RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15187
(298 letters)
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 102 bits (256), Expect = 8e-28
Identities = 45/96 (46%), Positives = 60/96 (62%), Gaps = 21/96 (21%)
Query: 142 PKGGNTIFVQGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCA 201
P+ GNT++V G G++EE L++ FS FG I ++SME EK GFVTF+
Sbjct: 1 PRKGNTLYVHGYGLTEEILKKAFSPFGNIINISMEKEKNCGFVTFEK------------- 47
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
ES+D+AI E+NGT VQGV+LKVSLAR+
Sbjct: 48 --------MESADRAIAELNGTTVQGVQLKVSLARK 75
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 59.5 bits (145), Expect = 8e-12
Identities = 31/92 (33%), Positives = 43/92 (46%), Gaps = 25/92 (27%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDC 200
T+FV +EE LR+ FS FGK+ SV + E K +GF
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGF----------------- 43
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
FV F+S E ++KA+ +NG + G LKV
Sbjct: 44 --AFVEFESEEDAEKALEALNGKELDGRPLKV 73
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 56.9 bits (138), Expect = 9e-11
Identities = 35/87 (40%), Positives = 44/87 (50%), Gaps = 22/87 (25%)
Query: 154 GISEEFLRQHFSIFGKICSVS-MEVEKG--RGFVTFDSPESSDKAITDDCARGFVTFDSP 210
I +E LR+ FS FG I S M EKG +GF GFV F SP
Sbjct: 12 SIDDERLREEFSPFGTITSAKVMTDEKGRSKGF-------------------GFVCFSSP 52
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLARR 237
E + KA+TE+NG + G L V+LA+R
Sbjct: 53 EEATKAVTEMNGRIIGGKPLYVALAQR 79
>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 = 54.5 bits (132), Expect = 5e-10
Identities = 33/99 (33%), Positives = 48/99 (48%), Gaps = 25/99 (25%)
Query: 145 GNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPESSDKAITD 198
GN +FV G +E+ L FS FG++ + + E G RGF
Sbjct: 1 GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGF--------------- 45
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFVTF+S E +D AI ++NG ++G +KV A+R
Sbjct: 46 ----GFVTFESVEDADAAIRDLNGKELEGRVIKVEKAKR 80
>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 = 54.2 bits (131), Expect = 6e-10
Identities = 32/91 (35%), Positives = 45/91 (49%), Gaps = 24/91 (26%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSM---EVEKGRGFVTFDSPESSDKAITDDCAR 202
+FV +EE LR+ FS FG+I SV + + K +GF
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGF------------------- 41
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
FV F+SPE ++KA+ +NG + G KLKVS
Sbjct: 42 AFVEFESPEDAEKALEALNGKELDGRKLKVS 72
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 48.4 bits (116), Expect = 9e-08
Identities = 29/89 (32%), Positives = 42/89 (47%), Gaps = 23/89 (25%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
T++V G++EE L++ FS FG I V V K +G+ F
Sbjct: 2 TVYVGNLPHGLTEEELQRTFSPFGAIEEV--RVFKDKGY-------------------AF 40
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVS 233
V FD+ E++ AI VNGT + G +K S
Sbjct: 41 VRFDTHEAAATAIVAVNGTSINGQTVKCS 69
>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 = 47.6 bits (114), Expect = 1e-07
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 23/78 (29%)
Query: 160 LRQHFSIFGKICSVSMEVEK----GRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDK 215
L Q F+ FG + S + V+K + F GFV++D+PES+
Sbjct: 15 LYQLFAPFGNVISAKVFVDKNTGQSKCF-------------------GFVSYDNPESAQA 55
Query: 216 AITEVNGTHVQGVKLKVS 233
AI +NG V G +LKV
Sbjct: 56 AIKAMNGFQVGGKRLKVQ 73
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 47.6 bits (114), Expect = 2e-07
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 24/89 (26%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSM---EVEKGRGFVTFDSPESSDKAITDDCAR 202
+FV +EE L+ FS FG I S+ + E + +GF
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGF------------------- 41
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLK 231
FV F+ E ++KA+ +NG + G +L+
Sbjct: 42 AFVEFEDEEDAEKALEALNGKELGGRELR 70
>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 = 52.1 bits (125), Expect = 2e-07
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 22/88 (25%)
