESKGYGFVEY 48
>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 = 38.0 bits (89), Expect = 3e-04
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
KLF+G L T + L+A FE++G + + V+K+ +GF+ E + ++A+
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKA 52
Query: 105 -RPHEIDGRVV 114
+E G+ +
Sbjct: 53 LNGYEFMGKRI 63
>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 = 38.4 bits (90), Expect = 4e-04
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVM---KDPVTKRSRGFGFITYSESKMVDEAM 102
L++G L+ + ++ L F ++G + V +M + +R+R GF+ + + A+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 103 SNRPHEIDGRVVE 115
E+DG+ V
Sbjct: 64 ----DELDGKDVM 72
>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 = 38.0 bits (89), Expect = 4e-04
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
+++G L + ++ L+ F +G I +V V KD +G+ F+ +
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFD 44
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 37.7 bits (88), Expect = 4e-04
Identities = 17/68 (25%), Positives = 38/68 (55%), Gaps = 12/68 (17%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+++IG L YR + ++ FF+ +G I ++ + GFGF+ + + + D+A+
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAV-- 50
Query: 105 RPHEIDGR 112
+E++G+
Sbjct: 51 --YELNGK 56
Score = 30.8 bits (70), Expect = 0.13
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLD 182
+F YG I +N+ K GF F+EF+D D V +
Sbjct: 18 RFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYE 52
>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 = 37.6 bits (88), Expect = 4e-04
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKM 97
++I GL T D+ L+ + +G+I+ + D T + +G+GF+ + +
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEA 54
Score = 30.7 bits (70), Expect = 0.13
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 144 QYGTIESVNMVTNKETGAKRGFAFIEFD 171
+G I S + +K+T +G+ F++FD
Sbjct: 23 PFGKIISTKAILDKKTNKCKGYGFVDFD 50
>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 = 37.7 bits (88), Expect = 5e-04
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
+F+ LDY+ LK F+ G++V + +D +SRG G + +
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFE 47
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM1
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 74
Score = 37.5 bits (87), Expect = 5e-04
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 9/72 (12%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRG--FGFITYSESKMVDEAMS 103
L++G LD R +D LK F+ G + +V ++ D K ++G +GF+ Y +S + A+
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD---KNNKGVNYGFVEYHQSHDAEIALQ 57
Query: 104 NRPHEIDGRVVE 115
++GR +E
Sbjct: 58 T----LNGRQIE 65
>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 = 37.5 bits (87), Expect = 6e-04
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFE-QWGEIVDVVVMKDPVTKRSRGFGFITYSESK 96
+F+G L N+ L + F+ ++ +M DPVT SRG+GF+ +S+
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDEN 55
Score = 27.1 bits (60), Expect = 3.9
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
+ + +S ++T+ TG RG+ F+ F D +
Sbjct: 26 FPSCKSAKIMTDPVTGVSRGYGFVRFSDEN 55
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. The additional
cytoplasmic localization of SAFB2 implies that it could
play additional roles in the cytoplasmic compartment
which are distinct from the nuclear functions shared
with SAFB1.
Length = 76
Score = 37.4 bits (86), Expect = 6e-04
Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R L++ GL T LK F ++G++V V+ + + +R +GF+T S S+ + ++
Sbjct: 2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCIN 61
Query: 104 N-RPHEIDGRVVETK 117
+ E+ GR++ +
Sbjct: 62 HLHRTELHGRMISVE 76
>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 = 37.6 bits (88), Expect = 6e-04
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F +G ++SV + K G+ RGFAF+EF
Sbjct: 21 FSPFGQVKSVRL-PKKFDGSHRGFAFVEF 48
Score = 29.5 bits (67), Expect = 0.48
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
KL + + + L+ F +G++ V + K RGF F+ + + AM
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKK-FDGSHRGFAFVEFVTKQEAQNAME 59
>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 = 37.2 bits (87), Expect = 6e-04
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
+++G LD + ++ L F Q G +V+V + KD VT+ +G+GF+ +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEF 47
Score = 29.5 bits (67), Expect = 0.42
Identities = 11/39 (28%), Positives = 22/39 (56%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVD 177
+ F Q G + +V++ ++ T A +G+ F+EF + D
Sbjct: 16 WELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDAD 54
>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 = 37.6 bits (87), Expect = 7e-04
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 8/76 (10%)
Query: 33 EDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
ED Q + R LFIG LD+ ++ L+ F+++G I++ VV+K P + + F+ +
Sbjct: 2 EDDQ----RATRNLFIGNLDHNVSEVELRRAFDKYG-IIEEVVIKRPARGQGGAYAFLKF 56
Query: 93 SESKMVDE---AMSNR 105
M AMS R
Sbjct: 57 QNLDMAHRAKVAMSGR 72
>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 = 37.4 bits (87), Expect = 7e-04
Identities = 13/48 (27%), Positives = 29/48 (60%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
++++G + + +D+++ F +G I + + DPVT + +GF F+ Y
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEY 49
Score = 33.2 bits (76), Expect = 0.020
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
F +G I+S++M + T +GFAF+E++
Sbjct: 21 FSPFGPIKSIDMSWDPVTMKHKGFAFVEYE 50
>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 = 37.3 bits (87), Expect = 8e-04
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+F+G L + L F + G+I++V ++K + F FI + + A+
Sbjct: 4 YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVE 61
Query: 104 NRPHEI 109
+ H +
Sbjct: 62 SENHSM 67
Score = 31.1 bits (71), Expect = 0.11
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+ F ++G I VN++ K FAFI+F+
Sbjct: 22 ERFSRHGKILEVNLI--KRANHTNAFAFIKFER 52
>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 = 37.7 bits (88), Expect = 8e-04
Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRG--FGFITYSESKMVDEA 101
R +++G + T L+ F+ +GEI ++ + R G +GF+TY + A
Sbjct: 3 RVIYVGKIPIDTTRSELRQRFQPFGEIEEIT-----LHFRDDGDNYGFVTYRYACDAFRA 57
Query: 102 MSNRPHE 108
+ + +
Sbjct: 58 IEHGNDD 64
>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 = 37.2 bits (86), Expect = 8e-04
Identities = 17/70 (24%), Positives = 37/70 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+++G +DY + + L+A F G I V ++ D + +G+ +I ++ V+ A++
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61
Query: 106 PHEIDGRVVE 115
GRV++
Sbjct: 62 ESSFRGRVIK 71
Score = 34.8 bits (80), Expect = 0.005
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 7/56 (12%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVING 196
+F G I V ++ +K +G +G+A+IEF D V+ V +D+ G
Sbjct: 19 HFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV-------ALDESSFRG 67
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 36.7 bits (85), Expect = 0.001
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 12/76 (15%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+F+G +D T+ + L+A FE +G ++ VM+ F F+ D A+
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIE- 52
Query: 105 RPHEIDGRVVETKRAV 120
E++GR + ++ V
Sbjct: 53 ---ELNGRELHGRKLV 65
>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 = 36.9 bits (86), Expect = 0.001
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFG---FITYSESKMVDEAM 102
+F+ L + LK F + G ++ V D RS+GFG F + +++ E
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPEDAQRAIEMF 59
Query: 103 SNRPHEIDGRVVETK 117
+ ++++GR +E +
Sbjct: 60 NG--YDLEGRELEVR 72
>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 = 37.1 bits (85), Expect = 0.001
Identities = 18/62 (29%), Positives = 30/62 (48%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
S L+I GL T D L + +G+IV + D T + +G+GF+ + +A
Sbjct: 6 SKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKA 65
Query: 102 MS 103
+S
Sbjct: 66 VS 67
Score = 28.3 bits (62), Expect = 1.5
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
YG I S + +K T +G+ F++FD K V
Sbjct: 31 YGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV 66
>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 = 37.0 bits (86), Expect = 0.001
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
RKLF+G L + +D ++ FE +G I + +++ P S+G F+ +S
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGP-DGNSKGCAFVKFS 50
>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 = 36.9 bits (86), Expect = 0.001
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+F+ L ++ L F +G + +V V++D T + +G+GF+T + +EA S
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTN---YEEAYS 58
Score = 31.9 bits (73), Expect = 0.059
Identities = 7/33 (21%), Positives = 18/33 (54%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
F +G + +V ++ + T +G+ F+ +Y+
Sbjct: 22 FSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE 54
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 37.0 bits (85), Expect = 0.001
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 41 ESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDE 100
+S L + L + LK+ F GEI +++D +T +S G+GF+ Y + K ++
Sbjct: 2 DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61
Query: 101 AMSNRPHEIDGRVVETK 117
A++ ++G ++TK
Sbjct: 62 AINT----LNGLRLQTK 74
Score = 30.5 bits (68), Expect = 0.26
Identities = 15/44 (34%), Positives = 22/44 (50%)
Query: 137 EQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
E FG G IES +V +K TG G+ F+ + D +K +
Sbjct: 20 ELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63
>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 = 36.4 bits (84), Expect = 0.001
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 14/70 (20%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY--------SESK 96
+LF+G L +D K F ++GE +V + K +GFGFI ++++
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFINK------GKGFGFIKLESRALAEIAKAE 56
Query: 97 MVDEAMSNRP 106
+ D M R
Sbjct: 57 LDDTPMRGRQ 66
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end)
protein family. This subfamily corresponds to the RRM2
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and component of the NXF1
pathway. It binds to NXF1 and serves as receptor for the
RNA export element RTE. It also possess mRNA export
activity and can facilitate the access of DEAD-box
protein DBP5 to mRNA at the nuclear pore complex (NPC).
