RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10362
(388 letters)
>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 = 129 bits (326), Expect = 2e-37
Identities = 46/66 (69%), Positives = 53/66 (80%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+RYFS+YGEV+DCV+MK+ T RSRGFGFV F DPN VG V+ PHTLDGRTIDPKPC
Sbjct: 17 RRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHTLDGRTIDPKPCT 76
Query: 278 PRTLQK 283
PR +Q
Sbjct: 77 PRGMQP 82
Score = 35.6 bits (82), Expect = 0.005
Identities = 15/32 (46%), Positives = 24/32 (75%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGL T+ LR +F++YG+V++ VIM
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIM 32
>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 = 109 bits (275), Expect = 6e-30
Identities = 39/55 (70%), Positives = 46/55 (83%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YFS+YGEV+DCV+MK+ TGRSRGFGFVTFADP++V V+ PH LDGR IDPK
Sbjct: 18 YFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGREIDPK 72
Score = 42.2 bits (100), Expect = 1e-05
Identities = 15/34 (44%), Positives = 23/34 (67%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
F+GGL + TE LR +F++YG+V++ VIM
Sbjct: 2 FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPI 35
>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 = 91.3 bits (227), Expect = 4e-23
Identities = 32/55 (58%), Positives = 43/55 (78%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YFS++GE+ +C+VM++ T RSRGFGFVTF+DP +V V+ PH LDG+ IDPK
Sbjct: 18 YFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKIDPK 72
Score = 35.1 bits (81), Expect = 0.005
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVIM-SPRTIRA 330
F+GGL T LR +F+++G++ E ++M P T R+
Sbjct: 2 FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRS 39
>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 = 82.4 bits (204), Expect = 8e-20
Identities = 33/60 (55%), Positives = 42/60 (70%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
YFS++GE+ DCVVMK+ T RSRGFGFVTFA + V + PH +DGR ++PK PR
Sbjct: 19 YFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVDGREVEPKRAVPR 78
Score = 41.6 bits (98), Expect = 3e-05
Identities = 14/40 (35%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM-SPRTIRA 330
K+F+GGL T+ L+ +F+++G++ + V+M P T R+
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRS 40
>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 = 80.3 bits (198), Expect = 5e-19
Identities = 33/60 (55%), Positives = 43/60 (71%), Gaps = 1/60 (1%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
YF ++GEV DC VM+++ TGRSRGFGF+TF P +V V++ H LDG+ IDPK PR
Sbjct: 18 YFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKK-EHILDGKIIDPKRAIPR 76
Score = 34.5 bits (79), Expect = 0.011
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+F+GGL T+ LR +F ++G+V + +M
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVM 31
>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 = 76.8 bits (189), Expect = 9e-18
Identities = 31/55 (56%), Positives = 38/55 (69%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YFS++GEV+DC + + TGRSRGFGFV F D +V V+ H LDGR IDPK
Sbjct: 18 YFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQKEHKLDGRVIDPK 72
Score = 32.9 bits (75), Expect = 0.030
Identities = 21/63 (33%), Positives = 40/63 (63%), Gaps = 8/63 (12%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI-MSPRTIRA-GITRVPTQELPVQKEATAVQ 350
+F+GGL + T+ DL+ +F+++G+V++ I + P T R+ G V + K+A +V+
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFV------LFKDAASVE 54
Query: 351 QVL 353
+VL
Sbjct: 55 KVL 57
>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 = 75.0 bits (184), Expect = 5e-17
Identities = 29/55 (52%), Positives = 39/55 (70%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YF+++GEV DC + + TGRSRGFGF+ F D ++V V++ H LDGR IDPK
Sbjct: 19 YFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQKEHRLDGRLIDPK 73
Score = 35.7 bits (82), Expect = 0.004
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 8/64 (12%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI-MSPRTIRA-GITRVPTQELPVQKEATAV 349
K+F+GGL + ++ DL+ +F ++G+V + I M P T R+ G + + K+A++V
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFI------LFKDASSV 54
Query: 350 QQVL 353
++VL
Sbjct: 55 EKVL 58
>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 = 72.3 bits (177), Expect = 4e-16
Identities = 30/55 (54%), Positives = 38/55 (69%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
Y SR+GEV+DC + + TGRSRGFGFV F D +V V++ H LDG+ IDPK
Sbjct: 19 YLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPK 73
Score = 33.0 bits (75), Expect = 0.036
Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 8/64 (12%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS-PRTIRA-GITRVPTQELPVQKEATAV 349
K+F+GGL + ++ DL + +R+G+V++ I + P T R+ G V + K+A +V
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFV------LFKDAASV 54
Query: 350 QQVL 353
+VL
Sbjct: 55 DKVL 58
>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 = 72.0 bits (177), Expect = 4e-16
Identities = 26/60 (43%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
YFS +GE++ V K+ +TG+S+GFGFV FAD + V+ H +DGR D K N +
Sbjct: 19 YFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ-RHMIDGRWCDVKIPNSK 77
Score = 33.1 bits (76), Expect = 0.034
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 297 GLPSNVTETDLRTFFNRYGKVMEVVIM 323
GLP TE DL+ +F+ +G+++ V +
Sbjct: 6 GLPWKTTEQDLKDYFSTFGELLMVQVK 32
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 69.9 bits (172), Expect = 3e-15
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTID 272
+ FS++G+V ++++ ETG+S+GF FV F + ++ LDGR +
Sbjct: 17 RELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72
Score = 54.5 bits (132), Expect = 7e-10
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
+F+G LP + TE +LR F+++GKV V ++ +
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKE 36
>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 = 69.3 bits (169), Expect = 4e-15
Identities = 32/55 (58%), Positives = 42/55 (76%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YFS++GE+ +C+VM++ T RSRGFGFVTFADP +V V+ H LD +TIDPK
Sbjct: 19 YFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQPHHELDSKTIDPK 73
Score = 31.2 bits (70), Expect = 0.15
Identities = 14/40 (35%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM-SPRTIRA 330
K+F+GGL + LR +F+++G++ E ++M P T R+
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRS 40
>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 = 69.3 bits (169), Expect = 5e-15
Identities = 30/57 (52%), Positives = 39/57 (68%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+ YF ++GEV +C+VM++ T RSRGFGFVTF D V V+ H LD +TIDPK
Sbjct: 18 REYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK 74
Score = 34.6 bits (79), Expect = 0.010
Identities = 16/40 (40%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM-SPRTIRA 330
K+F+GGL T+ LR +F ++G+V E ++M P T R+
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRS 41
>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 = 68.7 bits (168), Expect = 9e-15
Identities = 25/58 (43%), Positives = 40/58 (68%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
+R+F+RYG++ +CVVM + T RSRGFGF+TF+ + ++ PH++DG I+ K
Sbjct: 20 RRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQPHSIDGNQIELKR 77
Score = 40.9 bits (96), Expect = 6e-05
Identities = 18/40 (45%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVME-VVIMSPRTIRA 330
K+F+GGL +++ LR F RYGK+ E VV++ P T R+
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRS 43
>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 = 68.2 bits (167), Expect = 1e-14
Identities = 24/56 (42%), Positives = 37/56 (66%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
YFS++G+V+D +M++++TGRSRGFGFVTF + V V L G+ ++ K
Sbjct: 19 YFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAGMLELGGKQVEVKR 74
Score = 45.4 bits (108), Expect = 1e-06
Identities = 14/32 (43%), Positives = 26/32 (81%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGLP +VTE + + +F+++GKV++ +M
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLM 32
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 68.1 bits (166), Expect = 1e-14
Identities = 28/55 (50%), Positives = 38/55 (69%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YFS++GEV+DC + + TGRSRGFGFV F + +V V+ H L+G+ IDPK
Sbjct: 18 YFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPK 72
Score = 33.0 bits (75), Expect = 0.032
Identities = 19/65 (29%), Positives = 40/65 (61%), Gaps = 8/65 (12%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI-MSPRTIRA-GITRVPTQELPVQKEATAVQ 350
+F+GGL + T+ DL+ +F+++G+V++ + + P T R+ G V + KE+ +V
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFV------LFKESESVD 54
Query: 351 QVLRR 355
+V+ +
Sbjct: 55 KVMDQ 59
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 22/55 (40%), Positives = 34/55 (61%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YFS+YG V ++ + ETG+ RGF FVTF D + V ++ HT++G ++ K
Sbjct: 19 YFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQKYHTINGHRVEVK 73
Score = 46.9 bits (112), Expect = 4e-07
Identities = 17/36 (47%), Positives = 26/36 (72%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
K+F+GGL +VTE DLR +F++YG V V I++ +
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKE 36
>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 = 67.0 bits (164), Expect = 3e-14
Identities = 21/33 (63%), Positives = 28/33 (84%)
Query: 291 PKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGLP NVTETDLR +F+++G V EVV+M
Sbjct: 3 KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVM 35
Score = 63.5 bits (155), Expect = 5e-13
Identities = 23/59 (38%), Positives = 37/59 (62%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNP 278
YFS++G V + VVM ++E R RGFGF+TF ++V V+ H ++G+ ++ K P
Sbjct: 22 YFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEHFHDINGKKVEVKRAEP 80
>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 = 66.7 bits (162), Expect = 5e-14
Identities = 28/66 (42%), Positives = 45/66 (68%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDG 268
++ T + + Y+ ++G++ DCVVM++ + RSRGFGFVTF+ N V + PHT+DG
Sbjct: 11 SFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAARPHTIDG 70
Query: 269 RTIDPK 274
R ++PK
Sbjct: 71 RVVEPK 76
Score = 35.1 bits (80), Expect = 0.006
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 290 FPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
F K+F+GGL TE LR ++ ++GK+ + V+M
Sbjct: 2 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVM 35
>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 = 66.1 bits (162), Expect = 6e-14
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI 271
+ FS++G V + ++MK+ ETG SRGFGFVTF + I++ L+GR I
Sbjct: 19 EALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVI 73
Score = 46.4 bits (111), Expect = 6e-07
Identities = 15/37 (40%), Positives = 25/37 (67%), Gaps = 1/37 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS-PRT 327
K+F+ GL + TE +L F+++G+V EV++M P T
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPET 39
>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 = 63.2 bits (153), Expect = 7e-13
Identities = 26/66 (39%), Positives = 42/66 (63%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDG 268
++ T + + +F ++G + DCVVM++ T RSRGFGFVT++ V + PH +DG
Sbjct: 11 SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNARPHKVDG 70
Query: 269 RTIDPK 274
R ++PK
Sbjct: 71 RVVEPK 76
Score = 32.0 bits (72), Expect = 0.078
Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM-SPRTIRA 330
K+F+GGL T+ LR+ F ++G + + V+M P T R+
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRS 43
>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 = 62.8 bits (152), Expect = 1e-12
Identities = 25/57 (43%), Positives = 39/57 (68%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+ +F ++G + DCVVM++ +T RSRGFGFVT++ V + PH +DGR ++PK
Sbjct: 20 REHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSARPHKVDGRVVEPK 76
Score = 33.5 bits (76), Expect = 0.023
Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM-SPRTIRA 330
K+F+GGL T+ LR F ++G + + V+M P+T R+
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRS 43
>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 = 62.2 bits (152), Expect = 1e-12
Identities = 21/52 (40%), Positives = 35/52 (67%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRT 270
+YFS++GE+ + VV+ + +TG+SRG+GFVTF D + ++ +DGR
Sbjct: 19 KYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPNPIIDGRK 70
Score = 36.1 bits (84), Expect = 0.003
Identities = 16/37 (43%), Positives = 27/37 (72%), Gaps = 1/37 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVME-VVIMSPRT 327
K+F+GGLP + T+ LR +F+++G++ E VVI +T
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQT 38
>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 = 60.3 bits (147), Expect = 6e-12
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
FS++G + ++ +ETGRS+GF FV F D + ++ L GR +
Sbjct: 17 DLFSKFGPIESIRIV-RDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
Score = 48.4 bits (116), Expect = 9e-08
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
+F+G LP + TE DL+ F+++G + + I+ T R
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGR 37
>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 = 59.3 bits (144), Expect = 1e-11
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LD 267
++ ++ + F ++G V+ V+ + ETGRSRGFG+V F P + I+ LD
Sbjct: 8 SWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELD 67
Query: 268 GRTI 271
GR I
Sbjct: 68 GRPI 71
>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 = 58.3 bits (141), Expect = 4e-11
Identities = 26/64 (40%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LD 267
++ T Q ++ FS+YG++ + VV+K+ ET RSRGFGFVTF +P++ + +D
Sbjct: 9 SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVD 68
Query: 268 GRTI 271
GR I
Sbjct: 69 GRQI 72
Score = 35.2 bits (81), Expect = 0.005
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K+F+GGL + E L F++YG++ EVV++ R
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR 36
>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 = 57.7 bits (140), Expect = 5e-11
Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
+ FS++GE+ ++++ G+S+GF FV F P + ++ LDGR +
Sbjct: 16 RELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEALNGKELDGRKL 69
Score = 52.3 bits (126), Expect = 4e-09
Identities = 13/37 (35%), Positives = 24/37 (64%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
+F+G LP + TE DLR F+++G++ V I+ + +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGK 37
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 61.5 bits (148), Expect = 1e-10
Identities = 26/123 (21%), Positives = 49/123 (39%), Gaps = 20/123 (16%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTIDPKPC 276
+ F ++G V ++++ ETG+SRGF FV F + I+ L+GR + +
Sbjct: 133 RELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKA 192
Query: 277 NPRTLQKPKKNSSFPKVF-------------------LGGLPSNVTETDLRTFFNRYGKV 317
P + + + +++ F +G LP E +L F G +
Sbjct: 193 QPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDI 252
Query: 318 MEV 320
+
Sbjct: 253 VRA 255
Score = 41.5 bits (96), Expect = 4e-04
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 283 KPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ K +F+G LP +VTE DLR F ++G V V ++
Sbjct: 108 RQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLV 148
>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 = 56.5 bits (137), Expect = 1e-10
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
F ++GEV V+ + ETGRSRGFGFV I+ GRT+
Sbjct: 19 LFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTL 71
Score = 40.3 bits (95), Expect = 9e-05
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRTIRA 330
+++G LP NVTE DL+ F ++G+V VI T R+
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRS 40
>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 = 55.8 bits (135), Expect = 3e-10
Identities = 20/55 (36%), Positives = 34/55 (61%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+ YFS++G+V C V + ETG S+G+GFV+F+ + + +Q H L+G +
Sbjct: 17 KEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQKHILEGNKLQ 71
Score = 33.4 bits (77), Expect = 0.020
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKV 317
K+F+G LP V +L+ +F+++GKV
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKV 26
>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 = 60.2 bits (146), Expect = 7e-10
Identities = 26/104 (25%), Positives = 48/104 (46%), Gaps = 2/104 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDG-RTIDPKPCNPR 279
FS++G ++ C V + E G+SRG+GFV F + IQ L + + +
Sbjct: 109 FSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK 167
Query: 280 TLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
++ F +++ L +V E LR F ++G++ +M
Sbjct: 168 HEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVM 211
Score = 50.6 bits (121), Expect = 7e-07
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
FS GE+ VM + E G SRGFGFV F++P + + GR + KP
Sbjct: 306 FSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVT----EMHGRMLGGKP 355
Score = 44.8 bits (106), Expect = 6e-05
Identities = 27/115 (23%), Positives = 30/115 (26%), Gaps = 11/115 (9%)
Query: 52 AMGPNMGMGTPSGPMAGMTPM---GPGNMMQGY-QGWGSTPQTQGFPGQWAPSSQTPMNG 107
+ MG+P G G P GP G GW P P NG
Sbjct: 380 PRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSM---MPTPMGPGGPLRPNG 436
Query: 108 YANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNN 162
A P + A Q PP Y PP PQS
Sbjct: 437 LA-PMNAVRAPSRNAQNAAQKPPMQPVMY--PPNYQSLPLSQDLP-QPQSTASQG 487
Score = 41.7 bits (98), Expect = 6e-04
Identities = 28/125 (22%), Positives = 49/125 (39%), Gaps = 27/125 (21%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID-------- 272
F+++GE+ VMK+ +GRSRGF FV F + ++G+ I
Sbjct: 199 FAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDA----AKAVEEMNGKKIGLAKEGKKL 253
Query: 273 ------PKPCNPRTL--------QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVM 318
+ L Q+ K + +++ L VT+ LR F+ G++
Sbjct: 254 YVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEIT 313
Query: 319 EVVIM 323
+M
Sbjct: 314 SAKVM 318
Score = 36.7 bits (85), Expect = 0.019
Identities = 21/123 (17%), Positives = 28/123 (22%), Gaps = 21/123 (17%)
Query: 17 LQQVEIKKAEPRDASNKGNDMGNNQWGPP--QSGGPMAMGP-------NMGMGTPSGPMA 67
LQ ++ G+ MG PP G M TP GP
Sbjct: 371 LQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGG 430
Query: 68 GMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQ 127
+ P G M + + PM P Y +
Sbjct: 431 PLRPNGLAPMNA---------VRAPSRNAQNAAQKPPMQPV---MYPPNYQSLPLSQDLP 478
Query: 128 APP 130
P
Sbjct: 479 QPQ 481
Score = 32.1 bits (73), Expect = 0.52
Identities = 18/82 (21%), Positives = 22/82 (26%), Gaps = 7/82 (8%)
Query: 124 PGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAG 183
G + G PP YG +G W P P P G
Sbjct: 383 RQLPMGSPMGGAMGQPPY------YGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRPNG 436
Query: 184 GAT-GAAPTGPNPSGPSAGKPP 204
A A + +A KPP
Sbjct: 437 LAPMNAVRAPSRNAQNAAQKPP 458
Score = 30.2 bits (68), Expect = 2.2
Identities = 23/100 (23%), Positives = 48/100 (48%), Gaps = 6/100 (6%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRT 280
F +G V+ V +++ T RS G+G+V F +P + ++ T++ + + KP
Sbjct: 21 FKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE----TMNFKRLGGKPIRIMW 76
Query: 281 LQK--PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVM 318
Q+ + S +F+ L +V L F+++G ++
Sbjct: 77 SQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNIL 116
>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 = 54.0 bits (130), Expect = 1e-09
Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 6/58 (10%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP---HTLDGRTIDPK 274
YFS++G+V D ++M + +T R RGFGFVTF + VV + C H ++ + ++ K
Sbjct: 19 YFSQFGKVEDAMLMFDKQTNRHRGFGFVTF---ESEDVVDKVCEIHFHEINNKMVECK 73
Score = 47.0 bits (112), Expect = 3e-07
Identities = 14/32 (43%), Positives = 26/32 (81%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGL +N TE D++ +F+++GKV + ++M
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLM 32
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 54.1 bits (131), Expect = 1e-09
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
+FS YG+V +++N + R RGF FV FA P + ++ LDGRT+
Sbjct: 17 EFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68
Score = 46.8 bits (112), Expect = 4e-07
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAG 331
+++ LP +VTE DLR FF+ YGKV V ++ + G
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRG 39
>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 = 53.3 bits (129), Expect = 2e-09
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F +YG++ VMK++E G+S+GFGFV F + ++ L+G+ ++ K
Sbjct: 22 FGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKAVEE----LNGKEVNGKK 71
Score = 36.4 bits (85), Expect = 0.002
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 290 FPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
F V++ L ++ + L+ F +YGK+ +M
Sbjct: 1 FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVM 34
>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 = 53.1 bits (127), Expect = 3e-09
Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 215 QYQQR-YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDP 273
+Y R YF +YG++ VM++ ++G+ RGF FVTF D + V ++ HT++G +
Sbjct: 14 EYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEV 73