Query: 154 GISEEFLRQHFSIFGKICSVSM---EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
+++E LR+ FS G+I S + E RGF GFV F +P
Sbjct: 296 TVTDEKLRELFSECGEITSAKVMLDEKGVSRGF-------------------GFVCFSNP 336
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLARRQ 238
E +++A+TE++G + G L V+LA+R+
Sbjct: 337 EEANRAVTEMHGRMLGGKPLYVALAQRK 364
Score = 41.7 bits (98), Expect = 3e-04
Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 18/92 (19%)
Query: 152 GAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
++E+ LR+ F+ FG+I S ++ + F FV F+ E
Sbjct: 187 DPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGF----------------AFVNFEKHE 230
Query: 212 SSDKAITEVNGTHVQGVKL--KVSLARRQLKV 241
+ KA+ E+NG + K K+ + R Q +
Sbjct: 231 DAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRA 262
Score = 36.3 bits (84), Expect = 0.017
Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 24/101 (23%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVE-KGRGFVTFDSPES 191
P+ + G IFV+ + + L FS FG I C V+ + K RG+
Sbjct: 80 DPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGY-------- 131
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
GFV F+ ES+ AI +VNG + ++ V
Sbjct: 132 -----------GFVHFEKEESAKAAIQKVNGMLLNDKEVYV 161
Score = 27.5 bits (61), Expect = 9.4
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKAI 196
++E L F FG + SV + + G G+V F +P +++A+
Sbjct: 12 VTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERAL 59
>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 = 47.3 bits (113), Expect = 2e-07
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
T+FV G ++E+ LR F FG+I V + KG GFV F +++ AI
Sbjct: 3 TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAI 54
>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 = 45.7 bits (109), Expect = 8e-07
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 23/85 (27%)
Query: 156 SEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
+EE L+ F FG++ S + E + RGF GFV ++ E
Sbjct: 12 TEEDLKDLFGQFGEVTSARVITDRETGRSRGF-------------------GFVEMETAE 52
Query: 212 SSDKAITEVNGTHVQGVKLKVSLAR 236
++ AI ++NGT G L V+ AR
Sbjct: 53 EANAAIEKLNGTDFGGRTLTVNEAR 77
>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 = 45.5 bits (108), Expect = 9e-07
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 21/78 (26%)
Query: 160 LRQHFSIFGKICSVSMEV-EKG-RGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAI 217
LRQ F FG I V + E+G +GF GFVTF + +D+A
Sbjct: 17 LRQMFGQFGPILDVEIIFNERGSKGF-------------------GFVTFANSADADRAR 57
Query: 218 TEVNGTHVQGVKLKVSLA 235
+++GT V+G K++V+ A
Sbjct: 58 EKLHGTVVEGRKIEVNNA 75
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKAI 196
+FV G ++EE LR++FS +G + SV + +K G FVTFD + DK +
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58
>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 = 44.4 bits (106), Expect = 1e-06
Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 20/76 (26%)
Query: 160 LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITE 219
L + FS FG + + + +K FV F + E+++KA+
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPG--------------------FAFVEFSTEEAAEKAVQY 40
Query: 220 VNGTHVQGVKLKVSLA 235
+NG G L+V +
Sbjct: 41 LNGVLFGGRPLRVDYS 56
>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 = 45.0 bits (106), Expect = 1e-06
Identities = 18/45 (40%), Positives = 29/45 (64%)
Query: 152 GAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+G++E+ +RQ FS FG+I + + EKG F+ F + ES+ AI
Sbjct: 9 ASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAI 53
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 44.8 bits (107), Expect = 1e-06
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+ L +HFS FG I ++ + V F + E + KA
Sbjct: 15 NITKLNEHFSKFGTIVNIQVNYNPESALVQFSTSEEAKKAY 55
>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 = 45.0 bits (107), Expect = 2e-06
Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSM-----EVEKGRGFVTFDSPESSDKAITD 198
N IFV G +EE LR FS FG + V + V KG GFVTF++ E ++K +
Sbjct: 3 NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAM 62
Query: 199 D 199
Sbjct: 63 G 63