RNA-binding protein 15B (RBM15B), also termed one
twenty-two 3 (OTT3), is a paralog of RBM15 and therefore
has post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 36.6 bits (85), Expect = 0.001
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA-- 101
R LF+G L+ ++ L+ FE++G + DV + K P + + F+ + M A
Sbjct: 3 RTLFVGNLEITITEEELRRAFERYGVVEDVDI-KRPPRGQGNAYAFVKFLNLDMAHRAKV 61
Query: 102 -MSNR 105
MS +
Sbjct: 62 AMSGQ 66
>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 = 36.7 bits (85), Expect = 0.001
Identities = 15/58 (25%), Positives = 32/58 (55%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+++G +DY + L+A F G + V ++ D + +GF +I +S+ + V A++
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALA 59
Score = 36.3 bits (84), Expect = 0.002
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 2/42 (4%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVD 177
LE +F G++ V ++ +K +G +GFA+IEF D + V
Sbjct: 16 LEA--HFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 55
>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 = 36.4 bits (84), Expect = 0.001
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 5/72 (6%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R LF+ L Y D LK FE +I + S+G +I + ++A+
Sbjct: 4 RTLFVKNLPYNITVDELKEVFEDAVDI--RLPSGK--DGSSKGIAYIEFKTEAEAEKALE 59
Query: 104 NRP-HEIDGRVV 114
+ E+DGR +
Sbjct: 60 EKQGAEVDGRSI 71
>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 = 36.7 bits (85), Expect = 0.002
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVT--KRSRGFGFITYSESKMVDEAM 102
K+F+G + ++ L+ FEQ+G + + V++D +S+G F+T+ K EA
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA- 61
Query: 103 SNRPHEI 109
N H +
Sbjct: 62 QNALHNM 68
>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 = 36.2 bits (84), Expect = 0.002
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS-- 103
L++ GL T LK F ++G++V ++ + + +R FGF+T + + + +
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 104 NRPHEIDGRVV 114
+R E+ GRV+
Sbjct: 62 HRT-ELHGRVI 71
Score = 27.3 bits (61), Expect = 2.5
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDK 178
F +YG + +VTN + R F F+ + K
Sbjct: 18 QLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAK 56
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 35.7 bits (82), Expect = 0.002
Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 12/82 (14%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
++FIG L+ + ++ FF+ +G I D+ + RGFGF+ + + + D+A+
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDAV-- 50
Query: 105 RPHEIDGRVVETKRAVPREVKV 126
+E+DG+ + +R +
Sbjct: 51 --YELDGKELCNERVTIEHARA 70
Score = 28.4 bits (63), Expect = 0.93
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 8/32 (25%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+F YG I +++ KRGF F+EFDD
Sbjct: 19 FFKGYGRIRDIDL--------KRGFGFVEFDD 42
>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 = 36.2 bits (84), Expect = 0.002
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 13/89 (14%)
Query: 46 LFIGGLDYRTNDDSLKA----FFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
+F+ L +DD L+A F ++G +V V V++D R R + F+ ++ A
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNA 61
Query: 102 MSN-RPHEIDGRVVETKRAVPREVKVRRV 129
++ + +DGR + +RA KV R
Sbjct: 62 LAKGQGTILDGRHIRCERA-----KVNRT 85
>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 = 35.7 bits (83), Expect = 0.003
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 13/70 (18%)
Query: 44 RKLFIGGLDYRTNDDSLKAF----FEQWGEIVDVVVMKDPVTKRSRGFGFITY---SESK 96
R L++GG+ + ++ F +WG+I D+ V+ S+G F+ Y + ++
Sbjct: 2 RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLP------SKGIAFVRYKYRASAE 55
Query: 97 MVDEAMSNRP 106
EAM+++
Sbjct: 56 FAKEAMADQS 65
>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 = 35.7 bits (83), Expect = 0.003
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
L++ GL L+A F +G I+ ++ D VT SRG GFI +
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF 49
Score = 35.0 bits (81), Expect = 0.005
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 133 QIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
Q LE + F YG I + ++ + TG RG FI FD
Sbjct: 14 QQELEAL--FSPYGRIITSRILCDNVTGLSRGVGFIRFDKRI 53
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 35.7 bits (82), Expect = 0.003
Identities = 18/84 (21%), Positives = 46/84 (54%), Gaps = 12/84 (14%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+++IG L Y+ + ++ FF+ +G+I++V + G+GF+ + + + D+A+
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAV-- 50
Query: 105 RPHEIDGRVVETKRAVPREVKVRR 128
+E++G+ + +R + + R
Sbjct: 51 --YELNGKDLCGERVIVEHARGPR 72
Score = 26.1 bits (57), Expect = 6.0
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 8/42 (19%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLD 182
+F YG I V++ K G+ F+EFDD D V +
Sbjct: 19 FFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYE 52
>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 = 35.9 bits (83), Expect = 0.003
Identities = 13/42 (30%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVL 181
F ++G ++SV +VTN+ +G +G A++E+++ + VL
Sbjct: 21 KLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVL 61
Score = 33.5 bits (77), Expect = 0.019
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRS---RGFGFITY-SESKMVDE 100
KLF+ GL + + L+ F++ G + V + VT RS +G ++ Y +ES
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRL----VTNRSGKPKGLAYVEYENESSASQA 59
Query: 101 AMSNRPHEIDGRVV 114
+ EI + +
Sbjct: 60 VLKMDGTEIKEKTI 73
>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 = 35.4 bits (82), Expect = 0.004
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 142 FGQYG-TIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVL 181
F G T+ SV ++ NK TG G+ F+EF D ++ +
Sbjct: 20 FASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60
Score = 34.6 bits (80), Expect = 0.007
Identities = 13/70 (18%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGE-IVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L++G L+ +++ +K F GE ++ V ++++ +T G+ F+ +++ + +
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCL-- 59
Query: 105 RPHEIDGRVV 114
H+++G+ +
Sbjct: 60 --HKLNGKPI 67
>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 = 35.4 bits (81), Expect = 0.004
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L + L D L++ F GE+ +++D V S G+GF+ Y +K + A++
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61
>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 = 35.0 bits (81), Expect = 0.004
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R + +GG+D ++D LK FF GE+ V + D S F F+ +++++ A++
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAESALSALN 58
Score = 26.5 bits (59), Expect = 4.2
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
++F G + V + +++ A+ FAF+EF D
Sbjct: 19 EFFSNCGEVTRVRLCGDRQHSAR--FAFVEFAD 49
>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 = 35.4 bits (81), Expect = 0.005
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
L+I GL ++ F ++G I++ V+ D T SRG FI + + +EA+++
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61
Score = 33.4 bits (76), Expect = 0.022
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
D F ++G I + ++ ++ TG RG AFI FD
Sbjct: 19 DMFSRFGRIINSRVLVDQATGLSRGVAFIRFD 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 = 35.1 bits (81), Expect = 0.005
Identities = 14/46 (30%), Positives = 29/46 (63%)
Query: 58 DSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
D +++ F GEI +++D VT +S G+GF+ Y + + ++A++
Sbjct: 16 DEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61
Score = 32.8 bits (75), Expect = 0.031
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F G IES ++ +K TG G+ F+ + D + +K +
Sbjct: 22 FSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60
>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 = 35.0 bits (81), Expect = 0.005
Identities = 11/28 (39%), Positives = 21/28 (75%)
Query: 147 TIESVNMVTNKETGAKRGFAFIEFDDYD 174
+++SV +V +KET +GF ++EF+D +
Sbjct: 26 SVKSVRLVRDKETDKFKGFCYVEFEDVE 53
>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 = 35.1 bits (80), Expect = 0.005