Query: 274 KPCNPR 279
K +
Sbjct: 74 KKALSK 79
Score = 39.6 bits (92), Expect = 2e-04
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
K+F+GG+ + E LR +F +YGK+ + +M R
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQ 37
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 52.2 bits (126), Expect = 5e-09
Identities = 17/29 (58%), Positives = 21/29 (72%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
FSRYG + V+ + +TGRSRGFGFV F
Sbjct: 20 FSRYGPIEKVQVVYDQKTGRSRGFGFVYF 48
Score = 36.1 bits (84), Expect = 0.003
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
VF GL TE DLR F+RYG + +V +
Sbjct: 4 VF--GLSLYTTERDLREVFSRYGPIEKVQV 31
>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 = 51.8 bits (124), Expect = 9e-09
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
A+ + +FS + VV+ + ETG SRG+GFVTFA +
Sbjct: 8 AFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLED 53
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 50.7 bits (122), Expect = 2e-08
Identities = 19/43 (44%), Positives = 32/43 (74%), Gaps = 3/43 (6%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
++F+GG+P + TE +LR FF+R+G V +V I+ T RAG+++
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKII---TDRAGVSK 43
Score = 45.3 bits (108), Expect = 1e-06
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+FSR+G V D V + + G S+G+GFVTF + ++ G+ ++ P
Sbjct: 21 DFFSRFGSVKD-VKIITDRAGVSKGYGFVTFETQEDAEKILAMGNLNFRGKKLNIGPAI 78
>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 = 49.4 bits (119), Expect = 3e-08
Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI 271
+ FS +G V ++K GF FV F+ +Q GR +
Sbjct: 3 KLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPL 51
>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 = 50.0 bits (120), Expect = 3e-08
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+ F G + C ++++ TG+S G+GFV + D N+ I TL+G I K
Sbjct: 18 RSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN----TLNGFEIRNK 70
Score = 30.0 bits (68), Expect = 0.36
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 298 LPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
LP ++T+ +LR+ F G + I+ R
Sbjct: 8 LPQDMTQEELRSLFEAIGPIESCKIVRDR 36
>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 = 50.0 bits (119), Expect = 3e-08
Identities = 25/60 (41%), Positives = 38/60 (63%), Gaps = 6/60 (10%)
Query: 212 TYAQYQQRYFSRYG--EVIDCVVMKNNETGRSRGFGFVTFADPNNVG-VVIQNCPHTLDG 268
T + + YF +YG EVI+ +M + +G+ RGF FVTF D ++V +VIQ HT++G
Sbjct: 12 TEEHHLRDYFEQYGKIEVIE--IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY-HTVNG 68
Score = 40.4 bits (94), Expect = 8e-05
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K+F+GG+ + E LR +F +YGK+ + IM+ R
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR 36
>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 = 49.9 bits (120), Expect = 4e-08
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
+YFS++G V + ++ +TG+S+G+ FV F P
Sbjct: 18 KYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51
Score = 32.5 bits (75), Expect = 0.045
Identities = 12/36 (33%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
V++G LP E +LR +F+++G V + + S +T
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKT 37
>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 = 49.2 bits (117), Expect = 5e-08
Identities = 20/57 (35%), Positives = 35/57 (61%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
++YF ++G+V D ++M + T R RGFGFVTF + V V + H ++ + ++ K
Sbjct: 17 KQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECK 73
Score = 40.4 bits (94), Expect = 7e-05
Identities = 14/36 (38%), Positives = 25/36 (69%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
K+F+GGL N T D++ +F ++GKV + ++M +T
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKT 36
>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 = 53.7 bits (129), Expect = 7e-08
Identities = 30/113 (26%), Positives = 50/113 (44%), Gaps = 11/113 (9%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC--- 276
+FS+ G+V D +K+ + RS+G +V F D +V + L GR I +
Sbjct: 109 FFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAE 168
Query: 277 ------NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
N F K+++G L N+TE +LR F +G + +V +
Sbjct: 169 KNRAAKAATHQPGDIPN--FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLH 219
Score = 41.4 bits (97), Expect = 5e-04
Identities = 14/34 (41%), Positives = 24/34 (70%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
++ F +G++ D + ++ ETGRS+GFGF+ F D
Sbjct: 204 RQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHD 237
Score = 29.9 bits (67), Expect = 2.8
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
VF+ L E DL FF++ GKV +V + R R
Sbjct: 92 VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSR 128
>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 = 48.9 bits (116), Expect = 9e-08
Identities = 20/57 (35%), Positives = 36/57 (63%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
++YF ++G+V D ++M + T R RGFGFVTF + + V V + H ++ + ++ K
Sbjct: 21 KQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECK 77
Score = 42.0 bits (98), Expect = 3e-05
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
K+F+GGL +N D++ +F ++GKV + ++M +T
Sbjct: 5 KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKT 40
>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 = 48.4 bits (116), Expect = 1e-07
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
F +GE+ + + + ET RS+GF FV+F P +
Sbjct: 20 FEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEH 53
Score = 37.3 bits (87), Expect = 0.001
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
++F+ LP TE +LR F +G++ EV
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEV 29
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 48.4 bits (116), Expect = 2e-07
Identities = 19/52 (36%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQN-CPHTLDGRTI 271
FS+YGE++D ++++ +TG+S+GF F+ + D + + + N L GRTI
Sbjct: 30 FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTI 81
Score = 37.2 bits (87), Expect = 0.001
Identities = 12/35 (34%), Positives = 27/35 (77%), Gaps = 2/35 (5%)
Query: 286 KNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
K+S++ +++GGLP +TE D+ F++YG+++++
Sbjct: 7 KDSAY--IYIGGLPYELTEGDILCVFSQYGEIVDI 39
>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 = 48.1 bits (114), Expect = 2e-07
Identities = 19/57 (33%), Positives = 34/57 (59%)
Query: 212 TYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDG 268
T + + YF YG++ ++ + ++G+ RGFGFVTF D + V ++ HT++G
Sbjct: 12 TEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTING 68
Score = 35.1 bits (80), Expect = 0.007
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K+F+GG+ + E LR +F YGK+ + I++ R
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDR 36
>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 = 47.5 bits (114), Expect = 3e-07
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K+F+G LP TE D+R F YG + EV I+ +
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDK 35
Score = 45.2 bits (108), Expect = 1e-06
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
F YG + + ++++ +TG+S+G FV F+
Sbjct: 20 FEEYGNIEEVTIIRDKDTGQSKGCAFVKFSS 50
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 49.3 bits (117), Expect = 3e-07
Identities = 28/72 (38%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLD 267
++GT + F+ +G+V+D V+ + ETGRSRGFGFV F D I L+
Sbjct: 43 SWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN 102
Query: 268 GRTIDPKPCNPR 279
GR I P N R
Sbjct: 103 GRHIRVNPANDR 114
>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 = 47.3 bits (113), Expect = 3e-07
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 9/59 (15%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLD-----GRTI 271
+ FS+YG+V+ ++K+ ET +S+G F+ F D + C L+ GRT+
Sbjct: 19 HKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDA----HKCVKALNNKELFGRTL 73
Score = 39.6 bits (93), Expect = 2e-04
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
V++ LP ++T DL F++YGKV++V I+ + R
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETR 40
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 47.4 bits (113), Expect = 3e-07
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITRVPTQELPVQKEATAVQQ 351
++F+G LP ++TE +L+ FF +G V+EV I S R+P V + AVQ+
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGG----RLPNFGFVVFDDPEAVQK 60
Query: 352 VL 353
+L
Sbjct: 61 IL 62
Score = 40.8 bits (96), Expect = 6e-05
Identities = 15/44 (34%), Positives = 22/44 (50%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP 263
+F +G V++ + GR FGFV F DP V ++ N P
Sbjct: 23 FFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANKP 66
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 46.9 bits (112), Expect = 3e-07
Identities = 18/39 (46%), Positives = 28/39 (71%), Gaps = 2/39 (5%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRA 330
KVF+G L ++TE DLR +F+++G+V +V I P+ RA
Sbjct: 2 KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI--PKPFRA 38
Score = 46.1 bits (110), Expect = 6e-07
Identities = 17/34 (50%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPN 253
YFS++GEV D + K R F FVTFADP
Sbjct: 20 YFSQFGEVTDVYIPKP-----FRAFAFVTFADPE 48
>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 = 46.5 bits (111), Expect = 4e-07
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
R F +YGEV D + ++ T SRGF FV F D + + +DG+ +D
Sbjct: 17 RVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAM----DAMDGKELD 66
Score = 30.0 bits (68), Expect = 0.34
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 297 GLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
L T DLR F +YG+V +V I PR
Sbjct: 5 NLTYRTTPDDLRRVFEKYGEVGDVYI--PR 32
>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 = 46.1 bits (110), Expect = 8e-07
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
FS +G + VM + E GRS+GFGFV F+ P + ++GR I KP
Sbjct: 22 FSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVT----EMNGRIIGGKP 71
>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 = 45.7 bits (109), Expect = 8e-07
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
F +GE+ + ++ ETGRS+G+GF+ FAD
Sbjct: 19 FEPFGEIEFVQLQRDPETGRSKGYGFIQFADA 50
Score = 29.5 bits (67), Expect = 0.49
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
++G L N+TE DLR F +G++ V +
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEFVQLQ 31
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 45.9 bits (109), Expect = 8e-07
Identities = 17/54 (31%), Positives = 30/54 (55%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
F +G++ ++K+ TG S+GFG+V F P+ V ++NC + +PK
Sbjct: 21 FKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCDKSFKAVLAEPK 74
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 45.7 bits (109), Expect = 9e-07
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 9/71 (12%)
Query: 204 PADYSAYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP 263
P +++ Y F+ +G VI V + TG+S+ FGFV++ +P + I+
Sbjct: 7 PNEFTDQDLYQ-----LFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIK--- 58
Query: 264 HTLDGRTIDPK 274
++G + K
Sbjct: 59 -AMNGFQVGGK 68
>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 = 45.3 bits (108), Expect = 1e-06
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G LP T +LR F +YG V E ++
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVV 32
Score = 34.1 bits (79), Expect = 0.011
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 12/57 (21%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
F +YG V +C V+KN +GFV + + I+ L+G K N
Sbjct: 20 FEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKA----LNGYEFMGKRIN 64
>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 = 45.3 bits (108), Expect = 2e-06
Identities = 16/35 (45%), Positives = 25/35 (71%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPN 253
R FS+Y V+++ TG+S+G+GFV+F+DPN
Sbjct: 25 RAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN 59
Score = 27.6 bits (62), Expect = 3.3
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
++F+G L + VT+ L F++Y + V+ RT
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRT 44
>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 = 44.5 bits (106), Expect = 2e-06
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
F +G++ D + + ET + RGF FV F +P + I N + L GRTI
Sbjct: 19 FIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTI 70
Score = 30.3 bits (69), Expect = 0.27
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
+++GGL V E L F +G + ++ I
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQI 30
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 44.5 bits (106), Expect = 2e-06
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
+F GEV D VM+ + G+SR FGFV F
Sbjct: 20 HFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSE 51
Score = 34.1 bits (79), Expect = 0.014
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
++ + LP VTE LR F G+V +V +M RT R G +R
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVM--RT-RDGKSR 41
>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 = 44.5 bits (106), Expect = 3e-06
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFA 250
+ +FS G + C V+K+ + + RGFG+VTFA
Sbjct: 17 EEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFA 49
Score = 31.8 bits (73), Expect = 0.080
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
+F+ LP + T+ L FF+ G + +
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFV 31
>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 = 44.8 bits (106), Expect = 3e-06
Identities = 14/43 (32%), Positives = 28/43 (65%)
Query: 210 YGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
+G + ++YFS++G V + V ++ +TG S+ +GF+ F +P
Sbjct: 9 HGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNP 51
Score = 29.8 bits (67), Expect = 0.54
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEV 320
+++G LP E +L+ +F+++G V V
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNV 29
>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 = 44.9 bits (107), Expect = 3e-06
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDG 268
Y T +R F YG + ++++ +TG+ RG+ F+ F ++ + DG
Sbjct: 10 NYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA----DG 65
Query: 269 RTID 272
+ ID
Sbjct: 66 KKID 69
Score = 31.1 bits (71), Expect = 0.23
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 290 FPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
F +F+ L + TE+ LR F YG + + +
Sbjct: 1 FKTLFVARLNYDTTESKLRREFEEYGPIKRIRL 33
>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 = 44.2 bits (105), Expect = 3e-06
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+F GEV+D + ++++ GRS+GFG V FA ++ L GR I
Sbjct: 19 FFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKSGEELLGREI 69
Score = 38.1 bits (89), Expect = 5e-04
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
+F+G L + + DL FF G+V++V I
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQ 33
>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 = 44.1 bits (104), Expect = 4e-06
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITRVPTQEL 340
++F+G LP ++TE ++R F +YGK E+ I + G R+ T+ L
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGF--GFIRLETRTL 49
>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 = 43.8 bits (104), Expect = 4e-06
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
FS G V+ ++ + +TG+ +G+GF F D I+N L+G + +
Sbjct: 19 FSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN----LNGYEFNGRA 69
Score = 33.4 bits (77), Expect = 0.024
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
VF+G +P + TE L F+ G V+ +++ R
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDR 34
>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 = 44.0 bits (104), Expect = 5e-06
Identities = 18/43 (41%), Positives = 28/43 (65%), Gaps = 3/43 (6%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
++F+GG+ E DLR FF++YG V EV I+ RAG+++
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIV---NDRAGVSK 43
Score = 39.4 bits (92), Expect = 2e-04
Identities = 16/43 (37%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ 260
+++FS+YG V + V + N+ G S+G+GFVTF + ++Q
Sbjct: 20 RKFFSQYGTVKE-VKIVNDRAGVSKGYGFVTFETQEDAQKILQ 61
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 43.4 bits (103), Expect = 6e-06
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 13/55 (23%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI-------------MSPRTIRAGITR 334
V + LP + TE +R FF G++ EV I + A +T+
Sbjct: 3 VKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEALAALTK 57
>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 = 43.3 bits (102), Expect = 8e-06
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 6/59 (10%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP--CN 277
FS + D VM + ++GRSRG+GFV+F + +N + ++G+ + +P CN
Sbjct: 20 FSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDA----ENAINEMNGKWLGSRPIRCN 74
>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 = 43.1 bits (102), Expect = 8e-06
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
+V++G LP E D+ FF YG++ E+ +
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL 31
Score = 36.9 bits (86), Expect = 0.001
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 12/54 (22%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+R+F YG + + + +KN GFGFV F DP + + + L+G+ +
Sbjct: 17 ERFFKGYGRIRE-INLKN-------GFGFVEFEDPRDADDAV----YELNGKEL 58
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 47.7 bits (114), Expect = 8e-06
Identities = 34/152 (22%), Positives = 41/152 (26%), Gaps = 3/152 (1%)
Query: 85 GSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWG--SSYGAPPQQ 142
G P G G AP+S P A P+AP AP A S+ AP
Sbjct: 589 GPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVA 648
Query: 143 TGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNP-SGPSAG 201
+ S G+ W P P PA A A P P+A
Sbjct: 649 APEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAAT 708
Query: 202 KPPADYSAYGTYAQYQQRYFSRYGEVIDCVVM 233
P + S D V
Sbjct: 709 PPAGQADDPAAQPPQAAQGASAPSPAADDPVP 740
Score = 45.0 bits (107), Expect = 6e-05
Identities = 25/164 (15%), Positives = 32/164 (19%), Gaps = 11/164 (6%)
Query: 43 GPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQ 102
P +G A P P G G + G P +
Sbjct: 626 APAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAP 685
Query: 103 TPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNN 162
P A A P Q PPQ S +
Sbjct: 686 APAAPAAPAGAAPAQPAPAPAATP-PAGQADDPAAQPPQAAQGASAPSPAADDPV----- 739
Query: 163 WNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPAD 206
P P P + P+A PP+
Sbjct: 740 ----PLPPEPDDPPDPAGAPAQPPPPPAPAP-AAAPAAAPPPSP 778
Score = 38.4 bits (90), Expect = 0.006
Identities = 31/130 (23%), Positives = 35/130 (26%), Gaps = 8/130 (6%)
Query: 80 GYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAP---PGPQAPPQWGSSY 136
G G P A + P A P+A AP P P P S
Sbjct: 386 GVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPA 445
Query: 137 GAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPS 196
G P + + Q PT A PPA A AAP P
Sbjct: 446 GNAPAGGAPSPPPAAAPSAQPA-----PAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAP 500
Query: 197 GPSAGKPPAD 206
AG A
Sbjct: 501 AAPAGADDAA 510
Score = 38.0 bits (89), Expect = 0.008
Identities = 25/166 (15%), Positives = 29/166 (17%), Gaps = 21/166 (12%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQT 103
P P A G + P PG + S
Sbjct: 615 PAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGV--------AAPEHHPKHVAVPDASDGG 666
Query: 104 PMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNW 163
A APP AP + GA P Q
Sbjct: 667 DGWPAKAGGAA-----PAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQP 721
Query: 164 NWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
P P+ A P P P P
Sbjct: 722 --------PQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPP 759
Score = 38.0 bits (89), Expect = 0.009
Identities = 24/147 (16%), Positives = 35/147 (23%), Gaps = 1/147 (0%)
Query: 73 GPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQW 132
GP G +G + + P++ A P+ AP
Sbjct: 589 GPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGV- 647
Query: 133 GSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTG 192
+ P + G P G P P PAA A AP
Sbjct: 648 AAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAA 707
Query: 193 PNPSGPSAGKPPADYSAYGTYAQYQQR 219
P+G + A +
Sbjct: 708 TPPAGQADDPAAQPPQAAQGASAPSPA 734
Score = 35.0 bits (81), Expect = 0.082
Identities = 22/125 (17%), Positives = 31/125 (24%), Gaps = 8/125 (6%)
Query: 98 APSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWG--------SSYGAPPQQTGYGSYG 149
+ + G A A + A P P + AP
Sbjct: 380 RLERRLGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAP 439
Query: 150 PTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
+ P P+ A P A AAP P+ P+ PA +A
Sbjct: 440 APPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAA 499
Query: 210 YGTYA 214
A
Sbjct: 500 PAAPA 504
Score = 33.8 bits (78), Expect = 0.17
Identities = 27/117 (23%), Positives = 33/117 (28%), Gaps = 8/117 (6%)
Query: 85 GSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTG 144
+ P P AP++ A P APP P G + PP
Sbjct: 403 AAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAP 462
Query: 145 YGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAG 201
P A P PAA P A A AAP P + +A