>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 = 2e-06
Identities = 25/93 (26%), Positives = 38/93 (40%), Gaps = 17/93 (18%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
T+FV+ ++E L + FS G I R FV D + G+
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPI---------KRCFVVKDKGSKKCRGF------GY 45
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
VTF E + +A+ E T G K+ V A++
Sbjct: 46 VTFALEEDAKRALEEKKKTKFGGRKIHVEFAKK 78
>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 = 44.1 bits (105), Expect = 2e-06
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 22/76 (28%)
Query: 160 LRQHFSIFGKI--CSVSM-EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKA 216
L FS FG I C V+ E +G+ GFV F++ E++ +A
Sbjct: 19 LYDTFSAFGNILSCKVATDENGGSKGY-------------------GFVHFETEEAAVRA 59
Query: 217 ITEVNGTHVQGVKLKV 232
I +VNG + K+ V
Sbjct: 60 IEKVNGMLLNDKKVFV 75
>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 = 44.3 bits (105), Expect = 3e-06
Identities = 21/81 (25%), Positives = 32/81 (39%), Gaps = 15/81 (18%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+++E LR F G I S + D+ GFV + +
Sbjct: 12 MTQEELRSLFEAIGPIESCKI---------------VRDRITGQSLGYGFVDYVDENDAQ 56
Query: 215 KAITEVNGTHVQGVKLKVSLA 235
KAI +NG ++ +LKVS A
Sbjct: 57 KAINTLNGFEIRNKRLKVSYA 77
>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 = 43.9 bits (103), Expect = 4e-06
Identities = 22/52 (42%), Positives = 34/52 (65%), Gaps = 2/52 (3%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
T++ G +G++E+ +RQ FS FG+I V + +KG FV F+S ES+ AI
Sbjct: 2 TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAI 53
>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 = 42.2 bits (100), Expect = 1e-05
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 23/84 (27%)
Query: 154 GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDS 209
I+E+ LR F FG+I V + E + +G+ GF+ F
Sbjct: 9 NITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGY-------------------GFIQFAD 49
Query: 210 PESSDKAITEVNGTHVQGVKLKVS 233
E + KA+ ++NG + G +KV
Sbjct: 50 AEDAKKALEQLNGFELAGRPIKVG 73
>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 = 42.1 bits (99), Expect = 1e-05
Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 23/84 (27%)
Query: 156 SEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
+E+ L Q FS +G+I V + E ++ RGF GFVTF++P+
Sbjct: 13 NEQSLEQVFSKYGQISEVVVVKDRETQRSRGF-------------------GFVTFENPD 53
Query: 212 SSDKAITEVNGTHVQGVKLKVSLA 235
+ A+ +NG V G +++V A
Sbjct: 54 DAKDAMMAMNGKSVDGRQIRVDQA 77
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM1 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 76
Score = 42.0 bits (99), Expect = 2e-05
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 25/95 (26%)
Query: 147 TIFVQGAG--ISEEFLRQHFSIFGKI--CSVSMEVEKGR--GFVTFDSPESSDKAITDDC 200
T+FV + +E+L+ F FG + V + E GR GF
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGF----------------- 43
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
G+V F+SPE + KAI ++G + G + V +
Sbjct: 44 --GYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 41.5 bits (98), Expect = 2e-05
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE-KGRGFVTFDSPESSDKAITDD 199
++EE LRQ+FS FG++ V + + FVTF PE + +D
Sbjct: 12 MTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQSLCGED 57
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 41.5 bits (98), Expect = 2e-05
Identities = 20/51 (39%), Positives = 34/51 (66%), Gaps = 2/51 (3%)
Query: 147 TIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
T++V G G ++E+ LR HF FG+I S+++ + FVTF + E+++KA
Sbjct: 3 TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKA 53
>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 = 41.4 bits (98), Expect = 2e-05
Identities = 30/92 (32%), Positives = 45/92 (48%), Gaps = 24/92 (26%)
Query: 152 GAGISEEFLRQHFSIFGKICSVS-MEVEKG--RGFVTFDSPESSDKAITDDCARGFVTFD 208
G + +E L++ F +GKI S M+ ++G +GF GFV F+
Sbjct: 10 GEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGF-------------------GFVNFE 50