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT---YSESKM 97
+F+ L ++ L F +G + +V V++D T + +GFGF+T Y E+ M
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAM 58
Score = 28.9 bits (64), Expect = 0.82
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
FG +G + +V ++ + T +GF F+ +YD
Sbjct: 22 FGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYD 54
>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 = 35.2 bits (81), Expect = 0.005
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 45 KLFIGGLDYRTND-DSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
KL I L + LK F ++G++ + + + K GF F+T + K + A+
Sbjct: 2 KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALE 60
Query: 104 N-RPHEIDGRVVETKRAVPRE 123
N EIDGR V AV +
Sbjct: 61 NTNGLEIDGRPVAVDWAVQKN 81
>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 = 35.0 bits (81), Expect = 0.006
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +YGT+ V++ K TG +GFAFIEF+
Sbjct: 20 FSKYGTVVYVSLPRYKHTGDIKGFAFIEFET 50
Score = 34.6 bits (80), Expect = 0.007
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA--MS 103
+++ L + LKA F ++G +V V + + T +GF FI + + +A
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 104 NRPHE 108
N P E
Sbjct: 62 NNPPE 66
>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 = 34.7 bits (79), Expect = 0.006
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L+I GL T D L + +G+IV + D T + +G+GF+ + +A++
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61
Score = 27.8 bits (61), Expect = 1.7
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
YG I S + +K T +G+ F++FD K V
Sbjct: 25 YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60
>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 = 34.5 bits (79), Expect = 0.006
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R LF+G LD + ++ + F Q G ++ V + KD K + F F+ + V AM+
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGK-PKQFAFVNFKHEVSVPYAMN 60
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM1 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically binds mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone, and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs);
DND1 harbors only two RRMs. .
Length = 78
Score = 34.5 bits (80), Expect = 0.008
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+F+G + +D L FE+ G I ++ +M D +RG+ F+TY+ + A+
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAVKQL 62
Query: 106 P-HEI 109
+EI
Sbjct: 63 HNYEI 67
>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 = 34.5 bits (80), Expect = 0.008
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT 91
LF+GGL + L+ F ++G + DV ++K RGF +I
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYID 47
Score = 32.1 bits (74), Expect = 0.052
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFD 171
F ++GT+ V ++ K+ G RGFA+I+
Sbjct: 20 FSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49
>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 = 34.2 bits (79), Expect = 0.009
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 56 NDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+D L+ FE +G I DV + + R FGF+ Y + +A+
Sbjct: 13 KEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALK 59
>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 = 34.6 bits (79), Expect = 0.009
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 3/36 (8%)
Query: 59 SLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
SL A F Q+G +VD+V +K T + RG F+ + E
Sbjct: 21 SLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKE 53
>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 = 37.3 bits (86), Expect = 0.009
Identities = 34/147 (23%), Positives = 69/147 (46%), Gaps = 20/147 (13%)
Query: 39 EPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMV 98
+P ++F+G + +D L FE+ G I ++ +M D + ++RG+ F+T+ +
Sbjct: 54 QPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEA 112
Query: 99 DEAMSN-RPHEI-DGRV------VETKR----AVPREVKVRRVTKVQIALEQMDYFGQYG 146
EA+ +EI GR+ V+ R +P+ K + LE+ + G
Sbjct: 113 KEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEI------LEEFSKVTE-G 165
Query: 147 TIESVNMVTNKETGAKRGFAFIEFDDY 173
++ + + + RGFAF+E++ +
Sbjct: 166 VVDVIVYHSAADKKKNRGFAFVEYESH 192
Score = 35.4 bits (81), Expect = 0.041
Identities = 39/149 (26%), Positives = 66/149 (44%), Gaps = 31/149 (20%)
Query: 45 KLFIGGL-DYRTNDDSLKAFFEQWGEIVDVVVMKDPVTK-RSRGFGFITYSESKMVDEAM 102
+LF+GG+ + ++ L+ F + +VDV+V K ++RGF F+ Y + AM
Sbjct: 140 RLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAA--AM 197
Query: 103 SNR---PHEID--GRVVETKRAVPRE---------VKVRRVTKVQIAL-EQM--DYFGQY 145
+ R P I G V+ A P E VK+ V + E++ F ++
Sbjct: 198 ARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEF 257
Query: 146 --GTIESVNMVTNKETGAKRGFAFIEFDD 172
G +E V + R +AF+ F+D
Sbjct: 258 KPGKVERVKKI--------RDYAFVHFED 278
>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 = 33.9 bits (78), Expect = 0.010
Identities = 16/79 (20%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRG-FGFITYSESKMVDE 100
+ R +F+ G T+++ L +F +G +++V++ KD +G + + + + VD+
Sbjct: 1 AERSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDK 54
Query: 101 AMSNRPHEIDGRVVETKRA 119
+S H ++G + +
Sbjct: 55 VLSEPQHTLNGHRLRVRPR 73
Score = 33.1 bits (76), Expect = 0.021
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 5/46 (10%)
Query: 135 ALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
+ MDYF +G + +V M +K+ G +A +EFD + VDK++
Sbjct: 16 EEQLMDYFSAFGPVMNVIM--DKDKGV---YAIVEFDSKEGVDKVL 56
>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 = 34.3 bits (78), Expect = 0.010
Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
S L + L + ++ F GEI +++D +T +S G+GF+ Y + K ++A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 102 MSNRPHEIDGRVVETK 117
++ ++G ++TK
Sbjct: 61 INT----LNGLRLQTK 72
Score = 30.9 bits (69), Expect = 0.20
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
FG G IES +V +K TG G+ F+ + D +K +
Sbjct: 23 FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
>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 = 34.1 bits (78), Expect = 0.011
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
+LF+G L ++ ++ FE++G+ ++ + KD +GFGFI + + A
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIA 53
>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 = 33.8 bits (78), Expect = 0.013
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 6/47 (12%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
L++GGL R + L+ F Q+GEI + V V + + F+T+
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITV----VPR--QQCAFVTF 44
Score = 32.2 bits (74), Expect = 0.043
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 6/31 (19%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D+F Q+G I S+ +V ++ AF+ F
Sbjct: 20 DHFYQFGEIRSITVV------PRQQCAFVTF 44
>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 = 33.4 bits (77), Expect = 0.015
Identities = 15/77 (19%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWG--EIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
L++G L + T D+ L+ + G ++ + + +S+GF ++ ++ A +
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASE----AAAA 56
Query: 104 NRPHEIDGRVVETKRAV 120
+++GR K+ V
Sbjct: 57 AVKEKLEGREFNGKKCV 73
>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 = 33.4 bits (77), Expect = 0.015
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
L++ L T ++ L+ F ++GE+ V +KD + F+ + E +AM
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55
Query: 105 RPHEIDGRVVETKRAVP 121
E++G +E A P
Sbjct: 56 NGKELEGSPIEVSLAKP 72
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 34.2 bits (79), Expect = 0.015
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 44 RKLFIGGL--DYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
R LF+ L +R + L+ F Q G+ + P + RGF F+ Y+ ++ +EA
Sbjct: 3 RCLFVDRLPKTFR-DVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEA 60
Query: 102 MSNRPHEIDGRVVE 115
++G ++
Sbjct: 61 QQ----ALNGHSLQ 70
>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 = 33.5 bits (77), Expect = 0.018
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 150 SVNMVTNKETGAKRGFAFIEF 170
V ++ K TGA RGFAF+EF
Sbjct: 32 DVRLMRRKTTGASRGFAFVEF 52