Sbjct: 463 SAQPAPAPAAAPEP--------TAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAAT 511
Score = 32.7 bits (75), Expect = 0.36
Identities = 27/172 (15%), Positives = 32/172 (18%), Gaps = 33/172 (19%)
Query: 41 QWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPS 100
P S G G P+ P P P Q P A
Sbjct: 657 VAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAP-------AAPAGAAPAQPAPAPAAT- 708
Query: 101 SQTPMNGYANPSAPQGYTNWGAPPGP---QAPPQWGSSYGAPPQQTGYGSYGPTSGAPQS 157
P A Q PP + P + P P
Sbjct: 709 ----------PPAGQADDPAAQPPQAAQGASAPSPAADDPVPLP-----------PEPDD 747
Query: 158 GYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
P P PA PA + P+ D
Sbjct: 748 PPDPAGAPAQPP-PPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDR 798
>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 = 43.0 bits (102), Expect = 9e-06
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
+++G L VTE L F R+G + V IM PRT
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRT 38
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 42.7 bits (101), Expect = 1e-05
Identities = 14/30 (46%), Positives = 24/30 (80%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFA 250
F+ +GE+ D V+K+ +TG+S+G+GFV+F
Sbjct: 20 FAPFGEISDARVVKDMQTGKSKGYGFVSFV 49
Score = 29.6 bits (67), Expect = 0.44
Identities = 7/31 (22%), Positives = 16/31 (51%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+F+G L + LR F +G++ + ++
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVV 32
>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 = 42.5 bits (101), Expect = 1e-05
Identities = 14/35 (40%), Positives = 20/35 (57%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
+ F +G + + K+ ETG+SRGF FVTF
Sbjct: 17 RELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTR 51
Score = 29.4 bits (67), Expect = 0.55
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 298 LPSNVTETDLRTFFNRYGKVMEV 320
L + E DLR F +G + V
Sbjct: 7 LSEDADEDDLRELFRPFGPISRV 29
>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 = 11/32 (34%), Positives = 20/32 (62%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
FSR+G++ C V+++ +TG S + F+ F
Sbjct: 24 FSRFGKIKSCEVIRDKKTGDSLQYAFIEFETK 55
>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 = 41.8 bits (98), Expect = 2e-05
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G LP TE ++R+ F +YGKV+E I+
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDII 33
Score = 32.9 bits (75), Expect = 0.031
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 9/53 (16%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPH-TLDGRTID 272
F +YG+V++C ++KN +GFV D I+N H L G I+
Sbjct: 21 FEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRNLHHYKLHGVAIN 65
>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 = 41.8 bits (99), Expect = 3e-05
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 229 DCVVMKNNETGRSRGFGFVTFADPNNVGVV---IQNCPHT-LDGRTI 271
D ++++ TG SRGF FV F + + N +DGR +
Sbjct: 33 DVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVV 79
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 80
Score = 41.5 bits (98), Expect = 3e-05
Identities = 8/34 (23%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
FSR+G++++ ++K + F F+ F
Sbjct: 21 NERFSRHGKILEVNLIKRANHTNA--FAFIKFER 52
Score = 40.8 bits (96), Expect = 5e-05
Identities = 12/32 (37%), Positives = 23/32 (71%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
+F+G L +VT+ +L F+R+GK++EV ++
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIK 37
>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 = 41.5 bits (98), Expect = 3e-05
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 215 QYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
Y F+ GEV +++N +TG+S G+GFV FA
Sbjct: 14 AYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFAT 50
>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 = 41.7 bits (98), Expect = 3e-05
Identities = 17/35 (48%), Positives = 26/35 (74%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
VF+GG+ + ET++R+FF +YG V EV I++ RT
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRT 42
Score = 34.0 bits (78), Expect = 0.016
Identities = 15/42 (35%), Positives = 29/42 (69%), Gaps = 1/42 (2%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQN 261
+F++YG V + V + + TG S+G+GFV+F D +V ++++
Sbjct: 25 FFAKYGSVKE-VKIITDRTGVSKGYGFVSFYDDVDVQKIVES 65
>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 = 41.1 bits (97), Expect = 4e-05
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI 271
++ FS +G V + V + G+ +GF FV F + I+ + GR +
Sbjct: 17 KKLFSPFGFVWE-VTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPV 70
Score = 36.1 bits (84), Expect = 0.003
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 298 LPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
LP TE DL+ F+ +G V EV I PR
Sbjct: 7 LPFKCTEADLKKLFSPFGFVWEVTI--PR 33
>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 = 40.9 bits (96), Expect = 5e-05
Identities = 16/35 (45%), Positives = 24/35 (68%), Gaps = 2/35 (5%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
F ++G ++D V + NE G S+GFGFVTFA+ +
Sbjct: 20 MFGQFGPILD-VEIIFNERG-SKGFGFVTFANSAD 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 = 40.7 bits (96), Expect = 5e-05
Identities = 12/31 (38%), Positives = 24/31 (77%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
++F+G LP+++TE + + F++YG+V EV +
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFL 33
Score = 28.8 bits (65), Expect = 0.85
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 6/29 (20%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFV 247
FS+YGEV + + K +GFGF+
Sbjct: 20 ELFSKYGEVSEVFLNKE------KGFGFI 42
>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 = 40.3 bits (95), Expect = 7e-05
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEV 320
V++G LP +TE +L+ F+ +G + EV
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEV 30
>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 = 44.2 bits (104), Expect = 8e-05
Identities = 27/109 (24%), Positives = 56/109 (51%), Gaps = 14/109 (12%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDG-----RTIDPKP 275
F+ GE+ C ++++ TG+S G+GFV + P + + ++L+G +TI
Sbjct: 24 FTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAV----NSLNGLRLQNKTIKVSY 79
Query: 276 CNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
P + N +++ GLP +T+ +L + F+ +G+++ I+S
Sbjct: 80 ARPSSDSIKGAN-----LYVSGLPKTMTQHELESIFSPFGQIITSRILS 123
Score = 32.6 bits (74), Expect = 0.28
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRT 280
FS +G++I ++ +N TG S+G GF+ F + I+ TL+G T P C
Sbjct: 110 FSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIK----TLNGTT--PSGCTEPI 163
Query: 281 LQKPKKN--SSFPKVFLGGLPS 300
K N SS K L L +
Sbjct: 164 TVKFANNPSSSNSKGLLSQLEA 185
Score = 29.1 bits (65), Expect = 3.7
Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 8/111 (7%)
Query: 169 QNGPTTPAAGGPPAGGATGAAPTGPNPSGPS-AGKPPADYSAY------GTYAQYQQRYF 221
Q A T +G A A Y + T + F
Sbjct: 231 QQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLF 290
Query: 222 SRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
+G V + ++++ T + +G+GFV+ + + + I + +TL R +
Sbjct: 291 GPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVL 341
>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 = 40.7 bits (95), Expect = 8e-05
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNV--GVVIQNCPHTLDGRTIDPKPCN 277
+FS++G V V+ + +TG+ RGFGFV F + ++ V++ H ++G ++ K
Sbjct: 19 HFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKF--HPINGHRVEVKKAV 76
Query: 278 PR 279
P+
Sbjct: 77 PK 78
Score = 35.3 bits (81), Expect = 0.005
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K+F+GGL +V E DL F+++G V + +++ +
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADK 35
>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 = 40.0 bits (94), Expect = 9e-05
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
K+F+GGL TE +R +F ++G ++E+
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEI 29
Score = 38.9 bits (91), Expect = 2e-04
Identities = 14/55 (25%), Positives = 31/55 (56%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YF ++G +++ + + +T + RGF F+TF V +++ H + G+ ++ K
Sbjct: 19 YFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQFHVIGGKKVEVK 73
>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 = 39.9 bits (93), Expect = 1e-04
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITRVPTQEL 340
++F+G LP+++TE D + F +YG+ EV I R G R+ ++ L
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGF--GFIRLESRTL 49
>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 = 39.7 bits (93), Expect = 1e-04
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 212 TYAQYQQR-YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRT 270
Q + R FS GE+ C ++++ TG+S G+GFV + DP + I TL+G
Sbjct: 12 NMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN----TLNGLR 67
Query: 271 IDPK 274
+ K
Sbjct: 68 LQNK 71
>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 = 39.7 bits (93), Expect = 1e-04
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
F+G L +TE +LR F RYG V +V I P
Sbjct: 6 FVGNLEITITEEELRRAFERYGVVEDVDIKRPP 38
Score = 28.9 bits (65), Expect = 0.93
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
R F RYG V D + K G+ + FV F +
Sbjct: 21 RAFERYGVVEDVDI-KRPPRGQGNAYAFVKFLN 52
>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 = 39.9 bits (94), Expect = 2e-04
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPH-TLDGRTI 271
FSRYG++ ++++ TG S+G+ FV + + ++ +DG I
Sbjct: 24 FSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSEI 75
Score = 31.1 bits (71), Expect = 0.23
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKV 317
+F+G L TE LR F+RYG +
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDI 30
>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 = 39.5 bits (93), Expect = 2e-04
Identities = 15/30 (50%), Positives = 22/30 (73%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
+F+GGL +VTE+DL F+R+G V +V I
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEI 31
Score = 32.1 bits (74), Expect = 0.070
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 212 TYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
T + ++R FSR+G V D ++K + G RGF ++
Sbjct: 12 TESDLEER-FSRFGTVSDVEIIKKKDAGPDRGFAYIDL 48
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 221 FSRYGEVIDCVVMKNNETGRSR---GFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
FS++GEV + K + + R GF FVTF D ++ +Q L GR I
Sbjct: 21 FSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQLNGTELGGRKIS 75
Score = 33.0 bits (76), Expect = 0.038
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
++++ L + E DLR F+++G+V + I
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRI 32
>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 = 39.0 bits (92), Expect = 2e-04
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
FS++G V+D V K + RG FV F D
Sbjct: 23 LFSQFGPVLDIVASKTL---KMRGQAFVVFKD 51
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
VF+GGL VTE +LR+ F +G+++ V I
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKI 33
>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 = 38.6 bits (90), Expect = 3e-04
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G + + ++ +LR F YG V+ +M
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM 33
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 42.8 bits (101), Expect = 3e-04
Identities = 28/166 (16%), Positives = 30/166 (18%), Gaps = 14/166 (8%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQT 103
PQ P GM P G Q Q APS
Sbjct: 169 APQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQ-GHPEQVQPQQFLPAPSQAP 227
Query: 104 PMNGY---------ANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGS-YGPTSG 153
+ PP P PPQ PPQ +
Sbjct: 228 AQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQ---QPPQPQAQPPPQNQPTP 284
Query: 154 APQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPS 199
P G N PQ P P
Sbjct: 285 HPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQLSQQ 330
Score = 32.0 bits (73), Expect = 0.67
Identities = 20/87 (22%), Positives = 23/87 (26%), Gaps = 3/87 (3%)
Query: 121 GAPPGPQAPPQWGSSYGAPPQQTGYGSYGP---TSGAPQSGYGNNWNWNMPQNGPTTPAA 177
P PPQ G PP+Q + GP G PQ G+ Q P A
Sbjct: 167 QQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQA 226
Query: 178 GGPPAGGATGAAPTGPNPSGPSAGKPP 204
P P G
Sbjct: 227 PAQPPLPPQLPQQPPPLQQPQFPGLSQ 253
>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 = 38.9 bits (91), Expect = 3e-04
Identities = 14/45 (31%), Positives = 27/45 (60%)
Query: 210 YGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
Y ++ FS++GE+ + V + ++G+S+GF +V F DP +
Sbjct: 12 YSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPED 56
Score = 32.4 bits (74), Expect = 0.064
Identities = 11/37 (29%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
++F+ LP + E DL F+++G++ EV V + ++
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKS 40
>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 = 38.9 bits (91), Expect = 3e-04
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
VF+ G +E L +F+ +G VM V++ +
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDK 38
Score = 36.2 bits (84), Expect = 0.002
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRG-FGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
YFS +G V++ ++ K+ +G + V F V V+ HTL+G + +P
Sbjct: 22 YFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDKVLSEPQHTLNGHRLRVRP 72
>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 = 38.7 bits (91), Expect = 3e-04
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
FS YG V D + + E RG+ +V F P + I+ H +DG ID
Sbjct: 19 FSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK---H-MDGGQID 66
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 38.8 bits (91), Expect = 3e-04
Identities = 16/30 (53%), Positives = 20/30 (66%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
V+L GL +VTE L F+RYG V+ VVI
Sbjct: 10 VWLDGLDESVTEQYLTRHFSRYGPVVHVVI 39
Score = 31.1 bits (71), Expect = 0.15
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 215 QYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
QY R+FSRYG V+ V+ R RG V F
Sbjct: 22 QYLTRHFSRYGPVVHVVI------DRQRGQALVFFDK 52
>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 = 39.6 bits (92), Expect = 3e-04
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYG 315
KVF+GGLP ++TE D+ F R+G
Sbjct: 2 KVFVGGLPWDITEADILNSFRRFG 25
>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 = 38.7 bits (91), Expect = 4e-04
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 14/63 (22%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC----------PHTLDGR 269
FS++GEV ++K+ TG S+G FV F Q C +LDGR
Sbjct: 20 LFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKE----SAQKCLEAADNAEDSGLSLDGR 75
Query: 270 TID 272
+
Sbjct: 76 RLI 78
Score = 30.6 bits (70), Expect = 0.21
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKV 317
VF+ LP + TE +L+ F+++G+V
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEV 27
>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 = 41.9 bits (98), Expect = 4e-04
Identities = 53/226 (23%), Positives = 88/226 (38%), Gaps = 22/226 (9%)
Query: 108 YANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGY------GN 161
Y + G WG + P S Y PQ T + SY T + GY G
Sbjct: 13 YGYNNKSSGGRMWGMS---HSLPSGMSRYAFSPQDTDFSSYPSTGRQHRQGYNDFYGNGG 69
Query: 162 NWNWNMPQNGPTTPAAGGPP--AGGATGAAPTGPNPSGPS--AGKPPADYSAYGTYAQYQ 217
+ + G A + G+ G+ N SG + P D + YA
Sbjct: 70 SSACGLGSMGNMANMASTNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYA--- 126
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
F G + C +M++ +TG S G+ FV F + I+N L+G T+ K
Sbjct: 127 --LFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN----LNGITVRNKRLK 180
Query: 278 PRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ ++ +++ LP +T+ L T F +YG++++ I+
Sbjct: 181 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNIL 226
>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 = 38.4 bits (90), Expect = 4e-04
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 212 TYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNV--------GVVIQNCP 263
T Q+ + +RY V V+ + TGRS+G+GFV F D + GV + P
Sbjct: 14 TDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRP 73
Query: 264 HTL 266
+
Sbjct: 74 MRV 76
Score = 29.6 bits (67), Expect = 0.60
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 293 VFLGGLPSNVTETDLRTFF-NRYGKVMEV-VIMSPRT 327
+F+G L +VT+ L+ F RY V V+M P T
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVT 40
>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 = 38.4 bits (90), Expect = 4e-04
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
FS YG +I ++ +N TG SRG GF+ F
Sbjct: 21 FSPYGRIITSRILCDNVTGLSRGVGFIRF 49
Score = 27.3 bits (61), Expect = 3.5
Identities = 8/25 (32%), Positives = 17/25 (68%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKV 317
+++ GLP +T+ +L F+ YG++
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRI 27
>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 = 38.4 bits (89), Expect = 5e-04
Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
FSRYG + V+ + TGRSRGF FV F ++ +++ LDGR I
Sbjct: 20 FSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71
Score = 29.5 bits (66), Expect = 0.59
Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 297 GLPSNVTETDLRTFFNRYGKVMEV-VIMSPRTIRA-GITRVPTQELPVQKEA 346
GL TE DLR F+RYG + V V+ RT R+ G V + + KEA
Sbjct: 6 GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEA 57
>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 = 38.4 bits (89), Expect = 5e-04
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 278 PRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSP 325
P Q+ +N +F+G L NV+E +LR F++YG + EVVI P
Sbjct: 1 PEDDQRATRN-----LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRP 43
>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 = 37.6 bits (87), Expect = 6e-04
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
+V++G L +V E D++ FF YGK++E+
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEI 29
>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 = 37.9 bits (88), Expect = 6e-04
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPH--TLDG 268
F+ +G + +C V+++ G+SRG FVTFA I+ H T++G
Sbjct: 22 FAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQCALNAIKAMHHSQTMEG 70
Score = 28.6 bits (64), Expect = 1.2
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G L E D+R F +G + E ++
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVL 34
>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 = 37.6 bits (88), Expect = 7e-04
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ--NCPHTLDGRTID 272
F G V+ V +N+ GRS+GFG V F P + I+ N + L+GR ++
Sbjct: 19 FRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMFN-GYDLEGRELE 70
Score = 28.8 bits (65), Expect = 0.89
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRA---GITRVPTQE 339
+F+ LP +VT DL+ F G V+ + + R+ G + E
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPE 50
>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 = 37.6 bits (87), Expect = 7e-04
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K+F+G +P +TE ++R F +G V+EV I+ +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDK 35
Score = 29.5 bits (66), Expect = 0.59
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFA 250
F +G V++ ++K+ TG +G FV ++
Sbjct: 19 MFEEHGNVLEVAIIKDKRTGHQQGCCFVKYS 49
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 38.0 bits (89), Expect = 8e-04
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 10/68 (14%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITRVPTQELPVQKEATAVQQV 352
VF+G LP + DL+ F ++G + V S VP +E + K+ A+++
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRS----------VPVKEKKLPKKVAAIKKK 52
Query: 353 LRRSSTTK 360
Sbjct: 53 FHDKKDNV 60
>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 = 37.7 bits (88), Expect = 8e-04
Identities = 10/31 (32%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 221 FSRYGEVID-CVVMKNNETGRSRGFGFVTFA 250
FS +G ++ +M++ +TG S+GF F+++
Sbjct: 22 FSAFGVILQTPKIMRDPDTGNSKGFAFISYD 52
>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 = 37.4 bits (87), Expect = 0.001
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTI 328
V++G LP + +E +LR ++G + ++ I+ + I
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNI 41
>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 = 37.3 bits (87), Expect = 0.001
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
S +G V C ++ + TG S+G+GFV +A
Sbjct: 20 VSPFGAVERCFLVYSESTGESKGYGFVEYASK 51
>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 = 37.4 bits (87), Expect = 0.001
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 226 EVIDCVVMKNNETGRSRGFGFVTFA 250
E D +M+ TG SRGF FV F
Sbjct: 29 EPKDVRLMRRKTTGASRGFAFVEFM 53
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 37.1 bits (86), Expect = 0.001
Identities = 12/35 (34%), Positives = 24/35 (68%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
++++G LPS+V E DL F +YG++ ++ + + R
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRR 35
>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 = 37.2 bits (87), Expect = 0.001
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
F +G++ C + + ETG+ +G+GF+ + +P
Sbjct: 21 FEAFGKIKSCSLAPDPETGKHKGYGFIEYENP 52
Score = 29.2 bits (66), Expect = 0.84
Identities = 5/33 (15%), Positives = 19/33 (57%)