Query: 209 SPESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
+ E++ KA+ E+NG V G KL V R Q K
Sbjct: 51 NHEAAQKAVEELNGKEVNGKKLYV--GRAQKK 80
>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 = 41.1 bits (97), Expect = 3e-05
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 23/76 (30%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVEK----GRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
+EE LR+ F FG+I V + ++K +GF FV+F PE
Sbjct: 12 TEEELRELFEAFGEISEVHLPLDKETKRSKGF-------------------AFVSFMFPE 52
Query: 212 SSDKAITEVNGTHVQG 227
+ KA +E++G+ QG
Sbjct: 53 HAVKAYSELDGSIFQG 68
>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 = 41.3 bits (97), Expect = 3e-05
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 15/82 (18%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESS 213
++++ +R FS G+I S + DK GFV + PE +
Sbjct: 12 NMTQDEIRSLFSSIGEIESCKL---------------IRDKVTGQSLGYGFVNYVDPEDA 56
Query: 214 DKAITEVNGTHVQGVKLKVSLA 235
+KAI +NG +Q +KVS A
Sbjct: 57 EKAINTLNGLRLQNKTIKVSYA 78
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 40.5 bits (95), Expect = 5e-05
Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 8/56 (14%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKA 195
IFV G A +E+ ++++FS FGK+ + +K G GFVTF+S + DK
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 40.3 bits (95), Expect = 6e-05
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 12/59 (20%)
Query: 148 IFVQGAGIS----EEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAI 196
+F+ G+S EE LR++FS +G++ C + + GR GFVTF P S DK +
Sbjct: 1 LFI--GGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVL 57
>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 = 40.3 bits (95), Expect = 6e-05
Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 22/84 (26%)
Query: 155 ISEEFLRQHFSIFGKICSVSM---EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
+E L++ FS FG + V++ K +GF FV F S
Sbjct: 11 CTEADLKKLFSPFGFVWEVTIPRKPDGKKKGF-------------------AFVQFTSKA 51
Query: 212 SSDKAITEVNGTHVQGVKLKVSLA 235
++KAI VNG ++G + V A
Sbjct: 52 DAEKAIKGVNGKKIKGRPVAVDWA 75
>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 = 40.3 bits (95), Expect = 6e-05
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 19/83 (22%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDD---CARGFVTFDSPE 211
+ E+ LR FS FG++ S+ + P+ D+ A FVTF
Sbjct: 12 LDEDDLRGIFSKFGEVESIRI-------------PKKQDEKQGRLNNGFA--FVTFKDAS 56
Query: 212 SSDKAITEVNGTHVQGVKLKVSL 234
S++ A+ ++NGT + G K+ VSL
Sbjct: 57 SAENAL-QLNGTELGGRKISVSL 78
>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 = 40.3 bits (95), Expect = 8e-05
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 12/90 (13%)
Query: 147 TIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
T+FV+ +EE L++HF G + SV++ +K GF
Sbjct: 2 TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDP----------KGPGKLLSMGYGF 51
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
V F S E++ KA+ + GT + G L++ L
Sbjct: 52 VEFKSKEAAQKALKRLQGTVLDGHALELKL 81
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 40.0 bits (94), Expect = 9e-05
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 12/71 (16%)
Query: 144 GGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGF--VTFDSPESSDKA 195
IFV G ++E LR++FS FG + V + E ++ RGF +TF+S +S D+
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60
Query: 196 ITDDCARGFVT 206
F
Sbjct: 61 ----VNEHFHD 67
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 39.1 bits (92), Expect = 2e-04
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 21/79 (26%)
Query: 155 ISEEFLRQHFSIFGKICSVSM--EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPES 212
++EE LR+ FS +GK+ V + ++ RGF FV F SPE
Sbjct: 10 VTEEDLREFFSPYGKVEGVRLVRNKDRPRGF-------------------AFVEFASPED 50
Query: 213 SDKAITEVNGTHVQGVKLK 231
++ A+ ++NG + G L+
Sbjct: 51 AEAALKKLNGLVLDGRTLR 69
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 26/89 (29%)
Query: 155 ISEEFLRQHFSIFGKICSVSM-------EVEKGRGFVTFDSPESSDKAITDDCARGFVTF 207
++E L + FS +GKI + RG+ FVTF
Sbjct: 11 LTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGY-------------------CFVTF 51