Score = 28.5 bits (64), Expect = 1.2
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 72 DVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
DV +M+ T SRGF F+ E ++EA
Sbjct: 32 DVRLMRRKTTGASRGFAFV---EFMSLEEA 58
>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 = 33.3 bits (75), Expect = 0.021
Identities = 17/63 (26%), Positives = 31/63 (49%)
Query: 42 SLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
S L+I GL T D L + +G+IV + D T + +G+GF+ + +A
Sbjct: 3 SKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKA 62
Query: 102 MSN 104
+++
Sbjct: 63 VAS 65
Score = 28.3 bits (62), Expect = 1.3
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
YG I S + +K T +G+ F++FD K V
Sbjct: 28 YGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAV 63
>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 = 33.5 bits (76), Expect = 0.021
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
R +F L R L+ FF G++ DV ++ D ++RS+G ++ + E + V A+
Sbjct: 2 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 60
Score = 28.9 bits (64), Expect = 0.79
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
D+F G + V +++++ + +G A++EF
Sbjct: 20 DFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 50
>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 = 33.1 bits (75), Expect = 0.024
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT---YSESKM 97
+FI L ++ L F +G + +V V++D T + +GFGF+T Y E+ M
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAM 58
Score = 27.3 bits (60), Expect = 2.9
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
FG +G + +V ++ + T +GF F+ +Y+
Sbjct: 22 FGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYE 54
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). SNF contains two RNA recognition motifs (RRMs);
it can self-associate through RRM1, and each RRM can
recognize poly(U) RNA binding independently. .
Length = 78
Score = 33.0 bits (75), Expect = 0.025
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 46 LFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
++I L+ + + LK A F Q+G+I+D+V +K T + RG F+ + +
Sbjct: 2 IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALK---TLKMRGQAFVVFKD 51
>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 = 33.0 bits (75), Expect = 0.028
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTK-RSRGFGFITYSESKMVDEAM 102
+ L + L Y ++DSL+ FE+ ++ P R +G+ F+ + ++ EA+
Sbjct: 2 KVLVVNNLSYSASEDSLQEVFEK------ATSIRIPQNNGRPKGYAFVEFESAEDAKEAL 55
Query: 103 SN-RPHEIDGRVV 114
++ EI+GR +
Sbjct: 56 NSCNNTEIEGRSI 68
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 32.7 bits (75), Expect = 0.029
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
L+IG L + ++ LK FE++GEI + ++ RG ++
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCM 45
Score = 28.8 bits (65), Expect = 0.64
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 10/42 (23%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF----DDYDVVDKI 179
F +YG I+S++M+ RG A++ D + + K+
Sbjct: 23 FEEYGEIQSIDMIPP------RGCAYVCMETRQDAHRALQKL 58
>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 = 33.0 bits (76), Expect = 0.030
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++G LD T D L FF Q GE+ V + D T+ +R + F+ ++E V A+
Sbjct: 5 RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE-TQPTR-YAFVEFAEQTSVINALK 62
Query: 104 NRPHEIDGR 112
GR
Sbjct: 63 LNGAMFGGR 71
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 33.0 bits (75), Expect = 0.033
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 8/41 (19%)
Query: 140 DYFGQYGTIES--------VNMVTNKETGAKRGFAFIEFDD 172
DYF Q G I++ +N+ T++ETG +G A + FDD
Sbjct: 21 DYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 61
>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 = 32.8 bits (74), Expect = 0.034
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT---YSESKM 97
+F+ L +++ L F +G + +V V++D T + +GFGF+T Y E+ M
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60
Score = 29.7 bits (66), Expect = 0.51
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
FG +G + +V ++ + T +GF F+ +YD
Sbjct: 24 FGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYD 56
>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 = 32.8 bits (75), Expect = 0.034
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 7/63 (11%)
Query: 40 PESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVD 99
P + +F+GGL ++ ++ FEQ GEI+ + + K + F I ++E VD
Sbjct: 3 PPGCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMSK-------KNFCHIRFAEEFAVD 55
Query: 100 EAM 102
+A+
Sbjct: 56 KAI 58
>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 = 32.7 bits (74), Expect = 0.037
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
R +F L R L+ FF G++ DV ++ D ++RS+G ++ + + V A+
Sbjct: 2 RTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60
Score = 28.1 bits (62), Expect = 1.7
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
++F G + V M++++ + +G A++EF D
Sbjct: 20 EFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVD 52
>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 = 31.7 bits (73), Expect = 0.040
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 5/34 (14%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F +G +E + ++ K GFAF+EF
Sbjct: 2 YKLFSPFGNVEKIKLLKK-----KPGFAFVEFST 30
Score = 31.3 bits (72), Expect = 0.065
Identities = 11/56 (19%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 60 LKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN-RPHEIDGRVV 114
L F +G + + ++K GF F+ +S + ++A+ GR +
Sbjct: 1 LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPL 51
>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 = 32.5 bits (74), Expect = 0.041
Identities = 15/47 (31%), Positives = 23/47 (48%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
LFI L D L F +G ++ V D T +S+ FGF+++
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSF 53
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 32.2 bits (73), Expect = 0.043
Identities = 16/76 (21%), Positives = 43/76 (56%), Gaps = 12/76 (15%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
+++IG L Y + ++ FF +G+++++ + G+GF+ + +S+ D+A+
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAV-- 50
Query: 105 RPHEIDGRVVETKRAV 120
+E++G+ + +R +
Sbjct: 51 --YELNGKDLCGERVI 64
>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 = 32.3 bits (73), Expect = 0.043
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
LFI L D L F +G ++ V D T S+ FGF++Y A+
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAI--- 63
Query: 106 PHEIDGRVVETKR 118
++G + TKR
Sbjct: 64 -QAMNGFQIGTKR 75
>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 = 32.2 bits (74), Expect = 0.045
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 45 KLFIGGLDYRTNDDSLKA-FFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESK 96
+L + L + LK F + GEI DV +++ K SR FI Y +
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGK-SRRIAFIGYKTEE 53
>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 = 32.6 bits (75), Expect = 0.050
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 139 MDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
D F ++G I+++++ ++ TG +G+A IE++
Sbjct: 24 HDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKK 59
>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 = 32.4 bits (73), Expect = 0.056
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFIT---YSESKM 97
+F+ L ++ L F +G + +V V++D T + +GFGF+T Y E+ M
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60
Score = 29.3 bits (65), Expect = 0.68
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
FG +G + +V ++ + T +GF F+ +YD
Sbjct: 24 FGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYD 56
>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 = 31.7 bits (73), Expect = 0.065
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN- 104
L++G L + T ++ + F + G+I +++ D TK GF F+ Y + + A+
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 105 RPHEIDGRVVET 116
++D R++
Sbjct: 61 NGTKLDDRIIRV 72
Score = 29.4 bits (67), Expect = 0.45
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F + G I+ + M ++ T GF F+E+