Query: 291 PKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
++++ + +++E D+++ F +GK+ +
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLA 33
>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 = 37.0 bits (86), Expect = 0.001
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC 276
F YGE+ + + ++GR +GFG+V F+ Q L G + +P
Sbjct: 16 YEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQE----AAQAALDALGGTDLLGRPV 70
Score = 30.8 bits (70), Expect = 0.19
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRTIR 329
+F+G L + E + F YG++ V + P + R
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGR 38
>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 = 37.2 bits (86), Expect = 0.001
Identities = 18/33 (54%), Positives = 22/33 (66%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSP 325
+FLG L VTETDLR F+R+G + EV I P
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIKRP 42
>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 = 36.9 bits (85), Expect = 0.001
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 16/62 (25%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+R+F YG + D + +K RGFGFV F DP + + + LDG+ + CN
Sbjct: 17 ERFFKGYGRIRD-IDLK-------RGFGFVEFDDPRDA----DDAVYELDGKEL----CN 60
Query: 278 PR 279
R
Sbjct: 61 ER 62
>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 = 36.9 bits (86), Expect = 0.001
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
A T A+ ++ + GE+ D +++ E G+SR F+ +
Sbjct: 10 ASLTEAELKEHFSKHGGEITDVKLLRT-EDGKSRRIAFIGYKT 51
>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 = 36.6 bits (85), Expect = 0.001
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
FS+YG+V+ ++ N + +R FGFVT A IQ+ T L GR I
Sbjct: 20 FSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVI 71
Score = 34.2 bits (79), Expect = 0.010
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 296 GGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
GL S DL+ F++YGKV+ ++ + R+
Sbjct: 5 SGLSSTTKAADLKQLFSKYGKVVGAKIVTNARS 37
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 36.8 bits (86), Expect = 0.001
Identities = 13/54 (24%), Positives = 25/54 (46%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+ +FS D + + ++ GR G +V FA P + ++ + + GR I
Sbjct: 17 RDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNKMGGRYI 70
Score = 31.8 bits (73), Expect = 0.082
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYG 315
V L GLP + TE D+R FF+
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLD 24
>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 = 36.8 bits (86), Expect = 0.002
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
FS +G ++ C V + E G S+G+GFV F
Sbjct: 23 FSAFGNILSCKVATD-ENGGSKGYGFVHFETE 53
>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 = 37.0 bits (85), Expect = 0.002
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
F GE+ C ++++ TG+S G+GFV + DPN+ I +TL+G + K
Sbjct: 24 FGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI----NTLNGLKLQTK 73
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 75
Score = 36.7 bits (85), Expect = 0.002
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAG 331
+++G LP NV E + F RYG+V V I+ R G
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGG 40
>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 = 36.6 bits (85), Expect = 0.002
Identities = 14/42 (33%), Positives = 26/42 (61%)
Query: 286 KNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
K+ K+F+G +P N+ E DLR F ++GK+ E+ ++ +
Sbjct: 1 KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKY 42
Score = 30.1 bits (68), Expect = 0.42
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPH---TLDG--RTIDPKP 275
F ++G++ + V+K+ TG +G F+T+ + + Q+ H TL G R I KP
Sbjct: 26 FEQFGKIYELTVLKDKYTGMHKGCAFLTYCARES-ALKAQSALHEQKTLPGMNRPIQVKP 84
Query: 276 CNP 278
+
Sbjct: 85 ADS 87
>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 = 36.4 bits (85), Expect = 0.002
Identities = 12/36 (33%), Positives = 23/36 (63%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNV 255
+FS+ G+V D ++++ + RS+G +V F D +V
Sbjct: 19 FFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54
Score = 31.0 bits (71), Expect = 0.14
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRTIRA-GITRV 335
VF+ L V E DL FF++ GKV +V +I + R+ G+ V
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYV 46
>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 = 36.2 bits (84), Expect = 0.002
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
++++G LP ++ E D+ F +YG + + + + R
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRR 35
>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 = 36.0 bits (83), Expect = 0.002
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVME 319
K+F+G + + T +LR F +G+V+E
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVE 29
>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 617
Score = 39.8 bits (93), Expect = 0.002
Identities = 35/183 (19%), Positives = 44/183 (24%), Gaps = 39/183 (21%)
Query: 55 PNMGMGTPSGPMAGMT--PMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPS 112
P+ G P P A T P P + Y+G+G PG Q P A P+
Sbjct: 90 PSAGEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPG-LPRQDQLPT---ARPA 145
Query: 113 APQGYTN-----WGAPP---GPQAPP--------------------QWGSSYGAPPQQTG 144
P W G Q + Y A +
Sbjct: 146 YPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERDREPYDAGRPEYD 205
Query: 145 YGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPP--AGGATGAAPTGPNPSGPSAGK 202
P + P+ P AG G P PSA
Sbjct: 206 QRRRDYDHPRPDWDRPRRDRTDRPE---PPPGAGHVHRGGPGPPERDDAPVVPIRPSAPG 262
Query: 203 PPA 205
P A
Sbjct: 263 PLA 265
Score = 28.6 bits (64), Expect = 7.4
Identities = 25/105 (23%), Positives = 33/105 (31%), Gaps = 2/105 (1%)
Query: 122 APPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPP 181
P P + P + Y YG + G +P P PA P
Sbjct: 95 PAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDR-PPGLPRQDQLPTARPAYPAYQQRP 153
Query: 182 AGGATGAAPTGPNPSGPSAGKPP-ADYSAYGTYAQYQQRYFSRYG 225
GA A G PP A Y++ +YA Q+R Y
Sbjct: 154 EPGAWPRAADDYGWQQQRLGFPPRAPYASPASYAPEQERDREPYD 198
>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 = 36.1 bits (84), Expect = 0.002
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 226 EVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC 276
+V ++ G+S+GF +V FA V + L+GR + K C
Sbjct: 26 DVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEK----LEGREFNGKKC 72
>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 = 36.4 bits (85), Expect = 0.003
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGR-----SRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
+++F + G V + K + S G+GFV F ++ T LDG +
Sbjct: 18 KKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLDGHAL 77
Query: 272 D 272
+
Sbjct: 78 E 78
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 39.7 bits (92), Expect = 0.003
Identities = 56/245 (22%), Positives = 79/245 (32%), Gaps = 24/245 (9%)
Query: 19 QVEIKKAEPRDAS--NKGNDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGN 76
Q ++ + P D + ++GN+ +G G P A G P + G N
Sbjct: 314 QGDLVRGAPNDKNSFDRGNEKTYQIYGGFHDGSPNAASA----GAPFNGLGNQADGGHIN 369
Query: 77 MMQ--GYQGWGSTPQTQGFPGQWAPSSQTPMN-GYANPS-APQGYTNWG-APPGPQAPPQ 131
+ W P + A S+ N +N + GY+N G + PG P
Sbjct: 370 QVHPDARGAWAGGPHSNASYNCAAYSNAAQSNAAQSNAGFSNAGYSNPGNSNPGYNNAPN 429
Query: 132 WGSSYGAPPQQTGYGSYGPTSGAPQSG--YGNNWNWNMP-QNGPTTPAAGGPPAGGATGA 188
+ Y PP S P S P S Y N N P N P + A A A
Sbjct: 430 SNTPYNNPPNSNTPYSNPPNSNPPYSNLPYSNTPYSNAPLSNAPPSSAKDHH---SAYHA 486
Query: 189 APTGPNPSGPSAGKPPADYSAYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVT 248
A + P+A P A+ A + G + G T
Sbjct: 487 AYQHRAANQPAANLPTANQPA-------ANNFHGAAGNSVGNPFASRPFGSAPYGGNAAT 539
Query: 249 FADPN 253
ADPN
Sbjct: 540 TADPN 544
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 36.1 bits (84), Expect = 0.003
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
+ FS +G+V + K + G RGF FV F ++ T L GR +
Sbjct: 18 RELFSPFGQVKSVRLPKKFD-GSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHL 71
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 39.9 bits (93), Expect = 0.003
Identities = 39/167 (23%), Positives = 49/167 (29%), Gaps = 28/167 (16%)
Query: 50 PMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYA 109
P P+ P P G S P+ G+ A + +P
Sbjct: 2626 PPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGR-AAQASSPPQRPR 2684
Query: 110 NPSAPQG---YTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWN 166
+A T+ PP P P+ P S P P +
Sbjct: 2685 RRAARPTVGSLTSLADPPPPPPTPE--------PAPHALVSATPLPPGPAAA-------- 2728
Query: 167 MPQNGPTTPAAGGPPAGGATGAAPTGPN-------PSGPSAGKPPAD 206
Q P PAA PPA A A P GP +GP A PPA
Sbjct: 2729 -RQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAA 2774
Score = 32.2 bits (73), Expect = 0.52
Identities = 29/150 (19%), Positives = 37/150 (24%), Gaps = 10/150 (6%)
Query: 62 PSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWG 121
PS P P Q + G PS P +P P
Sbjct: 2577 PSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSP----- 2631
Query: 122 APPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQ--SGYGNNWNWNMPQNGPTTPAAGG 179
P P PP++ P+ G + P P AA
Sbjct: 2632 -SPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAA-- 2688
Query: 180 PPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
P G+ + P P P A SA
Sbjct: 2689 RPTVGSLTSLADPPPPPPTPEPAPHALVSA 2718
Score = 32.2 bits (73), Expect = 0.56
Identities = 38/183 (20%), Positives = 54/183 (29%), Gaps = 21/183 (11%)
Query: 27 PRDASNKGNDMGNNQWGPPQSGGPMAMGPNMGMGTPSG--PMAGMTPMGPGNMMQGYQGW 84
PR A G + PPQ A P +G T P TP + +
Sbjct: 2664 PRRARRLGRAAQAS--SPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPL 2721
Query: 85 GSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPP---GPQAPPQWGSSYGAPPQ 141
P P++ P A P+ P G PP GP AP + PP+
Sbjct: 2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPR 2781
Query: 142 QTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAG 201
+ + S + +S +P P A P + P+
Sbjct: 2782 RLTRPAVASLSESRESL--------------PSPWDPADPPAAVLAPAAALPPAASPAGP 2827
Query: 202 KPP 204
PP
Sbjct: 2828 LPP 2830
Score = 29.9 bits (67), Expect = 2.9
Identities = 28/165 (16%), Positives = 42/165 (25%), Gaps = 12/165 (7%)
Query: 45 PQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTP 104
P + + P+ P TP GP + P T P AP +
Sbjct: 2725 PAAARQASPALPAAPAPPAVPAGPATPGGPARP--------ARPPTTAGPPAPAPPAAPA 2776
Query: 105 MNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWN 164
+ + P W + P + P + +P +
Sbjct: 2777 --AGPPRRLTRPAVASLSESRESLPSPWDPA-DPPAAVLAPAAALPPAASPAGPLPPPTS 2833
Query: 165 WNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
P P P P AP G P + P A +A
Sbjct: 2834 -AQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAA 2877
Score = 29.9 bits (67), Expect = 3.2
Identities = 22/113 (19%), Positives = 30/113 (26%), Gaps = 11/113 (9%)
Query: 87 TPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYG 146
+ T+ F + P P PQ P P PP P G
Sbjct: 2892 SRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAG 2951
Query: 147 SYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPS 199
+ P+ PQ P G P P AP+ P+ +
Sbjct: 2952 AGEPSGAVPQ-----------PWLGALVPGRVAVPRFRVPQPAPSREAPASST 2993
Score = 29.5 bits (66), Expect = 3.9
Identities = 21/84 (25%), Positives = 23/84 (27%), Gaps = 7/84 (8%)
Query: 122 APPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPP 181
PP P A P PP + P + PQ P A
Sbjct: 2552 PPPLPPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAP-----PQ--SARPRAPVDD 2604
Query: 182 AGGATGAAPTGPNPSGPSAGKPPA 205
G G AP P P A PP
Sbjct: 2605 RGDPRGPAPPSPLPPDTHAPDPPP 2628
Score = 29.5 bits (66), Expect = 4.3
Identities = 33/182 (18%), Positives = 47/182 (25%), Gaps = 20/182 (10%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQT 103
PP + GP A P + + + P ++
Sbjct: 2760 PPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALP 2819
Query: 104 PMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYG--- 160
P A P P APP P PP G G P S +P +
Sbjct: 2820 PAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPA 2879
Query: 161 --------------NNWNWNMPQNGPT---TPAAGGPPAGGATGAAPTGPNPSGPSAGKP 203
+ ++ +P + P P A PP P P P P +P
Sbjct: 2880 RPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRP 2939
Query: 204 PA 205
Sbjct: 2940 QP 2941
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 36.2 bits (84), Expect = 0.003
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI--DPKP 275
+ F+ +GE+ D V+K+ +T S+G +V FA ++ ++ ++G+ + D KP
Sbjct: 20 REAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEE----MNGKCLGGDTKP 75
>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 = 35.7 bits (83), Expect = 0.003
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F R GEV V + + +GRS G V F + I+ +G +D +P
Sbjct: 21 FGRVGEVKK-VKINYDRSGRSEGTADVVFEKREDAERAIK----QFNGVLLDGQP 70
>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 = 35.7 bits (83), Expect = 0.003
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
KV++G L T+ +L F +YG + V
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSV 29
Score = 33.0 bits (76), Expect = 0.028
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+ F +YG + V +N GF FV F DP + ++ LDGR I
Sbjct: 17 EDEFEKYGPLRSVWVARN-----PPGFAFVEFEDPRDA----EDAVRALDGRRI 61
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 35.6 bits (83), Expect = 0.004
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKV 317
+++GGL + +L F+R+G +
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAI 25
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 35.7 bits (82), Expect = 0.004
Identities = 19/62 (30%), Positives = 36/62 (58%), Gaps = 7/62 (11%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITRVPTQELPVQKEATAVQQ 351
++F+G LP +V +++L+ FF +YG V+E+ I S ++P V ++ VQ+
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRINSG-------GKLPNFGFVVFDDSEPVQK 57
Query: 352 VL 353
+L
Sbjct: 58 IL 59
Score = 33.4 bits (76), Expect = 0.028
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDG 268
+ +F +YG V++ ++ N G+ FGFV F D V ++ N P G
Sbjct: 21 KEFFQQYGNVVE---LRINSGGKLPNFGFVVFDDSEPVQKILSNRPIMFRG 68
>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 = 35.3 bits (82), Expect = 0.004
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 8/36 (22%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
++GGL VTE DLR F ++G++ R+I
Sbjct: 5 YVGGLGERVTEKDLRDHFYQFGEI--------RSIT 32
>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 = 35.4 bits (82), Expect = 0.004
Identities = 16/62 (25%), Positives = 27/62 (43%)
Query: 210 YGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGR 269
Y T A+ +F G ++ + +TG+S+G FV F + ++ L GR
Sbjct: 10 YDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLKGR 69
Query: 270 TI 271
I
Sbjct: 70 KI 71
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 38.8 bits (90), Expect = 0.005
Identities = 32/184 (17%), Positives = 33/184 (17%), Gaps = 3/184 (1%)
Query: 37 MGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQ 96
MG GP Q M P G +G N M QG GQ
Sbjct: 125 MGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQ 184
Query: 97 WAPSSQTPMN--GYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGA 154
P Q G G P Q Q G
Sbjct: 185 QGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQG- 243
Query: 155 PQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTYA 214
P Q G G P P G P
Sbjct: 244 PADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLGMLPNQMQQMPGGG 303
Query: 215 QYQQ 218
Q
Sbjct: 304 QGGP 307
Score = 38.4 bits (89), Expect = 0.006
Identities = 41/180 (22%), Positives = 44/180 (24%), Gaps = 25/180 (13%)
Query: 38 GNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTP-----------------MGP------ 74
G GP GPM GP MG G + MGP
Sbjct: 81 GQGTRGPQ--MGPMGPGPGRPMGQQMGGPGTASNLLQSLNVRGQMPMGAAGMGPHQMSRV 138
Query: 75 GNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGS 134
G M G Q G Q+ G P P+ P G A A P G Q PPQ G
Sbjct: 139 GTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQPPQMGQ 198
Query: 135 SYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPN 194
G G Q Q GP A
Sbjct: 199 PGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQGPADAQAQMGQQQQGQ 258
Score = 36.5 bits (84), Expect = 0.022
Identities = 34/160 (21%), Positives = 37/160 (23%), Gaps = 7/160 (4%)
Query: 45 PQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTP 104
GP+ MG P P G G M Q Q G Q Q Q
Sbjct: 182 QGQQGPVGQQQPPQMGQPGMPGG----GGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQ 237
Query: 105 MNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGS-YGPTSGAPQSGYGNNW 163
M+ P+ Q PQ G Q Q G N
Sbjct: 238 MDQQQGPADAQAQMGQQQQGQGGMQPQQMQ--GGQMQVPMQQQPPQQQPQQSQLGMLPNQ 295
Query: 164 NWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKP 203
MP G P P GA P G
Sbjct: 296 MQQMPGGGQGGPGQPMGPPPQRPGAVPQGGQAVQQGVMSA 335
Score = 31.1 bits (70), Expect = 1.2
Identities = 32/167 (19%), Positives = 43/167 (25%), Gaps = 14/167 (8%)
Query: 38 GNNQWGPPQSGGPMAMGPN-MGMGTPSGPMAGMTPMGPGN----MMQGYQGWGSTPQTQG 92
G Q GP Q GP P + G + M+ + + Q Q
Sbjct: 301 GGGQGGPGQPMGPPPQRPGAVPQGGQAVQQGVMSAGQQQLKQMKLRNMRGQQQTQQQQQQ 360
Query: 93 FPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTS 152
G + Q MN + G Q P S P
Sbjct: 361 QGGNHPAAHQQQMNQQVGQGGQMVALGYLNIQGNQGGLGANPMQQGQPGMMSSPSPVPQV 420
Query: 153 GAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPS 199
QS MPQ + + G P + G PS P+
Sbjct: 421 QTNQS---------MPQPPQPSVPSPGGPGSQPPQSVSGGMIPSPPA 458
>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 = 35.2 bits (82), Expect = 0.005
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
VF+G LP ++ E +LR F G V V R +R
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAV-----RIVR 33
Score = 35.2 bits (82), Expect = 0.005
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ-NCPHTLDGRTI 271
++F G+V ++++ +TG +GFG+V F ++V + ++ N L GR I
Sbjct: 18 KHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNGIK-LKGRKI 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 = 34.9 bits (81), Expect = 0.005
Identities = 11/30 (36%), Positives = 22/30 (73%), Gaps = 1/30 (3%)
Query: 292 KVFLGGLPSN-VTETDLRTFFNRYGKVMEV 320
+VF+G L ++ V++ DL F++YGK++ +
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGI 31
Score = 34.1 bits (79), Expect = 0.010
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 12/51 (23%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
FS+YG+++ + K G+GFV F + + + +GR I
Sbjct: 22 FSKYGKILGISLHK--------GYGFVQFDNEEDA----RAAVAGENGREI 60
>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 = 35.5 bits (81), Expect = 0.005
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
F GE+ C ++++ TG+S G+GFV + DP + I +TL+G + K
Sbjct: 25 FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI----NTLNGLRLQTK 74
>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 = 35.2 bits (81), Expect = 0.005
Identities = 15/66 (22%), Positives = 32/66 (48%)
Query: 210 YGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGR 269
YG+ A+ + +FS G + ++ + +G +G+ ++ FA ++V + + GR
Sbjct: 9 YGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALDESSFRGR 68
Query: 270 TIDPKP 275
I P
Sbjct: 69 VIKVLP 74
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 38.5 bits (89), Expect = 0.006
Identities = 28/111 (25%), Positives = 36/111 (32%), Gaps = 6/111 (5%)
Query: 94 PGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSG 153
P QWAP + P P AP APPG P ++ A P G P +
Sbjct: 686 PIQWAPGTMQP-----PPRAPTPMRPPAAPPGRAQRPA-AATGRARPPAAAPGRARPPAA 739
Query: 154 APQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPP 204
AP + P PPA P P + P+ + P
Sbjct: 740 APGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPTPQPPPQAPPAPQQRP 790
Score = 30.8 bits (69), Expect = 1.6
Identities = 27/103 (26%), Positives = 31/103 (30%), Gaps = 4/103 (3%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQT 103
P + A P G P A P G + + P AP + T
Sbjct: 716 RPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPT 775
Query: 104 PMNGYANPSAPQGYTNWGAPPGPQAPPQWG--SSYGAPPQQTG 144
P P APQ P PQ PPQ G S P G
Sbjct: 776 PQPPPQAPPAPQQRPR--GAPTPQPPPQAGPTSMQLMPRAAPG 816
>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM2 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 93
Score = 34.9 bits (81), Expect = 0.008
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYG 315
V+ G LP VT+ DLR FF Y
Sbjct: 5 VYCGKLPKKVTDEDLREFFKDYN 27
>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 = 34.7 bits (80), Expect = 0.009
Identities = 15/44 (34%), Positives = 22/44 (50%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
A T +R F +YG ++D + + T R RGF +V F D
Sbjct: 9 ADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDV 52
Score = 30.0 bits (68), Expect = 0.39
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
+++ + DLR F +YG +++V I
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYI 32
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of nuclear
proteins consisting of Matrin 3 (MATR3), nuclear protein
220 (NP220) and similar proteins. MATR3 is a highly
conserved inner nuclear matrix protein that has been
implicated in various biological processes. NP220 is a
large nucleoplasmic DNA-binding protein that binds to
cytidine-rich sequences, such as CCCCC (G/C), in
double-stranded DNA (dsDNA). Both, Matrin 3 and NP220,
contain two RNA recognition motif (RRM), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a Cys2-His2 zinc finger-like motif at the
C-terminal region. .