Query: 208 DSPESSDKAITEVNGTHVQGVKLKVSLAR 236
++ E ++KA+ +NG G KL V A
Sbjct: 52 ETKEEAEKALKSLNGKTALGKKLVVRWAH 80
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 23/81 (28%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDK 215
+EE LR+ FS +G++ V K I D FV F+ + + K
Sbjct: 14 TEEQLRELFSEYGEVERV--------------------KKIKD---YAFVHFEERDDAVK 50
Query: 216 AITEVNGTHVQGVKLKVSLAR 236
A+ E+NG ++G ++VSLA+
Sbjct: 51 AMEEMNGKELEGSPIEVSLAK 71
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 38.6 bits (90), Expect = 2e-04
Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 19/73 (26%)
Query: 160 LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITE 219
+++ F G + V+M + F+TF++ E++ AI
Sbjct: 16 VKRLFETCGPVRKVTMLSRTVQPHA-------------------FITFENLEAAQLAIET 56
Query: 220 VNGTHVQGVKLKV 232
+NG V G +KV
Sbjct: 57 LNGASVDGNCIKV 69
>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 = 38.3 bits (90), Expect = 3e-04
Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 23/83 (27%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKG----RGFVTFDSPESSDKAITDDCARGFVTFDSP 210
++++ L++ FS +G + V + +++ RG+ +V F+SP
Sbjct: 10 VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGY-------------------AYVEFESP 50
Query: 211 ESSDKAITEVNGTHVQGVKLKVS 233
E ++KAI ++G + G ++ V
Sbjct: 51 EDAEKAIKHMDGGQIDGQEVTVE 73
>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 = 38.0 bits (89), Expect = 4e-04
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 23/85 (27%)
Query: 155 ISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPESSDKAITDDCARGFVTFDSP 210
+SE+ ++ F FGKI CS++ + E G +G+ GF+ +++P
Sbjct: 12 LSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGY-------------------GFIEYENP 52
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLA 235
+S+ AI +N + G +L+V A
Sbjct: 53 QSAQDAIASMNLFDLGGQQLRVGKA 77
>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 = 38.2 bits (89), Expect = 4e-04
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 8/60 (13%)
Query: 145 GNTIFVQGAGI--SEEFLRQHFSIFGKI--CSV----SMEVEKGRGFVTFDSPESSDKAI 196
+FV G + S+ LR+HF+ +GK+ C V + + +G GF+TF S + +D+A+
Sbjct: 2 LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
>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 = 38.0 bits (89), Expect = 4e-04
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 24/88 (27%)
Query: 155 ISEEFLRQHFSIFGKI---CSVSMEVEKG--RGFVTFDSPESSDKAITDDCARGFVTFDS 209
+ E+ L FS FG I + + + G +GF F+++DS
Sbjct: 13 VDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGF-------------------AFISYDS 53
Query: 210 PESSDKAITEVNGTHVQGVKLKVSLARR 237
E+SD AI +NG ++ + VS A +
Sbjct: 54 FEASDAAIEAMNGQYLCNRPITVSYAFK 81
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 38.0 bits (89), Expect = 4e-04
Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 25/92 (27%)
Query: 148 IFVQGAG--ISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCA 201
++V G + E+ L F FG I + + E +K RGF
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGF------------------ 42
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
FV F+ PE + AI +N + + G ++V+
Sbjct: 43 -AFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 41.1 bits (95), Expect = 4e-04
Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 17/102 (16%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDK 194
+ + + NT+FV ++EE LR+ F FG + V + ++ G
Sbjct: 107 SRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETG------------ 154
Query: 195 AITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F+S ES++KAI E+NG ++G L+V A+
Sbjct: 155 ---KSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193
>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 = 37.3 bits (87), Expect = 6e-04
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 148 IFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKAITDD 199
IFV G ++EE +++FS FGK+ + + G GFVTFDS + ++
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERV---- 57
Query: 200 CARGFVTFD 208
+ G +
Sbjct: 58 FSAGMLELG 66