Sbjct: 19 FSRCGDIKRIIMGLDRFTKTPCGFCFVEYYT 49
>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 = 31.9 bits (72), Expect = 0.066
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
++FIG L +D L E+ G+I ++ +M D +RG+ F+T+S + A+
Sbjct: 3 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAI 59
>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 = 31.4 bits (72), Expect = 0.077
Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
+L + L Y ++ L+ F + GE+ V + D + RS G + + + + + A+
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAI 58
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, 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. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 31.6 bits (72), Expect = 0.078
Identities = 17/66 (25%), Positives = 30/66 (45%)
Query: 50 GLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEI 109
GL Y +D + FF + D VV+ R G ++ ++ +M ++A+ EI
Sbjct: 8 GLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKHREEI 67
Query: 110 DGRVVE 115
R +E
Sbjct: 68 GNRYIE 73
>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 = 31.6 bits (72), Expect = 0.081
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 10/54 (18%)
Query: 118 RAVPREVKVRRVTKVQIALEQMDYFGQYGTIESVNMVTN-KETGAKRGFAFIEF 170
R +P E V+ + ++ F +G +++V + TG+ RGF F++F
Sbjct: 6 RNIPFEATVKELREL---------FSTFGELKTVRLPKKMTGTGSHRGFGFVDF 50
Score = 29.3 bits (66), Expect = 0.51
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRS-RGFGFITYS---ESKMVDE 100
K+ + + + L+ F +GE+ V + K S RGFGF+ + ++K +
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61
Query: 101 AMSNRPHEIDGRVV 114
A+ + H R+V
Sbjct: 62 ALCHSTHLYGRRLV 75
>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 = 31.9 bits (72), Expect = 0.083
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 46 LFIGGLDYRTNDDSLK----AFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
++I L+ + D LK A F ++G+I+D++V + + + RG F+ + E A
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 62
Query: 102 M 102
+
Sbjct: 63 L 63
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation
initiation factor 4B (eIF-4B) and similar proteins.
This subfamily corresponds to the RRM of eIF-4B, a
multi-domain RNA-binding protein that has been primarily
implicated in promoting the binding of 40S ribosomal
subunits to mRNA during translation initiation. It
contains two RNA-binding domains; the N-terminal
well-conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), binds the 18S rRNA of the 40S ribosomal subunit
and the C-terminal basic domain (BD), including two
arginine-rich motifs (ARMs), binds mRNA during
initiation, and is primarily responsible for the
stimulation of the helicase activity of eIF-4A. eIF-4B
also contains a DRYG domain (a region rich in Asp, Arg,
Tyr, and Gly amino acids) in the middle, which is
responsible for both, self-association of eIF-4B and
binding to the p170 subunit of eIF3. Additional research
indicates that eIF-4B can interact with the poly(A)
binding protein (PABP) in mammalian cells, which can
stimulate both, the eIF-4B-mediated activation of the
helicase activity of eIF-4A and binding of poly(A) by
PABP. eIF-4B has also been shown to interact
specifically with the internal ribosome entry sites
(IRES) of several picornaviruses which facilitate
cap-independent translation initiation. .
Length = 77
Score = 31.6 bits (72), Expect = 0.088
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 47 FIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDP-VTKRSRGFGFITYSESK-------MV 98
++G L Y ++ +K FF + V + ++P R RGFG+ + + +
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLN 63
Query: 99 DEAMSNRPHEID 110
DE++ NR +D
Sbjct: 64 DESLKNRRIRVD 75
>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 = 31.6 bits (71), Expect = 0.089
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 151 VNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDKVVVLEVDQEVIN 195
V ++ NK +G RGFAF+EF+ + D +E +Q +
Sbjct: 33 VRLMRNKSSGQSRGFAFVEFN-------HLQDATRWMEANQHSLM 70
>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 = 31.0 bits (71), Expect = 0.099
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 12/48 (25%)
Query: 125 KVRRVTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
+V+K LE++ F +YG I +++ +G+ F++FD+
Sbjct: 9 NTDKVSKED--LEEI--FSKYGKILGISL--------HKGYGFVQFDN 44
Score = 29.5 bits (67), Expect = 0.33
Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 15/77 (19%)
Query: 44 RKLFIGGL--DYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
++F+G L D + +D L+ F ++G+I+ + + K G+GF+ + + A
Sbjct: 1 SRVFVGNLNTDKVSKED-LEEIFSKYGKILGISLHK--------GYGFVQFDNEEDARAA 51
Query: 102 MSNRPHEIDGRVVETKR 118
++ +GR + ++
Sbjct: 52 VAGE----NGREIAGQK 64
>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 = 31.9 bits (73), Expect = 0.12
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 50 GLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESK 96
G T++D +K +F +GEI ++ DP T G I Y S
Sbjct: 9 GFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSP 55
Score = 29.6 bits (67), Expect = 0.80
Identities = 7/32 (21%), Positives = 12/32 (37%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
YF +G I + + T G I++
Sbjct: 22 YFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYG 53
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 84
Score = 31.4 bits (71), Expect = 0.13
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKR-----SRGFGFI---TYSESKM 97
LF+ L++ T + L F+ V V P KR S GFGF+ T +++
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 98 VDEAMSNRPHEIDGRVVETKRA 119
+AM +DG + K +
Sbjct: 63 ALKAMDGF--VLDGHTLVVKFS 82
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 30.6 bits (69), Expect = 0.16
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
K+ + L + ++ F +G++ V V K + +RGF F+ +S +K AM
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKK-FDQSARGFAFVEFSTAKEALNAM 58
Score = 28.6 bits (64), Expect = 0.97
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F YG ++SV V K + RGFAF+EF
Sbjct: 19 TLFSSYGQLKSVR-VPKKFDQSARGFAFVEF 48
>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 = 30.7 bits (70), Expect = 0.17
Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 10/58 (17%)
Query: 58 DSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNRPHEIDGRVVE 115
+ LK F +G I+++ + K+ + GF+T+ + + D A++ E++G V+
Sbjct: 17 EILKKAFSPFGNIINISMEKE------KNCGFVTFEKMESADRAIA----ELNGTTVQ 64
Score = 26.1 bits (58), Expect = 7.1
Identities = 7/40 (17%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 141 YFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F +G I +++M ++ F+ F+ + D+ +
Sbjct: 22 AFSPFGNIINISM------EKEKNCGFVTFEKMESADRAI 55
>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 = 30.7 bits (69), Expect = 0.19
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
R LF+G LD + L+ F+++G I +V + K P ++ +GF+ + M A
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVDI-KRPGRGQTSTYGFLKFENLDMAHRA 64
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 30.4 bits (68), Expect = 0.19
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
+F+ LDY+ LK F G +V +++D K SRG G +T+ + +A+S
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGK-SRGIGTVTFEQPIEAVQAIS 59
>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 = 30.3 bits (69), Expect = 0.22
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 5/43 (11%)
Query: 134 IALEQM-DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD-YD 174
I+ E++ D FG+YG I + + KET RG AF+ ++D YD
Sbjct: 14 ISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYD 53
Score = 26.0 bits (58), Expect = 6.5
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
R L++ L ++ + + L F ++G I + + T RG F+ Y
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYE 49
>gnl|CDD|240932 cd12488, RRM2_hnRNPR, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM2 of hnRNP R, a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. It contains an acidic auxiliary N-terminal
region, followed by two well-defined and one degenerated
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal RGG motif. hnRNP R binds RNA through
its RRM domains. .