Length = 76
Score = 34.5 bits (80), Expect = 0.009
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 292 KVFLGGLPS-NVTETDLRTFFNRYGKVMEVVIMSPR 326
V L LP TE +L +GKV + + R
Sbjct: 2 VVRLSNLPEGGYTEAELLKLAEPFGKVDHYIFLPNR 37
>gnl|CDD|241121 cd12677, RRM4_Nop4p, RNA recognition motif 4 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM4 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 156
Score = 36.1 bits (83), Expect = 0.009
Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 9/65 (13%)
Query: 231 VVM--KNNETGRSRGFGFVTFADPNNVGVVIQ--NC-----PHTLDGRTIDPKPCNPRTL 281
V + GRSRG+GF+ F + ++ N +D + N
Sbjct: 76 VETEKAGSTAGRSRGYGFMEFISHKYALMALRWLNGHAVTVKKIIDAEIEWARLPNIDYN 135
Query: 282 QKPKK 286
KP++
Sbjct: 136 DKPRR 140
>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 = 34.9 bits (80), Expect = 0.009
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 9/60 (15%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLD-----GRTID 272
+R F RYG ++D V + T R RGF +V F D + ++ H LD GR I+
Sbjct: 18 RREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDA----EDALHNLDRKWICGRQIE 73
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. The family
also includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 34.6 bits (80), Expect = 0.010
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC 276
FS++GEV VV+ + + GRS G G V F+ I+ C T P+P
Sbjct: 20 FSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAAIKRCSEGCFLLTASPRPV 74
>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 = 34.6 bits (79), Expect = 0.010
Identities = 15/49 (30%), Positives = 27/49 (55%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTL 266
+ YF +GEV + +N+T + RGF F+TF + V +++ H +
Sbjct: 17 REYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNV 65
Score = 29.6 bits (66), Expect = 0.61
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKV--MEVVIMSPRTIRAGITRVP-TQELPVQK 344
K+F+GGL + E +R +F +G+V +E+ + + R G + +E PV+K
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56
>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 = 34.6 bits (80), Expect = 0.010
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 5/54 (9%)
Query: 219 RYFSRYGEVIDCV-VMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
R F+ GE + V +++N TG G+ FV FAD + C H L+G+ I
Sbjct: 18 RAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATA----ERCLHKLNGKPI 67
>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 = 34.7 bits (79), Expect = 0.010
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
F GE+ C ++++ TG+S G+GFV + DP + I +TL+G + K
Sbjct: 23 FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI----NTLNGLRLQTK 72
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 34.0 bits (78), Expect = 0.011
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 5/53 (9%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVI-QNCPHTLDGRTI 271
YF ++G V+D V + + R FGFVTF + V ++ + PH + G +
Sbjct: 19 YFGQFGPVLD-VRIPYQQ---KRMFGFVTFENAETVKRILSKGNPHFICGSRV 67
>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 = 34.3 bits (78), Expect = 0.012
Identities = 13/29 (44%), Positives = 23/29 (79%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
F+ +G++ D V+K+ TG+S+G+GFV+F
Sbjct: 22 FAPFGKISDARVVKDMATGKSKGYGFVSF 50
>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 = 34.5 bits (80), Expect = 0.013
Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 8/51 (15%)
Query: 234 KNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP----CNPRT 280
K+ TG+ + FGF F DP L+G + K + +T
Sbjct: 34 KDPSTGKLKAFGFCEFEDPEGA----LRALRLLNGLELGGKKLLVKVDAKT 80
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1,
or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3,
or CUG-BP2, or NAPOR) belong to the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family
of RNA-binding proteins that have been implicated in
regulation of pre-mRNA splicing, and control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. The
human CELF-1 is a nuclear and cytoplasmic RNA-binding
protein that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for onset
of type 1 myotonic dystrophy (DM1), a neuromuscular
disease associated with an unstable CUG triplet
expansion in the 3'-UTR (3'-untranslated region) of the
DMPK (myotonic dystrophy protein kinase) gene; it
preferentially targets UGU-rich mRNA elements. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contain three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains): two consecutive RRMs (RRM1
and RRM2) situated in the N-terminal region followed by
a linker region and the third RRM (RRM3) close to the
C-terminus of the protein. The two N-terminal RRMs of
EDEN-BP are necessary for the interaction with EDEN as
well as a part of the linker region (between RRM2 and
RRM3). Oligomerization of EDEN-BP is required for
specific mRNA deadenylation and binding. CELF-2 is
expressed in all tissues at some level, but highest in
brain, heart, and thymus. It has been implicated in the
regulation of nuclear and cytoplasmic RNA processing
events, including alternative splicing, RNA editing,
stability and translation. CELF-2 shares high sequence
identity with CELF-1, but shows different binding
specificity; it binds preferentially to sequences with
UG repeats and UGUU motifs. It has been shown to bind to
a Bruno response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to the
3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2
of CELF-2, can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. This subgroup also
includes Drosophila melanogaster Bruno protein, which
plays a central role in regulation of Oskar (Osk)
expression in flies. It mediates repression by binding
to regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 84
Score = 34.4 bits (79), Expect = 0.013
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K+F+G +P + +E DLR F +YG V ++ ++ R
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDR 37
>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 = 34.2 bits (78), Expect = 0.013
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKV--MEVVIMSPRTIRAGITRVP-TQELPVQK 344
KVF+GGL + TE ++ +F +G++ +E+ + + R G V T E PVQK
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQK 56
Score = 33.5 bits (76), Expect = 0.021
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTL 266
+ YF +GE+ + + + +T RGF FVT+ D V ++++ H +
Sbjct: 17 KEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLESRYHQI 65
>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 = 34.6 bits (79), Expect = 0.014
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
FS+YG + D ++ + ++ RSRGF FV F +
Sbjct: 30 FSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60
Score = 28.1 bits (62), Expect = 2.3
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 291 PKVFLG--GLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
P LG GL TE DLR F++YG + +V I+ + R
Sbjct: 8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSR 48
>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 = 34.0 bits (79), Expect = 0.014
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPN 253
FS G V+ V ++ T RS G+ +V F +P
Sbjct: 20 FSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPA 52
Score = 32.9 bits (76), Expect = 0.038
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
++G L +VTE L F+ G V +S R R ITR
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPV-----LSIRVCRDLITR 38
>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 = 34.1 bits (79), Expect = 0.015
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 9/59 (15%)
Query: 224 YGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRTLQ 282
+G++ ++K++ TG S+G+ F + DP+ V L+G + L
Sbjct: 24 FGKLKAFNLVKDSATGLSKGYAFCEYLDPS----VTDQAIAGLNG-----MQLGDKKLT 73
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 34.2 bits (78), Expect = 0.015
Identities = 12/31 (38%), Positives = 23/31 (74%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
++F+G LP ++ E++L+ FF +G V+E+ I
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRI 37
>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 = 33.7 bits (77), Expect = 0.015
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
++F+G LP+++TE + + F +YG+ EV I
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFI 33
>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 = 33.9 bits (78), Expect = 0.016
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
F+G L T +DLR F R+G+++++ I
Sbjct: 6 FIGNLEKTTTYSDLREAFERFGEIIDIDI 34
>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 = 33.5 bits (77), Expect = 0.017
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
+F E+ + + ETG +GFG V FAD
Sbjct: 18 EFFKG-CEITSVRLATDKETGEFKGFGHVDFAD 49
>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 = 34.0 bits (78), Expect = 0.020
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVM 318
KVF+GGLP ++ E ++ F R+G ++
Sbjct: 2 KVFVGGLPPDIDEDEITASFRRFGPLV 28
>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 = 33.5 bits (77), Expect = 0.021
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPN 253
R F + C + ++ TG+S+GF +VT+++P
Sbjct: 18 RLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPA 52
>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 = 33.4 bits (76), Expect = 0.022
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
FS+YG +I ++++ TG SRG GF+ F
Sbjct: 21 FSQYGRIITSRILRDQLTGVSRGVGFIRF 49
Score = 27.2 bits (60), Expect = 4.0
Identities = 13/44 (29%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITRVP 336
+++ GLP +T+ +L F++YG+ I++ R +R +T V
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGR-----IITSRILRDQLTGVS 41
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 33.2 bits (76), Expect = 0.023
Identities = 11/32 (34%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 292 KVFLGGLPS-NVTETDLRTFFNRYGKVMEVVI 322
++F+G LP+ V++ DL F+ YG++ ++V+
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVL 32
>gnl|CDD|241167 cd12723, RRM1_CPEB1, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding
protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 100
Score = 33.9 bits (78), Expect = 0.024
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 291 PKVFLGGLPSNVTETDLRTFFNRYGKV 317
KVFLGG+P ++TE L F +G V
Sbjct: 3 CKVFLGGVPWDITEAGLINTFKPFGSV 29
>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 = 33.3 bits (76), Expect = 0.026
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
F YG ++ C ++++ TG RG FV +
Sbjct: 21 FEAYGNIVQCNLLRDKSTGLPRGVAFVRY 49
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of SXL which governs sexual differentiation
and X chromosome dosage compensation in Drosophila
melanogaster. It induces female-specific alternative
splicing of the transformer (tra) pre-mRNA by binding to
the tra uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 33.5 bits (77), Expect = 0.026
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
F G V +C ++++ TG S GFGFV + + I+ TL+G + K
Sbjct: 21 FLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR----TLNGLQLQNK 70
>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 = 33.1 bits (75), Expect = 0.028
Identities = 13/29 (44%), Positives = 22/29 (75%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
F+ +G + D V+K+ TG+S+G+GFV+F
Sbjct: 22 FAPFGRISDARVVKDMATGKSKGYGFVSF 50
>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 = 33.7 bits (78), Expect = 0.029
Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 218 QRYFSRYGEVIDCVVMKN------NETGRSRGFGFVTFAD 251
+R + ++ +M++ N G+S+G+GFV F +
Sbjct: 27 ERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTN 66
>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 = 33.1 bits (76), Expect = 0.031
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 228 IDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
++ V + + G+ + F FVTF +V IQ L GR +
Sbjct: 28 LEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGREL 72
>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 = 33.1 bits (76), Expect = 0.031
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
+ +GG+ +++E DL+ FF+ G+V V +
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRL 32
>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 = 33.2 bits (76), Expect = 0.031
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITRVPTQELPVQ--KEATAV 349
K+F+ GLP +VT+ +L F ++G V V ++ T R+G P V+ E++A
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLV---TNRSG---KPKGLAYVEYENESSAS 57
Query: 350 QQVLRRSSTT 359
Q VL+ T
Sbjct: 58 QAVLKMDGTE 67
>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 = 32.9 bits (75), Expect = 0.038
Identities = 15/40 (37%), Positives = 22/40 (55%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ 260
F +G VI V + T +S+ FGFV+F +P + IQ
Sbjct: 25 FLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQ 64
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM2 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 81
Score = 33.0 bits (75), Expect = 0.040
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
++ FS+YG +I ++ + TG SRG GF+ F
Sbjct: 19 EQLFSQYGRIITSRILVDQVTGISRGVGFIRF 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 = 32.8 bits (75), Expect = 0.041
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
FS+YG + + + + T + +GF FVT+ P +
Sbjct: 23 FSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEH 56
Score = 31.2 bits (71), Expect = 0.16
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
++F+ L TE DL F++YG + EV +
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHL 34
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 32.5 bits (75), Expect = 0.046
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 221 FSRYGEV-IDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
FS++G I + M +ETG+++G+ FV FA P + L+G +D K
Sbjct: 28 FSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEA----KEAVKALNGYKLDKK 78
>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 = 32.3 bits (74), Expect = 0.047
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 220 YFSRYGEV--IDCVVMKNNETGRSRGFGFVTFAD 251
YFS GE+ +D M +TGR RG F+TF
Sbjct: 18 YFSYCGEIEELDL--MTFPDTGRFRGIAFITFKT 49
Score = 30.0 bits (68), Expect = 0.29
Identities = 11/31 (35%), Positives = 23/31 (74%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
V++GG+P TE ++R++F+ G++ E+ +M
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLM 31
>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 = 32.3 bits (74), Expect = 0.048
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
++ F +G + D +K + G+ R FGFV +
Sbjct: 18 RKLFEAFGTITDVQ-LKYTKDGKFRKFGFVGY 48
>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 = 32.7 bits (75), Expect = 0.048
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ--NCPHTLDGRTIDPKP 275
FS+YG V+ + + TG +GF F+ F P + N P P
Sbjct: 20 FSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNNPPETATDKPGKFP 76
Score = 28.1 bits (63), Expect = 2.1
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
V++ LP N T L+ F++YG V+ V + PR
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSL--PR 33
>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 = 32.2 bits (74), Expect = 0.050
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 298 LPSNVTETDLRTFFNRYGKVMEVVIM 323
LP + TE LR F+ YG+V V +
Sbjct: 9 LPLSTTEEQLRELFSEYGEVERVKKI 34
>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 = 32.3 bits (74), Expect = 0.051
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+++G L VTE DL+ F YG++ + ++ PR
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPR 38
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44
(RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 32.6 bits (74), Expect = 0.051
Identities = 12/30 (40%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
V +GGL +V+E DLR+ F +Y +V + +
Sbjct: 2 VHVGGLSPSVSEGDLRSHFQKY-QVSVISL 30
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 32.5 bits (74), Expect = 0.051
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 222 SRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
SR+ +M + TG SRG+GFV F+D N+
Sbjct: 24 SRFPSCKSAKIMTDPVTGVSRGYGFVRFSDEND 56
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 32.3 bits (73), Expect = 0.058
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 12/51 (23%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
FS+YG+++ C V K GF FV + + N + DGR I
Sbjct: 23 FSKYGKIVGCSVHK--------GFAFVQYVNERNARAAVAG----EDGRMI 61
Score = 28.8 bits (64), Expect = 1.0
Identities = 10/28 (35%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 292 KVFLGGLPSN-VTETDLRTFFNRYGKVM 318
+VF+G L + V ++D+ F++YGK++
Sbjct: 3 RVFIGNLNTLVVKKSDVEAIFSKYGKIV 30
>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 = 32.4 bits (74), Expect = 0.061
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 218 QRYFSRYGEVIDCVVM--KNNETGRSRGFGFVTF 249
+ FS +GE + V + K TG RGFGFV F
Sbjct: 18 RELFSTFGE-LKTVRLPKKMTGTGSHRGFGFVDF 50
>gnl|CDD|227507 COG5180, PBP1, Protein interacting with poly(A)-binding protein
[RNA processing and modification].
Length = 654
Score = 35.1 bits (80), Expect = 0.062
Identities = 33/140 (23%), Positives = 45/140 (32%), Gaps = 17/140 (12%)
Query: 34 GNDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGF 93
G +MG P GGP A M G +G M P P M P Q
Sbjct: 517 GMNMGGMMGFP--MGGPSASPNPMMNGFAAGSMGMYMPFQPQPMF-------YHPSPQMM 567
Query: 94 PGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYG---SYGP 150
P S+ G + GP AP G P Q G S P
Sbjct: 568 PV--MGSNGAEEGGG---NISPHVPAGFMAAGPGAPMGAFGYPGGIPFQGMMGSGPSGMP 622
Query: 151 TSGAPQSGYGNNWNWNMPQN 170
+G+ +G++ N++ +
Sbjct: 623 ANGSAMHSHGHSRNYHQTSH 642
>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 = 31.9 bits (73), Expect = 0.070
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
FS+ GE+ D V + N G+S+G+ +V F +
Sbjct: 20 FSKCGEITD-VRLVKNYKGKSKGYAYVEFEN 49
Score = 29.5 bits (67), Expect = 0.42
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEV 320
VF+ L +V E +LR F++ G++ +V
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDV 29
>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 = 32.1 bits (73), Expect = 0.070
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 215 QYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
++ F RYG+V + + G+ GF FVT N + ++N +DGR +
Sbjct: 16 VKLKKIFGRYGKVRE-ATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPV 72
>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 = 31.9 bits (73), Expect = 0.075
Identities = 16/62 (25%), Positives = 29/62 (46%)
Query: 210 YGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGR 269
YGT + Q +F G + ++ + TG+ +GF ++ F D ++V + GR
Sbjct: 9 YGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNESEFRGR 68
Query: 270 TI 271
I
Sbjct: 69 QI 70
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 34.8 bits (80), Expect = 0.081
Identities = 28/164 (17%), Positives = 43/164 (26%), Gaps = 15/164 (9%)
Query: 45 PQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQG----WGSTPQTQGFPGQWAPS 100
S P + + + P+ P G P ++ S P A
Sbjct: 760 NPSLVPAKLAEALALLEPAEPQRGAGSSPPVRAEAAFRRPGRLRRSGPAADAASRT-ASK 818
Query: 101 SQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYG 160
++ + S G PPG A P P + + P + ++
Sbjct: 819 RKSRSHTPDGGSESSGPAR---PPGAAARP-------PPARSSESSKSKPAAAGGRARGK 868
Query: 161 NNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPP 204
N P P A PP A P P A +
Sbjct: 869 NGRRRPRPPEPRARPGAAAPPKAAAAAPPAGAPAPRPRPAPRVK 912
>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 = 32.2 bits (73), Expect = 0.085
Identities = 10/30 (33%), Positives = 21/30 (70%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
V++G +PS +T ++L+ F+ +G++ E I
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTI 34
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 31.5 bits (71), Expect = 0.092
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
+V++G L E D+ FF YGK++EV
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEV 29
Score = 30.3 bits (68), Expect = 0.26
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 8/37 (21%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
+R+F YG++++ V +KN G+GFV F D +
Sbjct: 17 ERFFKGYGKILE-VDLKN-------GYGFVEFDDLRD 45
>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 = 31.6 bits (72), Expect = 0.094
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
F G+V+ + ++ E G+SRG G V F P
Sbjct: 19 FKLAGKVVRADIKEDKE-GKSRGMGVVQFEHP 49
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 34.7 bits (79), Expect = 0.095
Identities = 27/143 (18%), Positives = 44/143 (30%), Gaps = 12/143 (8%)
Query: 103 TPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNN 162
+ +G A G PG Q P + G P S P + AP +
Sbjct: 379 SAPSGSAAEGPASGGAATIPTPGTQGPQGTAPAAGMTPS-----SAAPATPAPSAAPSPR 433
Query: 163 WNWNMPQNGPTTPAAGGPPAG----GATGAAPTGPNPSGPSAGKPPADYSAYGTYAQYQQ 218
W+ P P +G PP P P+ ++ PP A++
Sbjct: 434 VPWD--DAPPAPPRSGIPPRPAPRMPEASPVPGAPDSVASASDAPPT-LGDPSDTAEHTP 490
Query: 219 RYFSRYGEVIDCVVMKNNETGRS 241
+ ++ +N + GR
Sbjct: 491 SGPRTWDGFLEFCQGRNGQGGRL 513
Score = 29.6 bits (66), Expect = 2.9
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 1/64 (1%)
Query: 144 GYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAG-GATGAAPTGPNPSGPSAGK 202
G SG+ G + +P G P P AG + AAP P PS + +
Sbjct: 374 SGGGASAPSGSAAEGPASGGAATIPTPGTQGPQGTAPAAGMTPSSAAPATPAPSAAPSPR 433
Query: 203 PPAD 206
P D
Sbjct: 434 VPWD 437
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces
cerevisiae protein Nrd1, Schizosaccharomyces pombe
Rpb7-binding protein seb1 and similar proteins. This
subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1
is a novel heterogeneous nuclear ribonucleoprotein
(hnRNP)-like RNA-binding protein encoded by gene NRD1
(for nuclear pre-mRNA down-regulation) from yeast S.
cerevisiae. It is implicated in 3' end formation of
small nucleolar and small nuclear RNAs transcribed by
polymerase II, and plays a critical role in pre-mRNA
metabolism. Nrd1 contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a short arginine-, serine-,
and glutamate-rich segment similar to the regions rich
in RE and RS dipeptides (RE/RS domains) in many metazoan
splicing factors, and a proline- and glutamine-rich
C-terminal domain (P+Q domain) similar to domains found
in several yeast hnRNPs. Disruption of NRD1 gene is
lethal to yeast cells. Its N-terminal domain is
sufficient for viability, which may facilitate
interactions with RNA polymerase II where Nrd1 may
function as an auxiliary factor. By contrast, the RRM,
RE/RS domains, and P+Q domain are dispensable. Seb1 is
an RNA-binding protein encoded by gene seb1 (for seven
binding) from fission yeast S. pombe. It is essential
for cell viability and bound directly to Rpb7 subunit of
RNA polymerase II. Seb1 is involved in processing of
polymerase II transcripts. It also contains one RRM
motif and a region rich in arginine-serine dipeptides
(RS domain).