>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 = 37.5 bits (87), Expect = 6e-04
Identities = 29/95 (30%), Positives = 43/95 (45%), Gaps = 22/95 (23%)
Query: 142 PKGGNTIFVQGAGISEEF----LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
P+G N +F+ + +EF L Q F FG + S + V D+A
Sbjct: 2 PEGCN-LFIYH--LPQEFGDAELMQMFLPFGNVISAKVFV---------------DRATN 43
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
GFV+FD+P S+ AI +NG + +LKV
Sbjct: 44 QSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV 78
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 37.2 bits (87), Expect = 8e-04
Identities = 14/47 (29%), Positives = 22/47 (46%)
Query: 151 QGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
G G+S E L + F +G + + M K FV++ S E + A
Sbjct: 11 LGNGVSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYD 57
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of SXL which governs sexual differentiation
and X chromosome dosage compensation in Drosophila
melanogaster. It induces female-specific alternative
splicing of the transformer (tra) pre-mRNA by binding to
the tra uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 37.4 bits (87), Expect = 9e-04
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV + S E + +AI +NG +Q ++KV+ AR
Sbjct: 45 GFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYAR 78
>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 = 36.8 bits (86), Expect = 0.001
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 23/79 (29%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+S+E L + FS +GKI +S+ +G+ GFV FD+ E +
Sbjct: 13 VSKEDLEEIFSKYGKILGISLH----KGY-------------------GFVQFDNEEDAR 49
Query: 215 KAITEVNGTHVQGVKLKVS 233
A+ NG + G KL ++
Sbjct: 50 AAVAGENGREIAGQKLDIN 68
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 36.5 bits (85), Expect = 0.001
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
G+ + ES+++AIT ++G V GVKLKV
Sbjct: 38 GYAKYADRESAERAITTLHGKEVNGVKLKV 67
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 36.9 bits (86), Expect = 0.001
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 22/83 (26%)
Query: 155 ISEEFLRQHFSIFGKICSVSM-----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDS 209
++EE L Q F FG + SV + E E+ R +C GFV F +
Sbjct: 13 VTEEVLCQEFGRFGPLASVKIMWPRTEEERRRN---------------RNC--GFVAFMN 55
Query: 210 PESSDKAITEVNGTHVQGVKLKV 232
+++A+ E++G V G +LK+
Sbjct: 56 RADAERALDELDGKDVMGYELKL 78
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 36.5 bits (85), Expect = 0.001
Identities = 27/96 (28%), Positives = 37/96 (38%), Gaps = 25/96 (26%)
Query: 145 GNTIFVQGAG--ISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITD 198
G IFV E L Q FS FG + +V + K +G+
Sbjct: 1 GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGY--------------- 45
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
GFVT + E + AI +NG + G L+VS
Sbjct: 46 ----GFVTMTNYEEAYSAIASLNGYRLGGRVLQVSF 77
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 36.6 bits (85), Expect = 0.001
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 15/78 (19%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+ E+ +RQ FS FG I S+ M ++D K FV ++ PE++
Sbjct: 12 LGEDTIRQAFSPFGPIKSIDM---------SWDPVTMKHKGFA------FVEYEVPEAAQ 56
Query: 215 KAITEVNGTHVQGVKLKV 232
A+ ++NG + G +KV
Sbjct: 57 LALEQMNGVMLGGRNIKV 74
>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 = 36.2 bits (84), Expect = 0.001
Identities = 23/54 (42%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGR-GFVTFDSPESSDKAI 196
++FV G G SEE L +FS FG + +V M+ +KG V FDS E DK +
Sbjct: 3 RSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVL 56
>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 = 36.4 bits (85), Expect = 0.001
Identities = 24/82 (29%), Positives = 33/82 (40%), Gaps = 22/82 (26%)
Query: 157 EEFLRQHFSIFGKICSVS-MEVEKG--RGFVTFDSPESSDKAITDDCARGFVTFDSPESS 213
E+ LR+HF G++ V M G R F GFV F S E +
Sbjct: 14 EDRLREHFESKGEVTDVKVMRTRDGKSRRF-------------------GFVGFKSEEDA 54
Query: 214 DKAITEVNGTHVQGVKLKVSLA 235
+A+ N T + K+ V LA
Sbjct: 55 QQAVKYFNKTFIDTSKISVELA 76