Length = 85
Score = 30.5 bits (68), Expect = 0.22
Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 45 KLFIGGL-DYRTNDDSLKAFFEQWGEIVDVVVMKDPV-TKRSRGFGFITYSESKMVDEA- 101
+LF+G + +T ++ L+ F + +VDV++ P K++RGF F+ Y + K +A
Sbjct: 4 RLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQAR 63
Query: 102 ---MSNRPHEIDGRVVETKRAVP 121
MS + ++ G VV + A P
Sbjct: 64 RRLMSGKV-KVWGNVVTVEWADP 85
>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 = 30.8 bits (69), Expect = 0.24
Identities = 20/57 (35%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 36 QCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
Q PE LFI L D L F +G +V V D T S+ FGF++Y
Sbjct: 1 QKEGPEG-ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 56
>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 = 30.3 bits (69), Expect = 0.30
Identities = 13/51 (25%), Positives = 28/51 (54%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
+F+G + +DD ++ E+ G+++ +KDP T + + FGF + +
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFED 51
>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 = 29.8 bits (67), Expect = 0.30
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 10/40 (25%)
Query: 133 QIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
Q +E++ FG+YG ++ V+M K GFAF+ +D
Sbjct: 14 QSEIERL--FGKYGRVDRVDM--------KSGFAFVYMED 43
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 32.0 bits (72), Expect = 0.39
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 94 ESKMVDEAMSNRPHEIDGRVVETKRA----VPREVKVRRVTKVQIALEQMDYFGQYGTIE 149
E + + NR H + RVV+ +P +V V V L++ +YFGQYG I+
Sbjct: 92 EKERKEAEGQNRKHLSNIRVVQKNLVYVIGIPPKVADEEVAPV---LKRHEYFGQYGKIK 148
Query: 150 SVNMVTNKETGA 161
+ V NK+T +
Sbjct: 149 KI--VVNKKTSS 158
>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 = 29.6 bits (67), Expect = 0.39
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 21/55 (38%)
Query: 41 ESLRKLF--IGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
E L +LF I GL+Y + +DP T +S+GF ++TYS
Sbjct: 14 EQLHRLFDIIPGLEY-------------------CDLKRDPYTGKSKGFAYVTYS 49
>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 = 29.8 bits (67), Expect = 0.39
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESK 96
R ++I L + LK FE +GEI + V+ + R +GFITY S+
Sbjct: 3 RVIYIRNLSSSMSSTELKKRFEVFGEIEECKVL---IKSRGEKYGFITYRHSE 52
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 29.6 bits (66), Expect = 0.44
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSN 104
K+++G L N L+ F +G + V V ++P GF F+ + + + +A+
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV-- 58
Query: 105 RPHEIDGRVV 114
E+DGR +
Sbjct: 59 --RELDGRTL 66
Score = 29.2 bits (65), Expect = 0.62
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 9/60 (15%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDY----DVVDKIVLDKVVVLEVDQEVINGE 197
FG YG + SV + N GFAF+EF+D D V ++ + V E+ NGE
Sbjct: 25 FGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 79
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 29.3 bits (66), Expect = 0.48
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS-- 103
L+IG L N+ L+ FE+ V V++K G+ F+ + D+A+
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVK------KGGYAFVDCPDQSWADKAIEKL 54
Query: 104 NRPHEIDGRVVETKRAVPR 122
N + G+V+E + +VP+
Sbjct: 55 NGKI-LQGKVIEVEHSVPK 72
>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 85
Score = 29.3 bits (65), Expect = 0.58
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 45 KLFIGGL-DYRTNDDSLKAFFEQWGEIVDVVVMKDPV-TKRSRGFGFITYSESKMVDEA 101
+LF+G + +T + ++ F + + DV++ P K++RGF F+ Y + K +A
Sbjct: 4 RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQA 62
>gnl|CDD|183854 PRK13042, PRK13042, superantigen-like protein; Reviewed.
Length = 291
Score = 31.1 bits (70), Expect = 0.67
Identities = 31/114 (27%), Positives = 49/114 (42%), Gaps = 22/114 (19%)
Query: 88 GFITYSESKMVDEAMSNRPHEIDGRVV--ETKRAVPREVKVRRVTKVQIALEQMDY---- 141
G IT S SK VD H+ R+ + K + +V ++TK QI+L+++D+
Sbjct: 182 GGITKSNSKKVD-------HKAGVRITKEDNKGTISHDVSEFKITKEQISLKELDFKLRK 234
Query: 142 -----FGQYGTIESVNMVTNKETGAKRGF----AFIEFDDYDVVDKIVLDKVVV 186
YG + S +V + G K F E DV+D +D + V
Sbjct: 235 QLIEKHNLYGNVGSGKIVIKMKNGGKYTFELHKKLQENRMADVIDGTNIDNIEV 288
>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 = 29.0 bits (66), Expect = 0.81
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 136 LEQMDYFGQYGTIESVNMVTNKET 159
L++ +YFGQYG I+ + V N+ T
Sbjct: 23 LKKPEYFGQYGKIKKI--VINRNT 44
>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 = 28.7 bits (65), Expect = 0.83
Identities = 10/70 (14%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+++ G D ++ FFE++G++ ++ + +D K+ +G F+ + + + +
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDL-DKKFKGSVFVEFKTEEDAKKFLEKE 60
Query: 106 PHEIDGRVVE 115
+ + +
Sbjct: 61 KLKYKEKELT 70
Score = 26.8 bits (60), Expect = 4.0
Identities = 9/41 (21%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
++F ++G + ++ M + + K G F+EF + K +
Sbjct: 18 EFFEKFGKVNNIRMRRDLDKKFK-GSVFVEFKTEEDAKKFL 57
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 28.7 bits (64), Expect = 0.85
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYS 93
++F+G + +D L FE+ G+I + +M + + +RG+ F+ Y+
Sbjct: 2 CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYT 50
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 28.8 bits (64), Expect = 0.87
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
++F+G + +D L FE G I ++ +M D ++RG+ F+ Y++ A+
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAV 59
>gnl|CDD|241170 cd12726, RRM2_CPEB2_like, RNA recognition motif 2 found in
cytoplasmic polyadenylation element-binding protein
CPEB-2, CPEB-3, CPEB-4 and similar protiens. This
subgroup corresponds to the RRM2 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 = 81
Score = 28.6 bits (64), Expect = 0.98
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQ-WGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAM 102
+ +F+GG+ L ++ +G + + DP K +G G + +S + A+
Sbjct: 1 KTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAI 60
Query: 103 SNR-----PHEIDGRV 113
S R +ID RV
Sbjct: 61 SARFVQLQHGDIDKRV 76
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM4 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 29.1 bits (66), Expect = 1.0
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 28/75 (37%)
Query: 30 KAMEDSQCSEPESLRKLFIGGLDYRTNDDSLKAFFEQWGE----IVDVVVMKD-----PV 80
K++++ + L++LF+ KA E+ G+ I V +M+D P
Sbjct: 10 KSVDEKK------LKELFL------------KAVSERAGKKKPKIKQVKIMRDLKRVDPN 51
Query: 81 TK-RSRGFGFITYSE 94
K +S+G+GF+ ++
Sbjct: 52 GKGKSKGYGFVEFTN 66
Score = 26.4 bits (59), Expect = 7.7
Identities = 8/48 (16%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 133 QIALEQMDYF--GQYGTIESVNMVTNKE------TGAKRGFAFIEFDD 172
++ L+ + + I+ V ++ + + G +G+ F+EF +
Sbjct: 19 ELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTN 66
>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 = 28.2 bits (63), Expect = 1.1
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLDK 183
+YFGQ+G + V + KR F F+ F++ + V K +L K
Sbjct: 18 EYFGQFGPVLDVRI----PYQQKRMFGFVTFENAETV-KRILSK 56
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B shows high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 28.2 bits (63), Expect = 1.1
Identities = 15/74 (20%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMSNR 105
+F+ GL Y ++ +K FF ++ DV+ +K + + G + ++ + EA+