Length = 79
Score = 31.8 bits (72), Expect = 0.095
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
+F GG+ N+ E DLR+ F R+G+V ++
Sbjct: 6 LFPGGVTFNMIEYDLRSGFGRFGEVQSCIL 35
>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 = 31.9 bits (73), Expect = 0.099
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 220 YFS-RYGEVIDC-VVMKNNETGRSRGFGFVTFADPN 253
+FS RY VV+ N G SRG+GFV F+D +
Sbjct: 21 FFSKRYPSCKGAKVVLDQN--GNSRGYGFVRFSDES 54
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 31.7 bits (72), Expect = 0.10
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 10/62 (16%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFA---------DPNNVGVVIQNCPHTLDGRTI 271
FS YG V D +M++ E +SRG FV ++ N ++ C L R
Sbjct: 20 FSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKALNGVYTMRGCDQPLIVRFA 78
Query: 272 DP 273
DP
Sbjct: 79 DP 80
Score = 29.0 bits (65), Expect = 0.79
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G L TE ++ F+ YG+V ++ +M
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMM 32
>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 = 31.9 bits (72), Expect = 0.11
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
+R F RYG ++D V + T R RGF ++ F D
Sbjct: 18 RREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFED 51
>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 = 31.9 bits (73), Expect = 0.11
Identities = 8/30 (26%), Positives = 20/30 (66%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
+++G +P + T ++LR F +G++ E+ +
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITL 34
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 31.6 bits (71), Expect = 0.11
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
++ FS+YG +I ++ + TG SRG GF+ F
Sbjct: 20 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 51
Score = 27.8 bits (61), Expect = 2.7
Identities = 11/42 (26%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
+++ GLP +T+ +L F++YG+++ I+ + G++R
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV--TGVSR 44
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 31.7 bits (73), Expect = 0.12
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 8/48 (16%)
Query: 222 SRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGR 269
S++G V V KN+ G +V F Q C L+GR
Sbjct: 33 SKFGPVEHIKVDKNS----PEGVVYVKFKTVE----AAQKCIQALNGR 72
>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 = 31.5 bits (71), Expect = 0.13
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ 260
F +G VI V + +T S+ FGFV++ +P++ IQ
Sbjct: 25 FLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64
>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 = 31.5 bits (71), Expect = 0.13
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDG 268
+ YF +GE+ + + +T + RGF F+TF + + V V++ H + G
Sbjct: 22 REYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEKKFHNVSG 72
Score = 30.7 bits (69), Expect = 0.23
Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI-MSPRT-IRAGITRVP-TQELPVQK 344
K+F+GGL TE +R +F +G++ + + M P+T R G + +E PV+K
Sbjct: 6 KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61
>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 = 31.2 bits (70), Expect = 0.13
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
FS+YG+V+ V+ N + +R +GFVT + I + T L GR I
Sbjct: 22 FSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHLHRTELHGRMI 73
Score = 28.9 bits (64), Expect = 0.89
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVM 318
+++ GL S TDL+ F++YGKV+
Sbjct: 4 LWVSGLSSTTRATDLKNLFSKYGKVV 29
>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 = 31.2 bits (71), Expect = 0.14
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKV 317
VF+GGLP N TE +R F + G++
Sbjct: 9 VFVGGLPENATEEIIREVFEQCGEI 33
>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 = 31.1 bits (71), Expect = 0.14
Identities = 9/35 (25%), Positives = 20/35 (57%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
++ +G++I + + +T + +G+GFV F P
Sbjct: 18 EKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSP 52
Score = 27.6 bits (62), Expect = 2.0
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 291 PKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
V++ GLP N T+ DL +GK++ +
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAI 33
>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 = 31.6 bits (71), Expect = 0.14
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVI 259
+ +FS G+V D ++ + + RS+G +V F D ++V + I
Sbjct: 19 EEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60
Score = 28.5 bits (63), Expect = 1.8
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
VF L + + DL FF+ GKV +V ++S R R
Sbjct: 4 VFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSR 40
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains 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. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a specific
inhibitory effect on oestrogen action, SLTM is shown to
exert a generalized inhibitory effect on gene expression
associated with induction of apoptosis in a wide range
of cell lines. .
Length = 74
Score = 31.2 bits (70), Expect = 0.16
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
+++ GL SN DL+ F +YGKV+ +++
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVT 33
>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 = 31.2 bits (70), Expect = 0.16
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
FS GEV ++++ G S G+GFV + + + I TL+G + K
Sbjct: 22 FSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN----TLNGLRLQSK 71
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 86
Score = 31.4 bits (71), Expect = 0.16
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 232 VMKNNETGRSRGFGFVTFADPNNVGVVIQ-----NCPHTLDGRTI 271
++K+ +T ++RGF FV + ++Q + P +DG+TI
Sbjct: 36 LIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTI 80
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein (SXL).
SNF contains two RNA recognition motifs (RRMs); it can
self-associate through RRM1, and each RRM can recognize
poly(U) RNA binding independently. .
Length = 78
Score = 31.0 bits (70), Expect = 0.19
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
FS++G+++D V +K T + RG FV F D ++
Sbjct: 24 FSQFGQILDIVALK---TLKMRGQAFVVFKDISS 54
>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 = 31.4 bits (72), Expect = 0.21
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 293 VFLGGLPSNVTETDL---RTFFNRYGKVMEVVIMSPRTIRAGITR 334
V++ GLP + + ++ +F +YGK+ ++VI + T G
Sbjct: 8 VYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVI-NRNTSYNGSQG 51
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B shows high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 30.5 bits (69), Expect = 0.21
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 293 VFLGGLPSNVTETDLRTFF 311
VFL GLP E D++ FF
Sbjct: 2 VFLHGLPYTADEHDVKEFF 20
>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 = 30.8 bits (69), Expect = 0.23
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
FSR+G +I+ V+ + TG SRG F+ F
Sbjct: 21 FSRFGRIINSRVLVDQATGLSRGVAFIRF 49
Score = 27.3 bits (60), Expect = 4.7
Identities = 10/42 (23%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
+++ GLP +T+ D+ F+R+G+++ ++ + G++R
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQA--TGLSR 42
>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 = 30.6 bits (69), Expect = 0.24
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 224 YGEVIDCVVMKNNETGRSRGFGFVTF 249
YG + C ++ + TG S+G+GFV +
Sbjct: 23 YGNIERCFLVYSEVTGHSKGYGFVEY 48
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 32.8 bits (75), Expect = 0.26
Identities = 24/125 (19%), Positives = 42/125 (33%), Gaps = 8/125 (6%)
Query: 85 GSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTG 144
G P+ G+ G G + P P PP S YG+ ++G
Sbjct: 186 GPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGSGGTRSG 245
Query: 145 YGSYGP-----TSGAPQSGY--GNNWNWNMPQNGP-TTPAAGGPPAGGATGAAPTGPNPS 196
G +GP GY G+ N N + + P+ + ++ + + +
Sbjct: 246 QGGWGPGFWTGLGAGGALGYLFGSRRNNNSSYGRSYGSGSPSYSPSSSSNSSSSSSSSST 305
Query: 197 GPSAG 201
S+G
Sbjct: 306 RTSSG 310
Score = 31.2 bits (71), Expect = 0.81
Identities = 27/148 (18%), Positives = 44/148 (29%), Gaps = 22/148 (14%)
Query: 11 YITCFLLQQVEIKKAEPRDASNKGNDMGNNQWGPPQSGGPMAMGPNM--GMGTPSGPMAG 68
+++C ++ + G G G P + G +GP +G
Sbjct: 177 FLSCGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSG 236
Query: 69 MTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGY-------ANPSAPQGYTN-W 120
G G G GWG PG W GY N S + Y +
Sbjct: 237 ---YGSGGTRSGQGGWG--------PGFWTGLGAGGALGYLFGSRRNNNSSYGRSYGSGS 285
Query: 121 GAPPGPQAPPQWGSSYGAPPQQ-TGYGS 147
+ + SS + + +G+G
Sbjct: 286 PSYSPSSSSNSSSSSSSSSTRTSSGFGG 313
Score = 30.1 bits (68), Expect = 2.0
Identities = 23/119 (19%), Positives = 29/119 (24%), Gaps = 7/119 (5%)
Query: 90 TQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYG 149
+ P + G G G+ PGP P S G S
Sbjct: 178 LSCGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGY 237
Query: 150 PTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYS 208
+ G W G T G G G+ + G S G YS
Sbjct: 238 GSGGTRSGQ----GGW---GPGFWTGLGAGGALGYLFGSRRNNNSSYGRSYGSGSPSYS 289
Score = 28.2 bits (63), Expect = 8.1
Identities = 18/77 (23%), Positives = 27/77 (35%), Gaps = 2/77 (2%)
Query: 117 YTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPA 176
+ + G G P + G G G G G G P G+ ++ P P+
Sbjct: 177 FLSCGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGF--KSSFPPPYGPGAGPS 234
Query: 177 AGGPPAGGATGAAPTGP 193
+G G +G GP
Sbjct: 235 SGYGSGGTRSGQGGWGP 251
>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 = 30.7 bits (70), Expect = 0.28
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
++ FS+ G+ C + G+ RGF FV +A
Sbjct: 21 RKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATA 54
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 30.4 bits (69), Expect = 0.28
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
++ LP ++ E DL T YG+V +S R +R
Sbjct: 4 YISNLPLHMDEQDLETMLKPYGQV-----ISTRILR 34
>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 = 30.1 bits (68), Expect = 0.29
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
+F R G + +M ++G+ +GF FV F +
Sbjct: 17 AHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEE 49
Score = 30.1 bits (68), Expect = 0.35
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
+F+G L TE +LR F R G++ V +M+
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMT 32
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM2 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 86
Score = 30.7 bits (69), Expect = 0.29
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 232 VMKNNETGRSRGFGFVTFADPNNVGVVIQ-----NCPHTLDGRTI 271
++K+ +T ++RGF FV + ++Q + P +DG+TI
Sbjct: 36 LIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTI 80
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 30.7 bits (70), Expect = 0.29
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM-SPRTIR-AGITRV 335
V L N+ E L+ +YG+V EV I P+T + G+ RV
Sbjct: 5 VTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARV 49
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 30.6 bits (70), Expect = 0.32
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 291 PKVFLGGLPSNVTETDLRTFFNRYGKVME 319
V++ GLP ++T + F++ G + E
Sbjct: 2 TNVYVSGLPLDITVEEFVEVFSKCGIIKE 30
>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage
factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar
proteins. This subgroup corresponds to the RRM of
CFIm59. Cleavage factor Im (CFIm) is a highly conserved
component of the eukaryotic mRNA 3' processing machinery
that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. The two separate genes,
CPSF6 and CPSF7, code for two isoforms of the large
subunit, CFIm68 and CFIm59. The family includes CFIm59,
also termed cleavage and polyadenylation specificity
factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59). CFIm59 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. The N-terminal
RRM of CFIm59 mediates the interaction with CFIm25. It
also serves to enhance RNA binding and facilitate RNA
looping. .
Length = 90
Score = 30.3 bits (68), Expect = 0.34
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 227 VIDCVVMK---NNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTIDPKPCNPRTL 281
V D V +K N G+S+G+ V A N+V +++ P L+G +D +P + L
Sbjct: 27 VKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNL 85
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 29.7 bits (67), Expect = 0.36
Identities = 9/33 (27%), Positives = 21/33 (63%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSP 325
V++G LP ++ E ++ F +YG ++++ + P
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLP 34
>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 = 30.2 bits (68), Expect = 0.36
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+VF+G +P ++ E +L F R GK+ E +M
Sbjct: 3 EVFVGKIPRDMYEDELVPLFERAGKIYEFRLM 34
>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 = 30.4 bits (68), Expect = 0.37
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 3/31 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
FS++G V+D V +K T + RG FV F +
Sbjct: 26 FSQFGHVVDIVALK---TMKMRGQAFVIFKE 53
>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 = 30.4 bits (68), Expect = 0.37
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVI 259
+ +FS G+V D ++ + + RS+G +V F + +V + I
Sbjct: 19 EDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 60
Score = 28.5 bits (63), Expect = 1.6
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
VF L + + DL FF+ GKV +V I+S R R
Sbjct: 4 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSR 40
>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 = 30.7 bits (69), Expect = 0.37
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP 263
+FS++G V + + + TGR++G GFV F D ++N P
Sbjct: 21 HFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNAP 64
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 30.0 bits (68), Expect = 0.38
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 6/61 (9%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKV--MEVVIMSPRTIRAGITRVPTQELPVQKEATAV 349
K+ + +P +V DL + + YG V E V T + T E P Q +
Sbjct: 2 KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNV----TYESPEQAQQAVN 57
Query: 350 Q 350
+
Sbjct: 58 K 58
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 32.7 bits (74), Expect = 0.40
Identities = 32/143 (22%), Positives = 41/143 (28%), Gaps = 8/143 (5%)
Query: 86 STPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAP-PQWGSSYGAPPQQTG 144
+T TQ + P +QTP + Q W PGPQ P + PQQ+
Sbjct: 326 ATTATQSWAAPVEPVTQTPPVASVDVPPAQPTVAWQPVPGPQTGEPVIAPAPEGYPQQSQ 385
Query: 145 YGSYGPTSGAP-------QSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSG 197
Y P Q Y Q PA P AP P
Sbjct: 386 YAQPAVQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGN 445
Query: 198 PSAGKPPADYSAYGTYAQYQQRY 220
+ A + Q +Q Y
Sbjct: 446 AWQAEEQQSTFAPQSTYQTEQTY 468
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 32.5 bits (74), Expect = 0.41
Identities = 29/141 (20%), Positives = 38/141 (26%), Gaps = 27/141 (19%)
Query: 80 GYQGWGSTPQT--QGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYG 137
G G G+ P T Q AP++ P P+AP A +
Sbjct: 366 GQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPAR 425
Query: 138 APP--------QQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPA----GGA 185
P +Q G + PAA PA
Sbjct: 426 RSPAPEALAAARQASARGPGGAPAPAPAP-------------AAAPAAAARPAAAGPRPV 472
Query: 186 TGAAPTGPNPSGPSAGKPPAD 206
AA P + P+A PAD
Sbjct: 473 AAAAAAAPARAAPAAAPAPAD 493
Score = 32.5 bits (74), Expect = 0.47
Identities = 28/170 (16%), Positives = 35/170 (20%), Gaps = 14/170 (8%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQT 103
+ P P + GPG G P ++
Sbjct: 417 RAVAAAPARRSPAP---EALAAARQASARGPG----GAPAPAPAPAAAPAAAARPAAAGP 469
Query: 104 PMNGYANPSAPQGYTNWGAP-PGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNN 162
A +AP AP P PP W S P
Sbjct: 470 RPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFA------SPAPAQPDAAPAGWVA 523
Query: 163 WNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGT 212
+ P A A AP + P P SA G
Sbjct: 524 ESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGL 573
>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 = 29.8 bits (68), Expect = 0.41
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDP 273
F + G + + +M + +G +RG+ FVT+ + Q L I P
Sbjct: 22 FEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEA----AQRAVKQLHNYEIRP 69
Score = 28.3 bits (64), Expect = 1.4
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
VF+G +P ++ E +L F + G + E+ +M
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLM 34
>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 = 30.1 bits (67), Expect = 0.41
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTF 249
++ FS+YG +I ++ + TG SRG GF+ F
Sbjct: 23 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 54
Score = 27.1 bits (59), Expect = 5.7
Identities = 11/42 (26%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
+++ GLP +T+ +L F++YG+++ I+ + G++R
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV--TGVSR 47
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 32.6 bits (75), Expect = 0.42
Identities = 9/41 (21%), Positives = 13/41 (31%)
Query: 169 QNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
+ P+ GG P GG + +A PA
Sbjct: 389 EGPPSPGGGGGGPPGGGGAPGAPAAAAAPGAAAAAPAAGGP 429
Score = 30.6 bits (70), Expect = 1.5
Identities = 11/38 (28%), Positives = 12/38 (31%)
Query: 168 PQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPA 205
G GG A GA AA + A PA
Sbjct: 393 SPGGGGGGPPGGGGAPGAPAAAAAPGAAAAAPAAGGPA 430
>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 = 30.0 bits (67), Expect = 0.42
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G + E D+R F+ +G++ E I+
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEECRIL 34
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 29.9 bits (67), Expect = 0.43
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 234 KNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
+NN GR +G+ FV F + + +C +T ++GR+I
Sbjct: 32 QNN--GRPKGYAFVEFESAEDAKEALNSCNNTEIEGRSI 68
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM1 of the majority of family members that include
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), heterogeneous
nuclear ribonucleoprotein L (hnRNP-L), heterogeneous
nuclear ribonucleoprotein L-like (hnRNP-LL),
polypyrimidine tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTBP2
is highly homologous to PTB and is perhaps specific to
the vertebrates. Unlike PTB, PTBP2 is enriched in the
brain and in some neural cell lines. It binds more
stably to the downstream control sequence (DCS) RNA than
PTB does but is a weaker repressor of splicing in vitro.
PTBP2 also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. In
addition, this family also includes RNA-binding motif
protein 20 (RBM20) that is an alternative splicing
regulator associated with dilated cardiomyopathy (DCM)
and contains only one RRM. .
Length = 74
Score = 29.9 bits (68), Expect = 0.43
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ L LP +VTE+DL + +GKV V+++
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLL 32
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 29.5 bits (67), Expect = 0.43
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 206 DYSAYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFA 250
DYS ++ FS+YG+V D VV +G V FA
Sbjct: 15 DYSE-----DELRKIFSKYGDVSDVVVSSK-----KKGSAIVEFA 49
>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 = 29.7 bits (67), Expect = 0.45
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
+FS GE+ + + ETG S+GF ++ F
Sbjct: 23 HFSSCGEITRVSIPTDRETGASKGFAYIEFKS 54
>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 = 29.8 bits (67), Expect = 0.46
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
K+ + LP T+ D+RT F+ YG++ V +
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRV 32
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 77
Score = 29.9 bits (67), Expect = 0.46
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 212 TYAQYQQRYFSR-YGEVIDCVVMKNNETGRSRGFGFVTF 249
TY Q Q R +G + C ++ + TG S+G+GFV +
Sbjct: 10 TYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEY 48
>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 = 29.8 bits (68), Expect = 0.47
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRY 314
++++G LP +TE +L FFN+
Sbjct: 3 RLYVGNLPPGITEEELVDFFNQA 25
>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 = 30.1 bits (68), Expect = 0.49
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
+FS+YG ++ V+++ R R + FV F + ++ + T LDGR I
Sbjct: 25 EHFSKYGTLVFVKVLRDW---RQRPYAFVQFTNDDDAKNALAKGQGTILDGRHI 75
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 of MRD1. RBM19, also termed RNA-binding
domain-1 (RBD-1), is a nucleolar protein conserved in
eukaryotes involved in ribosome biogenesis by processing
rRNA and is essential for preimplantation development.
It has a unique domain organization containing 6
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). MRD1 is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well conserved in
yeast and its homologues exist in all eukaryotes. MRD1
is present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 29.5 bits (67), Expect = 0.50
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 298 LPSNVTETDLRTFFNRYGKVMEVVIMSPRTI 328
LP TE +LR F ++G + +++ RTI
Sbjct: 8 LPFGTTEEELRELFEKFGSLGRLLLPPSRTI 38
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 31.8 bits (72), Expect = 0.51
Identities = 30/97 (30%), Positives = 34/97 (35%), Gaps = 10/97 (10%)
Query: 117 YTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPA 176
Y N P P G +Y AP Q G G P G G P G P
Sbjct: 1 YGNMQNYPQAMNPQMGGGNYPAPGQPAQQGYANQGMGGPVGGGG------GPGAGGGAP- 53
Query: 177 AGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTY 213
GGP GG G+ GP G AG+ S + Y
Sbjct: 54 -GGPVGGGGGGSG--GPPGGGEVAGEAEDAMSEFDDY 87
Score = 31.0 bits (70), Expect = 0.87
Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 26 EPRDASNKG-NDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGW 84
E +DA+N +++ NN P GG G MG G G M M MGP GY G
Sbjct: 165 EEQDAANGVRDNVLNNLNNAPGGGGYGGGGGGMGGGGGGG-MGEMGGMGPQGGGGGYGGM 223
Query: 85 GSTPQTQGF 93
G+ Q +
Sbjct: 224 GAPGQGNAY 232
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs) connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 29.5 bits (67), Expect = 0.54
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 294 FLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTI 328
FL LP T+ L FN++ EV ++ R I
Sbjct: 6 FLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRGI 40
>gnl|CDD|217686 pfam03713, DUF305, Domain of unknown function (DUF305). Domain
found in small family of bacterial secreted proteins
with no known function. Also found in Paramecium
bursaria chlorella virus 1. This domain is short and
found in one or two copies. The domain has a conserved
HH motif that may be functionally important. This
domain belongs to the ferritin superfamily. It contains
two sequence similar repeats each of which is composed
of two alpha helices.
Length = 150
Score = 31.1 bits (71), Expect = 0.54
Identities = 9/34 (26%), Positives = 10/34 (29%), Gaps = 4/34 (11%)
Query: 40 NQWGPPQSGGPMAMGPNMGMGTPSGPMAGM-TPM 72
WG P G G M GM +P
Sbjct: 54 EAWGGPPPPSGSGHGGMGGEM---AGMPGMASPA 84
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 32.1 bits (73), Expect = 0.55
Identities = 28/160 (17%), Positives = 40/160 (25%), Gaps = 11/160 (6%)
Query: 51 MAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYAN 110
+A P + G P G+ G + + P A +
Sbjct: 356 LAFEPAVTGG--GAPGGGVPARVAGAVPAPGARAAAAVGASAVPAVTAVTGAAGAALAPK 413
Query: 111 PSAPQGYTNWGAPPGPQAPPQWGSSYGAP-PQQTGYGSYGPTSGAPQSGYGNNWNWNMPQ 169
+A T APP APP + + S +
Sbjct: 414 AAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADS--------RCDE 465
Query: 170 NGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
PA G + A+ A P P A P A A
Sbjct: 466 RDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPA 505
>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 = 32.2 bits (73), Expect = 0.55
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 267 DGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFN 312
+G I P P P Q ++ ++++GG+P E + FFN
Sbjct: 155 EGSIITPLPVLPYQQQATRQAR---RLYVGGIPPEFVEEAVVDFFN 197
Score = 31.4 bits (71), Expect = 0.82
Identities = 31/146 (21%), Positives = 53/146 (36%), Gaps = 51/146 (34%)
Query: 232 VMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN-------------- 277
++K+ TG S+G+ F + DP+ V I L+G+ +
Sbjct: 327 LIKDIATGLSKGYAFCEYKDPSVTDVAI----AALNGKDTGDNKLHVQRACVGANQATID 382
Query: 278 ------PRTLQKPKKNSSFPKVFLGGLPSNVTE--------------------TDLRTFF 311
P TL + S + +GG P+ V + D++T F
Sbjct: 383 TSNGMAPVTLLAKALSQSI--LQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEF 440
Query: 312 NRYGKVMEVVIMSPRTIRAGITRVPT 337
++YG ++ +VI PR R T
Sbjct: 441 SKYGPLINIVI--PRPNG---DRNST 461
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding
protein Raly. This subgroup corresponds to the RRM of
Raly, also termed autoantigen p542, or heterogeneous
nuclear ribonucleoprotein C-like 2, or hnRNP core
protein C-like 2, or hnRNP associated with lethal yellow
protein homolog, an RNA-binding protein that may play a
critical role in embryonic development. It is encoded by
Raly, a ubiquitously expressed gene of unknown function.
Raly shows a high degree of identity with the 5'
sequences of p542 gene encoding autoantigen, which can
cross-react with EBNA-1 of the Epstein Barr virus. Raly
contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes a unique
glycine/serine-rich stretch. .
Length = 76
Score = 29.2 bits (65), Expect = 0.62
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 15/62 (24%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNV-GVVIQNCPHTLDGRTID------P 273
FS+YG V+ C V K G+ FV +++ + G VI L G+T+D P
Sbjct: 23 FSKYGRVVGCSVHK--------GYAFVQYSNERHARGAVIGENGRVLAGQTLDINMAGEP 74
Query: 274 KP 275
KP
Sbjct: 75 KP 76
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 29.6 bits (67), Expect = 0.64
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 221 FSRYGEV--IDCVVMKNN-ETGRSRGFGFVTFA 250
FS+YG++ D + K+ G+ RG+ FVTF
Sbjct: 20 FSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFE 52
>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 = 29.2 bits (66), Expect = 0.65
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVT 248
+ FS +G V + V+++ T + +G+GFVT
Sbjct: 20 QLFSPFGAVTNVKVIRDLTTNKCKGYGFVT 49
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
or Set1 complex component, is encoded by SET1 from the
fission yeast S. pombe. It is essential for the H3
lysine-4 methylation. in vivo, and plays an important
role in telomere maintenance and DNA repair in an ATM
kinase Rad3-dependent pathway. spSet1p is the homology
counterpart of Saccharomyces cerevisiae Set1p (scSet1p).
However, it is more closely related to Set1 found in
mammalian. Moreover, unlike scSet1p, spSet1p is not
required for heterochromatin assembly in fission yeast.
spSet1p contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 86
Score = 29.6 bits (67), Expect = 0.69
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 9/79 (11%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVI-MSPRTIRA-GITRV-----PTQELPVQKE 345
+ + GL T +R F +G++ E + + PRT ++ GI RV P + +
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60
Query: 346 ATAVQQVL--RRSSTTKVQ 362
A A L RR +V+
Sbjct: 61 AKAAVDGLNGRRIGGKRVR 79
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 31.6 bits (72), Expect = 0.73
Identities = 18/80 (22%), Positives = 23/80 (28%), Gaps = 14/80 (17%)
Query: 85 GSTPQTQGFPGQWAPSSQ-------TPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYG 137
P P + S + P +P+ TN PPGP APP
Sbjct: 192 PGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPP------ 245
Query: 138 APPQQTGYGSYGPTSGAPQS 157
PP Q P +
Sbjct: 246 -PPVQQVPPLSTAKPTPPSA 264
>gnl|CDD|227493 COG5164, SPT5, Transcription elongation factor [Transcription].
Length = 607
Score = 31.5 bits (71), Expect = 0.74
Identities = 30/173 (17%), Positives = 42/173 (24%), Gaps = 28/173 (16%)
Query: 55 PNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTP--QTQGFPG-----QWAPSSQTPMNG 107
PN G + A + G G++ TP G W S G
Sbjct: 434 PNYATGGIAAGAAATSSGLSGYRTPGWKDGPKTPALNDPGIDWGDEKDNWYKGSLIHALG 493
Query: 108 YANPSAPQGYTNWGAPPGPQAPPQWGSSYGAP--------PQQTGYGSYGPTSGA----- 154
+ QA S+ P G+ G +G
Sbjct: 494 KGLALEDYRDGLFMTAWKGQATSASEISFVQPRWNNLVCVLDGEKKGTCGILNGINGDWG 553
Query: 155 ---PQSGYGNNWNWNMPQN-----GPTTPAAGGPPAGGATGAAPTGPNPSGPS 199
+S G+ +W M N A G G + N G S
Sbjct: 554 GTVIRSTKGSVVHWPMNDNSKKIYDGGASAWGNQDDGNRSAWQGNKSNYGGNS 606
>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 = 29.0 bits (65), Expect = 0.76
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
FS G V+ ++ + ETG+ +G+GF + D ++N + L+GR +
Sbjct: 19 FSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQL 70
Score = 27.5 bits (61), Expect = 3.3
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
VF+G +P TE L+ F+ G V+ ++ R
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR 34
>gnl|CDD|177328 PHA01929, PHA01929, putative scaffolding protein.
Length = 306
Score = 31.2 bits (70), Expect = 0.82
Identities = 24/84 (28%), Positives = 28/84 (33%), Gaps = 3/84 (3%)
Query: 122 APPGPQAPPQWGSSYGAPPQQTGYGSYGPT-SGAPQSGYGNNWNWNMPQNGPTTPAAGGP 180
A P PQ P P Q G + PQ + ++ Q P PA P
Sbjct: 23 AAPTPQPNPVIQPQAPVQPGQPGAPQQLAIPTQQPQPVPTSAMTPHVVQQAPAQPAPAAP 82
Query: 181 PAGGATGAAPTGPNPSGPSAGKPP 204
PA GA A P P A P
Sbjct: 83 PAAGA--ALPEALEVPPPPAFTPN 104
>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 = 28.8 bits (64), Expect = 0.99
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 232 VMKNNETGRSRGFGFVTFADPNN 254
++ + +TG S+GFGFV F+ +
Sbjct: 29 IVTDRDTGSSKGFGFVDFSSEED 51
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 28.9 bits (65), Expect = 1.0
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYG 315
VF+ LP N TE DL F G
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIG 23
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 28.9 bits (64), Expect = 1.1
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVI 259
F +G V + V+++ T + +GFGFVT + + + I
Sbjct: 22 FGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 28.9 bits (64), Expect = 1.1
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVI 259
F +G V + V+++ T + +GFGFVT + + + I
Sbjct: 24 FGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62
>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 = 28.6 bits (64), Expect = 1.2
Identities = 12/46 (26%), Positives = 24/46 (52%)
Query: 210 YGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNV 255
YG A+ + +F G V ++ + +G +GF ++ F+D +V
Sbjct: 9 YGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 54
>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 = 28.9 bits (64), Expect = 1.2
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVI 259
F +G V + V+++ T + +GFGFVT + + I
Sbjct: 22 FGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60
>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 = 28.6 bits (64), Expect = 1.2
Identities = 8/35 (22%), Positives = 21/35 (60%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
++++G LP ++ D+ F +YG + ++ + + R
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRR 35
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 28.5 bits (63), Expect = 1.3
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEV 320
V+ GG+ S +TE +R F+ +G++MEV
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEV 30
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM3
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 73
Score = 28.4 bits (63), Expect = 1.4
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEV 320
V+ GG+ S +TE +R F+ +G++ME+
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEI 30
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 31.0 bits (71), Expect = 1.4
Identities = 10/63 (15%), Positives = 14/63 (22%)
Query: 143 TGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGK 202
YG + + A PA A A P P+ +A
Sbjct: 34 ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAA 93
Query: 203 PPA 205
Sbjct: 94 AAP 96
Score = 29.1 bits (66), Expect = 5.0
Identities = 19/86 (22%), Positives = 26/86 (30%), Gaps = 13/86 (15%)
Query: 121 GAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGP 180
G+ P A ++ A + P + AP PAA
Sbjct: 39 GSTAAPTAAAAAAAA-AASAPAAAPAAKAPAAPAP------------APPAAAAPAAPPK 85
Query: 181 PAGGATGAAPTGPNPSGPSAGKPPAD 206
PA A AA P+ +A P A
Sbjct: 86 PAAAAAAAAAPAAPPAAAAAAAPAAA 111
Score = 29.1 bits (66), Expect = 5.4
Identities = 14/39 (35%), Positives = 16/39 (41%)
Query: 171 GPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
PT AA A A AAP P+ P+ P A A
Sbjct: 43 APTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPA 81
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The domain,
however, is found in various periplasmic ligand-binding
sensor proteins.
Length = 234
Score = 30.4 bits (69), Expect = 1.4
Identities = 10/43 (23%), Positives = 11/43 (25%)
Query: 111 PSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSG 153
P PP P A P WGS + Y
Sbjct: 91 APRPPPAAPAVQPPAPPARPGWGSGGPSQQGAGQQPGYAQPGP 133
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 28.6 bits (64), Expect = 1.5
Identities = 7/23 (30%), Positives = 16/23 (69%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYG 315
+++ LP + T+ +L ++F +YG
Sbjct: 3 LYISNLPPDTTQLELESWFTQYG 25
>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly
[ADP-ribose] polymerase PARP-10, RNA recognition motif 2
in PARP-14, RNA recognition motif in N-myc-interactor
(Nmi), interferon-induced 35 kDa protein (IFP 35),
RNA-binding protein 43 (RBM43) and similar proteins.
This subfamily corresponds to the RRM1 and RRM2 of
PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi),
interferon-induced 35 kDa protein (IFP 35) and
RNA-binding protein 43 (RBM43). PARP-10 is a novel
oncoprotein c-Myc-interacting protein with
poly(ADP-ribose) polymerase activity. It is localized to
the nuclear and cytoplasmic compartments. In addition to
PARP activity, PARP-10 is also involved in the control
of cell proliferation by inhibiting c-Myc- and
E1A-mediated cotransformation of primary cells. PARP-10
may also play a role in nuclear processes including the
regulation of chromatin, gene transcription, and
nuclear/cytoplasmic transport. PARP-10 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two overlapping C-terminal domains composed of
a glycine-rich region and a region with homology to
catalytic domains of PARP enzymes (PARP domain). In
addition, PARP-10 contains two ubiquitin-interacting
motifs (UIM). PARP-14, also termed aggressive lymphoma
protein 2, is a member of the B aggressive lymphoma
(BAL) family of macrodomain-containing PARPs. Like
PARP-10, PARP-14 also includes two RRMs at the
N-terminus. Nmi, also termed N-myc and STAT interactor,
is an interferon inducible protein that interacts with
c-Myc, N-Myc, Max and c-Fos, and other transcription
factors containing bHLH-ZIP, bHLH or ZIP domains.
Besides binding Myc proteins, Nmi also associates with
all the Stat family of transcription factors except
Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma)
stimulation, Nmi can enhance Stat-mediated
transcriptional activity through recruiting the Stat1
and Stat5 transcriptional coactivators, CREB-binding
protein (CBP) and p300. IFP 35 is an interferon-induced
leucine zipper protein that can specifically form
homodimers. Distinct from known bZIP proteins, IFP 35
lacks a basic domain critical for DNA binding. In
addition, IFP 35 may negatively regulate other bZIP
transcription factors by protein-protein interaction.
For instance, it can form heterodimers with B-ATF, a
member of the AP1 transcription factor family. Both Nmi
and IFP35 harbor one RRM. RBM43 is a putative
RNA-binding protein containing one RRM, but its
biological function remains unclear. .
Length = 74
Score = 28.4 bits (64), Expect = 1.5
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 240 RSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
R +G VTFAD V++ H L+G +
Sbjct: 39 REKGSALVTFADFKVAERVVKQKKHPLNGTQLS 71
>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein
(LMP2) protein. This family consists of several
Gammaherpesvirus latent membrane protein (LMP2)
proteins. Epstein-Barr virus is a human Gammaherpesvirus
that infects and establishes latency in B lymphocytes in
vivo. The latent membrane protein 2 (LMP2) gene is
expressed in latently infected B cells and encodes two
protein isoforms, LMP2A and LMP2B, that are identical
except for an additional N-terminal 119 aa cytoplasmic
domain which is present in the LMP2A isoform. LMP2A is
thought to play a key role in either the establishment
or the maintenance of latency and/or the reactivation of
productive infection from the latent state. The
significance of LMP2B and its role in pathogenesis
remain unclear.
Length = 489
Score = 30.6 bits (69), Expect = 1.5
Identities = 25/98 (25%), Positives = 33/98 (33%), Gaps = 14/98 (14%)
Query: 89 QTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTG---- 144
Q G G + G +NP P + + PGP P + + PP G
Sbjct: 7 QPLGAGGPRSHGGPDGDEGDSNPYYPSSFGSSWDRPGPPVPEDYDAPSHRPPPYGGSNGD 66
Query: 145 -YGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPP 181
+G Y P S Y + QNG G PP
Sbjct: 67 RHGGYQPLGQQDPSLYA-----GLGQNG----GGGLPP 95
Score = 28.3 bits (63), Expect = 7.3
Identities = 16/72 (22%), Positives = 23/72 (31%), Gaps = 9/72 (12%)
Query: 146 GSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPA 205
G+ GP S G + + P P++ G P + PS PP
Sbjct: 10 GAGGPRSHGGPDGDEGD-------SNPYYPSSFGSS--WDRPGPPVPEDYDAPSHRPPPY 60
Query: 206 DYSAYGTYAQYQ 217
S + YQ
Sbjct: 61 GGSNGDRHGGYQ 72
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 30.8 bits (69), Expect = 1.5
Identities = 28/115 (24%), Positives = 32/115 (27%), Gaps = 14/115 (12%)
Query: 86 STPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGY 145
S+ Q Q Q PS Q P PSAP P PPQ P Q
Sbjct: 166 SSAQQQLLQPQGPPSIQVPPGAALAPSAPPP-----TPSAQAVPPQGSPIAAQPAPQPQQ 220
Query: 146 GSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSA 200
S AP PQ P+ P P P+ P +
Sbjct: 221 PSPLSLISAPSLH---------PQRLPSPHPPLQPQTASQQSPQPPAPSSRHPQS 266
>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 = 28.9 bits (65), Expect = 1.6
Identities = 7/32 (21%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 297 GLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
G + +E ++ +F+ +G++ E+ P T
Sbjct: 9 GFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNT 40
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 30.6 bits (69), Expect = 1.7
Identities = 29/176 (16%), Positives = 45/176 (25%), Gaps = 42/176 (23%)
Query: 140 PQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPS 199
P + G T Q + +G ++ P G P PS
Sbjct: 194 PGRRDPGL-DQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPS--- 249
Query: 200 AGKPPADYSAYGTYAQYQQRY-----------------------------FSRYGEVIDC 230
+ Y A A Y F YG V
Sbjct: 250 --RYRPAYEAAP-LAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERV 306
Query: 231 VVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPCNPRTLQKPK 285
MKN + + ADP + + + L G+ + P + +Q P+
Sbjct: 307 KFMKN-----KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPR 357
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 30.5 bits (69), Expect = 1.7
Identities = 24/154 (15%), Positives = 39/154 (25%), Gaps = 20/154 (12%)
Query: 85 GSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPP--GPQAPPQWGSSYGAPPQQ 142
G P+ P P++ + A S ++ A P A G+
Sbjct: 372 GRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDP 431
Query: 143 TGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGK 202
P S APQ+ Q P + P+ P A +
Sbjct: 432 PAAVPVNPPSTAPQAV-------RPAQFKEEKK----IPVSKVSSLGPSTLRPIQEKAEQ 480
Query: 203 PPADYSAYGTYAQYQ-------QRYFSRYGEVID 229
+ T Q + Q Y+ +
Sbjct: 481 ATGNIKEAPTGTQKEIFTEEDLQYYWQEFAGTRP 514
>gnl|CDD|227665 COG5373, COG5373, Predicted membrane protein [Function unknown].
Length = 931
Score = 30.6 bits (69), Expect = 1.7
Identities = 24/109 (22%), Positives = 27/109 (24%), Gaps = 18/109 (16%)
Query: 96 QWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAP 155
+ G A P A AP + A P+ P
Sbjct: 31 ELRELRSLVAEGAAGPVAKAAEQMAAPEAAEAAPLPAAAESIASPEVPPPVPPAP----- 85
Query: 156 QSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPP 204
Q G PAA P A A AAP P PS P
Sbjct: 86 ------------AQEGEA-PAAEQPSAVPAPSAAPAPAEPVEPSLAANP 121
>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 = 28.2 bits (63), Expect = 1.8
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G L TE D+R F +G + E I+
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEECTIL 34
>gnl|CDD|187682 cd09624, DOMON_b558_566, DOMON-like heme-binding domain of CbsA.