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGL-DVEDVIFLKRHNGRNN-GNAIVKFATFQDAKEALKRH 59
Query: 106 PHEIDGRVVETKRA 119
+ R +E +
Sbjct: 60 RELMGSRYIELMLS 73
>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 = 28.3 bits (64), Expect = 1.2
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEA 101
+FI LD ++ +L F +G I+ V D S+G+GF+ + + A
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGG-SKGYGFVHFETEEAAVRA 59
>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 = 28.1 bits (63), Expect = 1.2
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 57 DDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
D+ ++ F G + + +++D T S GFGF+ Y
Sbjct: 14 DEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDY 49
Score = 27.0 bits (60), Expect = 3.3
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEF 170
F G +++ +V +K TG GF F+++
Sbjct: 21 FLAVGPVKNCKIVRDKRTGYSYGFGFVDY 49
>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 = 28.7 bits (64), Expect = 1.3
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRG--FGFITY 92
R ++IG + R LK F +GEI + + RS G +GF+TY
Sbjct: 3 RVVYIGKIPSRMTRSELKDRFSVFGEIEECTIH-----FRSEGDNYGFVTY 48
>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 = 28.2 bits (63), Expect = 1.3
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 4/39 (10%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIV 180
F G + V M++ + AFI F++ + +
Sbjct: 20 FETCGPVRKVTMLSRT----VQPHAFITFENLEAAQLAI 54
>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 = 27.9 bits (63), Expect = 1.4
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 10/44 (22%)
Query: 129 VTKVQIALEQMDYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
TK + F Q+ + V +V +RG AF+EF+
Sbjct: 14 TTKEML----EMLFNQFPGFKEVRLV------PRRGIAFVEFET 47
>gnl|CDD|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 3
(IGF2BP3). This subgroup corresponds to the RRM1 of
IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also
termed KH domain-containing protein overexpressed in
cancer (KOC), or VICKZ family member 3, an RNA-binding
protein that plays an important role in the
differentiation process during early embryogenesis. It
is known to bind to and repress the translation of IGF2
leader 3 mRNA. IGF2BP3 also acts as a
Glioblastoma-specific proproliferative and proinvasive
marker acting through IGF2 resulting in the activation
of oncogenic phosphatidylinositol
3-kinase/mitogen-activated protein kinase (PI3K/MAPK)
pathways. IGF2BP3 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 28.0 bits (62), Expect = 1.6
Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 16/86 (18%)
Query: 43 LRKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKR---SRGFGFITYSESKM-- 97
+ KL+IG L + L++ F+ K P + G+ F+ +
Sbjct: 1 MNKLYIGNLSENASPLDLESIFKDS---------KIPFSGPFLVKSGYAFVDCPDESWAM 51
Query: 98 -VDEAMSNRPHEIDGRVVETKRAVPR 122
+ +S + E+ G+V+E + +VP+
Sbjct: 52 KAIDTLSGKV-ELHGKVIEVEHSVPK 76
>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 = 27.7 bits (62), Expect = 1.6
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
D F +YG I+++++ K FAF+EF+D
Sbjct: 18 DLFYKYGPIKAIDL---KNRRRGPPFAFVEFED 47
>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 = 28.4 bits (63), Expect = 1.8
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIV 71
RK+F+GGL + + + F ++G +
Sbjct: 1 RKVFVGGLPWDITEADILNSFRRFGSLQ 28
>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 = 27.6 bits (61), Expect = 2.0
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 145 YGTIESVNMVTNKETGAKRGFAFIEFDDYDVVDKIVLD 182
YG IE +V ++ TG +G+ F+E+ D K L+
Sbjct: 23 YGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60
>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 = 28.0 bits (62), Expect = 2.0
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRG--FGFITY 92
R +++G + T L+ FE +GEI + V R G +GFITY
Sbjct: 3 RVIYVGKIRPDTTRTELRDRFEVFGEIEECT-----VNLRDDGDSYGFITY 48
>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 = 27.4 bits (61), Expect = 2.2
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSESKMVDEAMS 103
R +++ +D + ++ L A F G++VD V DP F FI +++ + A+S
Sbjct: 3 RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDP--NSVLRFAFIEFTDEEGARAALS 60
>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 = 27.3 bits (60), Expect = 2.5
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
F YG + +V + N GFAF+EF+D
Sbjct: 20 FSYYGPLRTVWIARNPP-----GFAFVEFED 45
>gnl|CDD|227226 COG4889, COG4889, Predicted helicase [General function prediction
only].
Length = 1518
Score = 29.8 bits (67), Expect = 2.5
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 183 KVVVLEVDQEVINGEDHRT-HGTHQEAKVDGV 213
KV+VL VD+EVI G G + +D V
Sbjct: 399 KVMVLAVDKEVIAGVLQSVLSGPSKGLALDDV 430
>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 = 27.1 bits (60), Expect = 2.6
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKD 78
K+F+G + D L+ FE++G +V+ +KD
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD 35
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM1 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 87
Score = 27.3 bits (60), Expect = 2.9
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 157 KETGAKRGFAFIEF 170
++TG RGFAF+EF
Sbjct: 42 RKTGVSRGFAFVEF 55
>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 = 3.0
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 7/36 (19%)
Query: 142 FGQYGTIESVNMVTNKETGAKRGFAFIEFDDYDVVD 177
FG YG I+ + +ET KR FIEF YDV
Sbjct: 22 FGAYGEIKEI-----RETPNKRHHKFIEF--YDVRS 50
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 27.1 bits (61), Expect = 3.0
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVM-KDPVTK----RSRGFGFITYSESKMV 98
R+L++G L ++ L FF Q + +PV + F F+ E + V
Sbjct: 2 RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFV---EFRTV 58
Query: 99 DEA 101
+EA
Sbjct: 59 EEA 61
>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 = 27.0 bits (60), Expect = 3.0
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDD 172
D F +YG I +++ K G+AFIEF+D
Sbjct: 18 DLFYKYGPIVDIDL---KLPPRPPGYAFIEFED 47
>gnl|CDD|187728 cd08700, FMT_C_OzmH_like, C-terminal subdomain of the
Formyltransferase-like domain found in OzmH-like
proteins. Domain found in OzmH-like proteins with
similarity to the C-terminal domain of
Formyltransferase. OzmH is one of the proteins involved
in the synthesis of Oxazolomycin (OZM), which is a
hybrid peptide-polyketide antibiotic that exhibits
potent antitumor and antiviral activities. OzmH is a
multi-domain protein consisting of a formyl transferase
domain, a flavin-utilizing monoxygenase domain, a LuxE
domain functioning as an acyl protein synthetase and a
phosphopantetheine (PP)-binding domain, which may
function as an acyl carrier. It shows sequence
similarity with other peptide-polyketide biosynthesis
proteins.
Length = 100
Score = 27.6 bits (62), Expect = 3.2
Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 1/67 (1%)
Query: 178 KIVLDKVVVLEVDQEVINGEDHRTHGTHQEAKVDGVT-TTNQTHGTIREVVGMDNSKVVA 236
KI+L V+L EV+ GT DG T T + + +D + V
Sbjct: 34 KILLADRVLLVGKAEVLAVSSGGAPGTVLAVDADGWTVATGDGAVRLSGLTDLDGAAVDL 93
Query: 237 GEIKEVG 243
+ + G
Sbjct: 94 AALAQAG 100
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma
Protein (EWS). This subgroup corresponds to the RRM of
EWS, also termed Ewing sarcoma breakpoint region 1
protein, a member of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the FET
family, EWS contains an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U RNA.