This family, conserved in some lineages of the
Crenarchaeota, represents a mono-heme cytochrome
b558/566. CbsA is reported to be a subunit in a
heterodimeric complex (CbsA-CbsB in Sulfolobus species),
and appears to be glycosylated.
Length = 279
Score = 30.0 bits (67), Expect = 2.0
Identities = 23/94 (24%), Positives = 30/94 (31%), Gaps = 5/94 (5%)
Query: 125 GPQAPPQWGSSYGAPPQQTGYGSYGPT--SGAPQSGYGNNWNWNMPQNGPTTPAAGGPPA 182
G P + G P G G T S A +G W WN T +G P
Sbjct: 141 GSVPPTSDTMNIGTPHMMPGTSGDGITGGSLAQSAGQAEIWMWNSNPRANNTQDSGYP-- 198
Query: 183 GGATGAAPTGPNPSGPSAGKPPADYSAYGTYAQY 216
GAT T P P + G + + +
Sbjct: 199 -GATWFNRTSPPPYFVATGATYENGYWIVEFVRP 231
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 28.1 bits (62), Expect = 2.0
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 295 LGGLPSNVTETDLRTFFNRYG 315
L +P +VTE DLRT F G
Sbjct: 8 LSNIPQSVTEEDLRTLFANTG 28
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 87
Score = 28.1 bits (62), Expect = 2.3
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 232 VMKNNETGRSRGFGFVTFADPNNVGVVIQ-----NCPHTLDGRTI 271
V+K+ +T +RGF F+ + ++Q + P ++DG+TI
Sbjct: 36 VIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLSIDGKTI 80
>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 = 27.6 bits (61), Expect = 2.4
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+VF+G +P +V E +L F G++ E+ +M
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRIYEMRLM 34
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 86
Score = 28.1 bits (62), Expect = 2.4
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVI 259
F +G V + V+++ T + +GFGFVT + + + I
Sbjct: 24 FGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62
>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 = 27.6 bits (61), Expect = 2.4
Identities = 11/42 (26%), Positives = 22/42 (52%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC 262
F + G + D +M + +G++RG+ F+TF ++ C
Sbjct: 22 FEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both, nuclear and
cytoplasmic, roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 27.7 bits (62), Expect = 2.6
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 291 PKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
P V + GLP VTE DL + +G + V +M
Sbjct: 3 PVVHVRGLPDGVTEADLVEALSEFGPISYVTMM 35
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 27.4 bits (61), Expect = 2.7
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
++++ P + +E+ +R F+ YG V EV ++S
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMIS 33
>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 = 28.1 bits (62), Expect = 2.7
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ 260
F +G V+ V + +T S+ FGFV++ +P + IQ
Sbjct: 28 FMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 67
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 27.7 bits (62), Expect = 2.8
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKV 317
+++ GLP +VTE L F G +
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGII 25
>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 = 27.3 bits (61), Expect = 2.8
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 294 FLGGLPSNVTETDLRTFF 311
+LG LP +VTE D++ FF
Sbjct: 5 YLGNLPYDVTEEDIKEFF 22
>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 = 27.7 bits (61), Expect = 2.8
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 232 VMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLD--GRTI-----DPKP 275
+M+N +G+SRGF FV F + ++ H+L G+ + DPKP
Sbjct: 35 LMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLMILGQKVSMHYSDPKP 85
>gnl|CDD|237015 PRK11901, PRK11901, hypothetical protein; Reviewed.
Length = 327
Score = 29.7 bits (67), Expect = 3.1
Identities = 29/127 (22%), Positives = 37/127 (29%), Gaps = 27/127 (21%)
Query: 100 SSQTPMNGYANPSAPQGYTNWGAPPGPQ---APPQWGSSYGAPPQQTGYGSY-------- 148
+Q+ + N S + PQ APP + A P QT G
Sbjct: 90 GNQSSPSAANNTSDGHDASGVKNTAPPQDISAPPISPTPTQAAPPQTPNGQQRIELPGNI 149
Query: 149 --------GPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPN--PSGP 198
G + A Q+ GN PT PA P G A P P
Sbjct: 150 SDALSQQQGQVNAASQNAQGNT------STLPTAPATVAPSKGAKVPATAETHPTPPQKP 203
Query: 199 SAGKPPA 205
+ KP
Sbjct: 204 ATKKPAV 210
>gnl|CDD|177553 PHA03185, PHA03185, UL14 tegument protein; Provisional.
Length = 214
Score = 29.2 bits (65), Expect = 3.3
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 168 PQNGPT-TPAAGGPPAGGATGA-APTGPNPSGPSAG 201
P + PT P AGG P GGA P P P+ P++
Sbjct: 168 PGSRPTSGPVAGGLPGGGAPAPPTPPRPGPTDPASE 203
>gnl|CDD|163257 TIGR03425, urea_degr_2, urea carboxylase-associated protein 2. A
number of bacteria degrade urea as a nitrogen source by
the urea carboxylase/allophanate hydrolase pathway,
which uses biotin and consumes ATP, rather than my means
of the nickel-dependent enzyme urease. This model
represents one of a pair of homologous, tandem
uncharacterized genes found together with the urea
carboxylase and allophanate hydrolase genes.
Length = 233
Score = 29.2 bits (66), Expect = 3.3
Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 238 TGRSRGFGFVTFADPNNVGVVIQNCPHTLDGR-TIDPKP 275
GRS +V + VV+ NCPH LD R PKP
Sbjct: 159 PGRSGAGDYVDLRAEMDTLVVLSNCPHPLDPRPDYQPKP 197
>gnl|CDD|227538 COG5213, FIP1, Polyadenylation factor I complex, subunit FIP1 [RNA
processing and modification].
Length = 266
Score = 28.9 bits (64), Expect = 3.9
Identities = 22/98 (22%), Positives = 30/98 (30%), Gaps = 7/98 (7%)
Query: 16 LLQQVEIKKAEPRDASNKGNDMGNNQWGPPQSGGPMAMGPNMGMG-TPSGPMAGMTPMGP 74
LLQQ + N+G + +G GMG P+GP P
Sbjct: 174 LLQQQGELNSGNDRDFNEGKIDDDGDGPNGANGSNDNGNMGNGMGGRPNGPAGPKEPSFG 233
Query: 75 GNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPS 112
G M G P + +Q P +G S
Sbjct: 234 GLGMFG----DFEPFP--YEEMGPGMNQGPNDGGKQNS 265
>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 = 3.9
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYG--KVMEVVIMSPRTIRAGITR 334
+ L GLP N+TE D+R + + +V +M +T G++R
Sbjct: 8 IMLRGLPINITENDIRELIESFEGPQPADVRLMKRKT---GVSR 48
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 29.3 bits (66), Expect = 4.0
Identities = 21/73 (28%), Positives = 26/73 (35%), Gaps = 5/73 (6%)
Query: 152 SGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTG----PNPSGPSAGKPPADY 207
GAP + W P P A PP A A P P P+ P+A PPA
Sbjct: 379 RGAP-APPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPARS 437
Query: 208 SAYGTYAQYQQRY 220
+ A R+
Sbjct: 438 ADPAAAASAGDRW 450
Score = 28.2 bits (63), Expect = 9.5
Identities = 17/97 (17%), Positives = 23/97 (23%), Gaps = 21/97 (21%)
Query: 121 GAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPT-TPAAGG 179
GAP P WG+ A P P + AP P A
Sbjct: 380 GAPAPP--SAAWGAPTPAAPAAP------PPAAAP------------PVPPAAPARPAAA 419
Query: 180 PPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTYAQY 216
PA A P + + + +
Sbjct: 420 RPAPAPAPPAAAAPPARSADPAAAASAGDRWRAFVAF 456
>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein.
Length = 753
Score = 29.4 bits (66), Expect = 4.1
Identities = 18/83 (21%), Positives = 23/83 (27%), Gaps = 11/83 (13%)
Query: 121 GAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGP 180
G P P P ++ A P + G P + P P GGP
Sbjct: 655 GGPGVPGPVPVGMPAHTARPSRVARG--DPVRPTAH---------HAALRAPQAPRPGGP 703
Query: 181 PAGGATGAAPTGPNPSGPSAGKP 203
P GG P + A
Sbjct: 704 PGGGGGLPPPPDLPAAAGPAPCG 726
>gnl|CDD|109783 pfam00739, X, Trans-activation protein X. This protein is found in
hepadnaviruses where it is indispensable for
replication.
Length = 142
Score = 28.0 bits (62), Expect = 4.3
Identities = 10/26 (38%), Positives = 11/26 (42%)
Query: 187 GAAPTGPNPSGPSAGKPPADYSAYGT 212
GA G GPS G P + SA
Sbjct: 22 GAESRGRPVPGPSGGLPSSPASAVSA 47
>gnl|CDD|221143 pfam11593, Med3, Mediator complex subunit 3 fungal. Mediator is a
large complex of up to 33 proteins that is conserved
from plants to fungi to humans - the number and
representation of individual subunits varying with
species. It is arranged into four different sections, a
core, a head, a tail and a kinase-activity part, and the
number of subunits within each of these is what varies
with species. Overall, Mediator regulates the
transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Mediator subunit
Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast
transcriptional co-repressor.
Length = 381
Score = 29.2 bits (65), Expect = 4.4
Identities = 18/77 (23%), Positives = 24/77 (31%), Gaps = 3/77 (3%)
Query: 43 GPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQ 102
P + PN M +P + M+PM N M G + S +
Sbjct: 245 PTPLMQLLNGVSPNNAMASP---LNNMSPMRNLNQMGNQNNGGQMTPSANNGNMNNQSRE 301
Query: 103 TPMNGYANPSAPQGYTN 119
MN PSA N
Sbjct: 302 NSMNQGMTPSASMINLN 318
>gnl|CDD|218994 pfam06333, Med13_C, Mediator complex subunit 13 C-terminal.
Mediator is a large complex of up to 33 proteins that is
conserved from plants through fungi to humans - the
number and representation of individual subunits varying
with species. It is arranged into four different
sections, a core, a head, a tail and a kinase-activity
part, and the number of subunits within each of these is
what varies with species. Overall, Mediator regulates
the transcriptional activity of RNA polymerase II but it
would appear that each of the four different sections
has a slightly different function. Med13 is part of the
ancillary kinase module, together with Med12, CDK8 and
CycC, which in yeast is implicated in transcriptional
repression, though most of this activity is likely
attributable to the CDK8 kinase. The large Med12 and
Med13 proteins are required for specific developmental
processes in Drosophila, zebrafish, and Caenorhabditis
elegans but their biochemical functions are not
understood.
Length = 406
Score = 29.2 bits (66), Expect = 4.4
Identities = 14/75 (18%), Positives = 19/75 (25%), Gaps = 1/75 (1%)
Query: 62 PSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWG 121
+ P P + STPQ+ PS N P G N
Sbjct: 227 TDPKLVPDPPTQPIPFSRFNTSNSSTPQSTPCTLS-FPSPDQFGNAPTPPLGENGNDNAP 285
Query: 122 APPGPQAPPQWGSSY 136
P +P +
Sbjct: 286 PVTPPGSPSESDPDS 300
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 29.0 bits (65), Expect = 4.7
Identities = 10/38 (26%), Positives = 12/38 (31%)
Query: 172 PTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
P T AG P A A+ A +A S
Sbjct: 5 PATEDAGRPAAPAASDDAAATDGAGANAAAPAAPAESD 42
>gnl|CDD|171499 PRK12438, PRK12438, hypothetical protein; Provisional.
Length = 991
Score = 29.1 bits (65), Expect = 4.9
Identities = 18/58 (31%), Positives = 20/58 (34%), Gaps = 1/58 (1%)
Query: 150 PTSGAPQSGYGNNWNWNMPQN-GPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPAD 206
T G + GY + Q GP T P G A A P G P P PP
Sbjct: 874 RTEGGVRVGYAPTLAEALDQVFGPGTGRVATAPGGDAASAPPPGAGPPAPPQAVPPPR 931
>gnl|CDD|177614 PHA03377, PHA03377, EBNA-3C; Provisional.
Length = 1000
Score = 29.3 bits (65), Expect = 5.1
Identities = 24/59 (40%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 80 GYQG-WGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYG 137
GY G WG Q + WA SQ P G+ +P P W AP P PPQW S G
Sbjct: 792 GYAGPWGLRAQHPRYRHSWAYWSQYP--GHGHPQGP-----W-APRPPHLPPQWDGSAG 842
Score = 28.9 bits (64), Expect = 6.0
Identities = 20/58 (34%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 99 PSSQTPMNGYANPSAPQG-YTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAP 155
PS Q P +G+ P A Q Y + P PQAP Y P Q S P P
Sbjct: 742 PSHQAPYSGHEEPQAQQAPYPGYWEPRPPQAPYL---GYQEPQAQGVQVSSYPGYAGP 796
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM3
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 72
Score = 26.6 bits (59), Expect = 5.2
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 298 LPSNVTETDLRTFFNRYGKVMEVVIMSPRTI 328
P T +LR F +GK+ V++ TI
Sbjct: 8 FPYGTTAEELRDLFEPHGKLTRVLMPPAGTI 38
>gnl|CDD|221459 pfam12200, DUF3597, Domain of unknown function (DUF3597). This
family of proteins is found in bacteria, eukaryotes and
viruses. Proteins in this family are typically between
126 and 281 amino acids in length. The function of this
domain is unknown. The structure of this domain has been
found to contain five helices with a long flexible loop
between helices one and two.
Length = 124
Score = 27.7 bits (62), Expect = 5.6
Identities = 8/29 (27%), Positives = 9/29 (31%)
Query: 168 PQNGPTTPAAGGPPAGGATGAAPTGPNPS 196
P A P A A A T P +
Sbjct: 16 AAPAPAAAPATAPAAAAAAAPAATPPAAA 44
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4, an
RNA-binding protein that is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. DND1 interacts specifically
with apolipoprotein B editing complex 3 (APOBEC3), a
multi-functional protein inhibiting retroviral
replication. The DND1-APOBEC3 interaction may play a
role in maintaining viability of germ cells and for
preventing germ cell tumor development. DND1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 26.7 bits (59), Expect = 5.8
Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 16/66 (24%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM----------------SPRTIRAGITRV 335
+VF+G +P +V E L F G + E +M R A I +
Sbjct: 3 EVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATL 62
Query: 336 PTQELP 341
ELP
Sbjct: 63 HNYELP 68
>gnl|CDD|215618 PLN03184, PLN03184, chloroplast Hsp70; Provisional.
Length = 673
Score = 28.7 bits (64), Expect = 5.9
Identities = 8/28 (28%), Positives = 11/28 (39%)
Query: 170 NGPTTPAAGGPPAGGATGAAPTGPNPSG 197
N P AG P G A ++ + G
Sbjct: 636 NQPGAGGAGPAPGGEAGSSSSSSSGGDG 663
>gnl|CDD|183756 PRK12799, motB, flagellar motor protein MotB; Reviewed.
Length = 421
Score = 28.5 bits (63), Expect = 6.0
Identities = 22/139 (15%), Positives = 38/139 (27%), Gaps = 19/139 (13%)
Query: 56 NMGMGTPSGPMAGMTPMGPGNMMQGYQGWG---STPQTQGFPGQWAPSSQTPMNGYANPS 112
+ + P+A +TP +P ++ T + A S
Sbjct: 292 QIDT-HGTVPVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSVTTQSATTTQASAVALSS 350
Query: 113 APQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGP 172
A ++ P P + P T ++ + N NGP
Sbjct: 351 AGVLPSDVTLPGTVALPAAEPVNMQPQPMST-----------TETQQSSTGNITSTANGP 399
Query: 173 TTPAAGGPPAGGATGAAPT 191
TT PA A+ +
Sbjct: 400 TTSL----PAAPASNIPVS 414
>gnl|CDD|235076 PRK02842, PRK02842, light-independent protochlorophyllide reductase
subunit N; Provisional.
Length = 427
Score = 28.3 bits (64), Expect = 7.8
Identities = 19/79 (24%), Positives = 28/79 (35%), Gaps = 13/79 (16%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYG-KVMEVVIMSPRTIRAGITRVP-----TQELPVQKEA 346
V +G L +V E L F + G V+ + R T +P T Q
Sbjct: 170 VLVGSLA-DVVEDQLTLEFKKLGIGVVGF--LPARR----FTELPAIGPGTVVALAQPFL 222
Query: 347 TAVQQVLRRSSTTKVQAPF 365
+ + LR + APF
Sbjct: 223 SDTARALRERGAKVLTAPF 241
>gnl|CDD|220708 pfam10349, WWbp, WW-domain ligand protein. The WWbp domain is
characterized by several short PY and PT-like motifs of
the PPPPY form. These appear to bind directly to the WW
domains of WWP1 and WWP2 and other such diverse proteins
as dystrophin and YAP (Yes-associated protein). This is
the WW-domain binding protein WWbp via PY and PY_like
motifs. The presence of a phosphotyrosine residue in the
pWBP-1 peptide abolishes WW domain binding which
suggests a potential regulatory role for tyrosine
phosphorylation in modulating WW domain-ligand
interactions. Given the likelihood that WWP1 and WWP2
function as E3 ubiquitin-protein ligases, it is possible
that initial substrate-specific recognition occurs via
WW domain-substrate protein interaction followed by
ubiquitin transfer and subsequent proteolysis. This
domain lies just downstream of the GRAM (pfam02893) in
many members.
Length = 111
Score = 27.0 bits (60), Expect = 8.6
Identities = 12/70 (17%), Positives = 18/70 (25%), Gaps = 5/70 (7%)
Query: 91 QGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGP 150
+ P P Y + Y + APP PP P Y + P
Sbjct: 36 RAQPVSRESGYYPPPGAYVHLEPLPAYGQYAAPPPYGPPP-----PYYPAPPGVYPTPPP 90
Query: 151 TSGAPQSGYG 160
+ +
Sbjct: 91 PNSGYMADPQ 100
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 28.0 bits (63), Expect = 9.1
Identities = 20/110 (18%), Positives = 27/110 (24%), Gaps = 18/110 (16%)
Query: 123 PPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPA 182
PPQ P P P P P T A
Sbjct: 520 TAKTPPPPQ------KSPPP-------PAPTPPLPQPTATAPPPTPPPPPPTATQASSNA 566
Query: 183 GGATGAAPTGPNPSGPSAGKPPADYSAYGTYAQYQQR---YFSRYGEVID 229
A + P P P S+ + + +F+ GE+ID
Sbjct: 567 PAQIPADSSPPPPIPEEPTPSPTKDSSPEEIDKAAKNLADFFN--GEIID 614
>gnl|CDD|219833 pfam08418, Pol_alpha_B_N, DNA polymerase alpha subunit B
N-terminal. This is the eukaryotic DNA polymerase alpha
subunit B N-terminal domain which is involved in complex
formation. Also see pfam04058.
Length = 239
Score = 27.7 bits (62), Expect = 9.7
Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 3/62 (4%)
Query: 170 NGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPP-ADYSAYGTYAQYQQRYFSRYGEVI 228
+TP + + + P++ P A + A++ R S GEV+
Sbjct: 103 RILSTPELPKRKRSFSASSLESPSLFFSPASFSPSAAPSTPSPNSAKFSSR--SNPGEVV 160
Query: 229 DC 230
+
Sbjct: 161 ET 162
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
0.312 0.132 0.420
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,117,427
Number of extensions: 1919448
Number of successful extensions: 3323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2719
Number of HSP's successfully gapped: 699
Length of query: 388
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 289
Effective length of database: 6,546,556
Effective search space: 1891954684
Effective search space used: 1891954684
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 60 (27.1 bits)