It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor gene.
.
Length = 84
Score = 27.2 bits (60), Expect = 3.7
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 8/44 (18%)
Query: 137 EQMDYFGQYGTIE--------SVNMVTNKETGAKRGFAFIEFDD 172
E D+F G ++ VN+ T+KETG +G A + ++D
Sbjct: 16 ELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYED 59
>gnl|CDD|237341 PRK13302, PRK13302, putative L-aspartate dehydrogenase;
Provisional.
Length = 271
Score = 28.7 bits (64), Expect = 4.0
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 146 GTIESVNMVTNKETGAKRGFAFIEFDDYDV 175
GTI SV M+T K +G F+ ++ D+
Sbjct: 138 GTIHSVKMITRKPPDGLKGAPFLVTNNIDI 167
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 26.7 bits (59), Expect = 4.0
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 8/35 (22%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRG--FAFIEFDD 172
D F +YG I +++ +RG FAF+EF+D
Sbjct: 18 DLFYKYGAIRDIDLKN------RRGPPFAFVEFED 46
>gnl|CDD|226078 COG3548, COG3548, Predicted integral membrane protein [Function
unknown].
Length = 197
Score = 28.1 bits (63), Expect = 4.2
Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 9/67 (13%)
Query: 233 KVVAGEIKEVGVVSLVVDGVVAKVATVGV-------DKMLIQSFILLLSIRDLLSYFMCF 285
+ A G + D V A + T+ V +Q+ LLS L+ Y + F
Sbjct: 3 REDAEAAMGKGRLEAFTDAVFAIIMTIMVLEIKVPKGGGRLQALAELLS--SLIIYALSF 60
Query: 286 LLYLSYY 292
L+ ++
Sbjct: 61 LVVAIFW 67
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family may share similar expression
patterns and functions. CPEB-2 is an RNA-binding protein
that is abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation; it directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a Zn-finger motif.
In addition, they do have conserved nuclear export
signals that are not present in CPEB-1. .
Length = 92
Score = 27.0 bits (60), Expect = 4.3
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSR---GFGFITYSESKMVDE 100
RK+F+GGL ++D + A F ++G +V V +K G+ F+ + E V
Sbjct: 1 RKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQA 59
Query: 101 AMS 103
+
Sbjct: 60 LID 62
>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 = 26.6 bits (59), Expect = 4.4
Identities = 10/47 (21%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 44 RKLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFI 90
R ++IG L +++ L+ E++G I + ++K+ + F+
Sbjct: 4 RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFV 44
>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 = 26.5 bits (59), Expect = 5.0
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 46 LFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITYSES 95
L++G LD +D L F Q G I ++++ + + F+ Y +
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDH 47
>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 = 26.1 bits (57), Expect = 5.3
Identities = 10/34 (29%), Positives = 21/34 (61%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKD 78
KL +G + + L+A FE++G +++ ++KD
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD 35
>gnl|CDD|238130 cd00212, PTS_IIB_glc, PTS_IIB, PTS system, glucose/sucrose specific
IIB subunit. The bacterial phosphoenolpyruvate: sugar
phosphotransferase system (PTS) is a multi-protein
system involved in the regulation of a variety of
metabolic and transcriptional processes. This family is
one of four structurally and functionally distinct group
IIB PTS system cytoplasmic enzymes, necessary for the
uptake of carbohydrates across the cytoplasmic membrane
and their phosphorylation.
Length = 78
Score = 26.3 bits (59), Expect = 5.4
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 8/47 (17%)
Query: 205 HQEAKVD--------GVTTTNQTHGTIREVVGMDNSKVVAGEIKEVG 243
E+KVD GV + G + ++G + V IK +G
Sbjct: 32 KDESKVDEAALKKLGGVKGVVKNGGQYQVIIGPGVADVYKEAIKLLG 78
>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 = 26.4 bits (59), Expect = 5.5
Identities = 8/35 (22%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 140 DYFGQYGTIESVNMVTNKETGAKRGFAFIEFDDYD 174
++F ++GTI ++ + N E+ A ++F +
Sbjct: 21 EHFSKFGTIVNIQVNYNPES------ALVQFSTSE 49
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 26.1 bits (58), Expect = 6.5
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 46 LFIGGLDYRTNDDSLKAFF-EQWGEIVDVVVMKDPVTKRSRGFGFITYSE 94
LF+G L +D L FF +++ V+ D SRG+GF+ +S+
Sbjct: 4 LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSD 52
>gnl|CDD|236239 PRK08322, PRK08322, acetolactate synthase; Reviewed.
Length = 547
Score = 28.3 bits (64), Expect = 6.8
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 70 IVDVVVMKDPVTKRSR 85
IVDVV M P+TK +R
Sbjct: 111 IVDVVAMMAPLTKWTR 126
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 27.8 bits (61), Expect = 8.7
Identities = 29/112 (25%), Positives = 48/112 (42%), Gaps = 18/112 (16%)
Query: 88 GFITYSESKMVDEAMSNRPHEIDGRVVETKRAVPREVKVRRVTKVQIALEQMDY------ 141
G IT + SK VD E+ + + + R+V +TK +I+L+++D+
Sbjct: 247 GGITKTNSKKVDHKA-----ELSITKKDNQGMISRDVSEYMITKEEISLKELDFKLRKQL 301
Query: 142 ---FGQYGTIESVNMVTNKETGAKRGF----AFIEFDDYDVVDKIVLDKVVV 186
YG + S +V + G K F E DV+D +DK+ V
Sbjct: 302 IEKHNLYGNMGSGTIVIKMKNGGKYTFELHKKLQEHRMADVIDGTNIDKIEV 353
>gnl|CDD|176191 cd05289, MDR_like_2, alcohol dehydrogenase and quinone
reductase-like medium chain degydrogenases/reductases.
Members identified as zinc-dependent alcohol
dehydrogenases and quinone oxidoreductase. QOR
catalyzes the conversion of a quinone + NAD(P)H to a
hydroquinone + NAD(P)+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR
actin the respiratory chains of bacteria and
mitochondria, while soluble QOR acts to protect from
toxic quinones (e.g. DT-diaphorase) or as a soluble
eye-lens protein in some vertebrates (e.g.
zeta-crystalin). QOR reduces quinones through a
semi-quinone intermediate via a NAD(P)H-dependent
single electron transfer. QOR is a member of the medium
chain dehydrogenase/reductase family, but lacks the
zinc-binding sites of the prototypical alcohol
dehydrogenases of this group. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG
motif after the first mononucleotide contact half
allows the close contact of the coenzyme with the ADH
backbone. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. In human
ADH catalysis, the zinc ion helps coordinate the
alcohol, followed by deprotonation of a histidine, the
ribose of NAD, a serine, then the alcohol, which allows
the transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 309
Score = 27.5 bits (62), Expect = 9.5
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 1 MKGVMQYIFKLVPGLEVAGTVV 22
+K L+PG +VAG VV
Sbjct: 51 LKAAFPLTLPLIPGHDVAGVVV 72
>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 = 25.7 bits (57), Expect = 9.5
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 45 KLFIGGLDYRTNDDSLKAFFEQWGEIVDVVVMKDPVTKRSRGFGFITY 92
KL + LD+ +DD +K F ++G + V D + RS G + +
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVF 48
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
0.321 0.138 0.392
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: 15,594,640
Number of extensions: 1531660
Number of successful extensions: 2073
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2000
Number of HSP's successfully gapped: 471
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.4 bits)