>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 = 36.1 bits (84), Expect = 0.001
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 21/79 (26%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESS 213
I+EE ++ FS +G++ V + K +GF GF+ D+ ++
Sbjct: 12 DITEEEFKELFSKYGEVSEVF--LNKEKGF-------------------GFIRLDTRTNA 50
Query: 214 DKAITEVNGTHVQGVKLKV 232
+KA E++G +G +L+V
Sbjct: 51 EKAKAELDGIMRKGRQLRV 69
>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 = 36.0 bits (84), Expect = 0.002
Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 20/93 (21%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFV-TFDSPESSDKAITDDCARGF 204
+FV G ++E L + FS FG + V + +K G F +
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGF----------------AY 45
Query: 205 VTFDSPESS-DKAITEVNGTHVQGVKLKVSLAR 236
+ + E+ K + +NGT +G LK+ A+
Sbjct: 46 IDLRTSEAQLKKCKSTLNGTKWKGSVLKIEEAK 78
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 37.3 bits (86), Expect = 0.002
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 25/94 (26%)
Query: 148 IFVQGA--GISEEFLRQHFSIFGKICS----VSMEVEKGRGFVTFDSPESSDKAITDDCA 201
+F+ G G + LR F+ FG + V E + RGF
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGF------------------ 78
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
GFV F+ ++ AI+E++G + G ++V+ A
Sbjct: 79 -GFVNFNDEGAATAAISEMDGKELNGRHIRVNPA 111
>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 = 38.8 bits (90), Expect = 0.002
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 15/83 (18%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESS 213
+++E +R F+ G+I S + DK GFV + PE +
Sbjct: 14 TMTQEEIRSLFTSIGEIESCKL---------------VRDKVTGQSLGYGFVNYVRPEDA 58
Query: 214 DKAITEVNGTHVQGVKLKVSLAR 236
+KA+ +NG +Q +KVS AR
Sbjct: 59 EKAVNSLNGLRLQNKTIKVSYAR 81
Score = 30.7 bits (69), Expect = 0.93
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 18/87 (20%)
Query: 139 NEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
++ KG N ++V G +++ L FS FG+I + + + G K +
Sbjct: 84 SDSIKGAN-LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGL---------SKGV 133
Query: 197 TDDCARGFVTFDSPESSDKAITEVNGT 223
GF+ FD + +D+AI +NGT
Sbjct: 134 ------GFIRFDKRDEADRAIKTLNGT 154
>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 = 36.0 bits (84), Expect = 0.002
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 156 SEEFLRQHFSIFGKICSV------SMEVEKGRGFVTFDSPESSDKAI 196
+EE L++ FS FG++ KG FV F + ES+ K +
Sbjct: 13 TEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59
>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 = 35.9 bits (83), Expect = 0.003
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 146 NTIFVQGAG--ISEEFLRQHFSIFG-----KICSVSMEVEKGRGFVTFDSPESSDKAITD 198
N IFV G +E LR+ FS +G KI + V KG GFVTF++ E + K + +
Sbjct: 3 NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQE 62
>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 = 35.9 bits (82), Expect = 0.003
Identities = 18/44 (40%), Positives = 23/44 (52%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + P +DKAI +NG +Q +KVS AR
Sbjct: 38 DKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYAR 81
>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 = 35.3 bits (82), Expect = 0.004
Identities = 13/44 (29%), Positives = 29/44 (65%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITD 198
++E++L +HFS +G + V ++ ++G+ V FD E++ A+ +
Sbjct: 19 VTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQAAVNE 62
>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 = 34.9 bits (81), Expect = 0.004
Identities = 28/91 (30%), Positives = 40/91 (43%), Gaps = 18/91 (19%)
Query: 147 TIFVQGAGIS--EEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
IFV G ++ LR++FS FG E+E V D + GF
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFG-------EIE--EAVVITDRQTGKSRGY------GF 46
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
VTF ES+++A + N + G K V+LA
Sbjct: 47 VTFKDKESAERACKDPNPI-IDGRKANVNLA 76
>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 = 35.0 bits (81), Expect = 0.005
Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 16/82 (19%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESS 213
GI E+ LR+ F FG I V ++ K F F GFV + + E +
Sbjct: 11 GIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKF----------------GFVGYKTEEEA 54
Query: 214 DKAITEVNGTHVQGVKLKVSLA 235
KA+ N + + K+ V +
Sbjct: 55 QKALKHFNNSFIDTSKITVEIC 76
>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 = 37.6 bits (87), Expect = 0.006
Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 26/100 (26%)
Query: 155 ISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
I+E+ LRQ F FG I V + E + +GF GF+ F
Sbjct: 198 ITEQELRQIFEPFGDIEDVQLHRDPETGRSKGF-------------------GFIQFHDA 238
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASS 250
E + +A+ +NG + G +KV A+ + DAA++
Sbjct: 239 EEAKEALEVMNGFELAGRPIKVGYAQ---DSTYLLDAANT 275
>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 = 34.6 bits (80), Expect = 0.006
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 183 FVTFDSPESSDKAITDD-CARGFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
T+ + ++ ++ T A VT++SPE + +A+ ++NG +G KLKVS
Sbjct: 21 LSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLNGHEYEGSKLKVS 72
>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 = 34.3 bits (79), Expect = 0.006
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
A GFV FDSPES AI G ++G KL + +++
Sbjct: 35 AYGFVQFDSPESCANAINCEQGKMIRGRKLHLEVSK 70
>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 = 34.5 bits (80), Expect = 0.006
Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 23/84 (27%)
Query: 156 SEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
+EE L + FS G + S + + K +G+ GF F+ E
Sbjct: 11 TEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGY-------------------GFCEFEDIE 51
Query: 212 SSDKAITEVNGTHVQGVKLKVSLA 235
++ AI +NG G L+V A
Sbjct: 52 TAASAIRNLNGYEFNGRALRVDFA 75
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 34.9 bits (81), Expect = 0.007
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 24/78 (30%)
Query: 160 LRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPESSDKAITDDCARGFVTFDSPESSDK 215
LR+ FS GK C +++ G RGF FV + + E +++
Sbjct: 20 LRKLFSQVGKPTFCQLAI-APNGQPRGF-------------------AFVEYATAEDAEE 59
Query: 216 AITEVNGTHVQGVKLKVS 233
A +NG +QG ++VS
Sbjct: 60 AQQALNGHSLQGSPIRVS 77
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 34.6 bits (79), Expect = 0.007
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 17/77 (22%)
Query: 160 LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITE 219
L++ FS G + +++E G+ + C G V FDSPES++KA
Sbjct: 16 LKEKFSQCGHVMFAEIKMENGK---------------SKGC--GTVRFDSPESAEKACRL 58
Query: 220 VNGTHVQGVKLKVSLAR 236
+NG + G ++ V L R
Sbjct: 59 MNGIKINGREIDVRLDR 75
>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 = 34.1 bits (79), Expect = 0.007
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 20/86 (23%)
Query: 152 GAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
G ++ L F +G + SV +V + P FV F+ P
Sbjct: 8 GPRATKRELEDEFEKYGPLRSV---------WVARNPP-----------GFAFVEFEDPR 47
Query: 212 SSDKAITEVNGTHVQGVKLKVSLARR 237
++ A+ ++G + G +++V L+R
Sbjct: 48 DAEDAVRALDGRRICGNRVRVELSRG 73
>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 = 34.2 bits (78), Expect = 0.010
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
IFV G E LR +F +GKI + + ++G G FVTFD +S DK +
Sbjct: 3 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 59
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 33.8 bits (77), Expect = 0.012
Identities = 26/95 (27%), Positives = 40/95 (42%), Gaps = 22/95 (23%)
Query: 142 PKGGNTIFVQGAGISEEF----LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
P+G N + +EF L Q F FG + S + + DK
Sbjct: 2 PEGCNLFIYH---LPQEFTDTDLAQTFLPFGNVISAKVFI---------------DKQTN 43
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
GFV++D+P+S+ AI +NG + +LKV
Sbjct: 44 LSKCFGFVSYDNPDSAQAAIQAMNGFQIGTKRLKV 78
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 33.8 bits (78), Expect = 0.012
Identities = 20/48 (41%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAIT 197
++E L + FGKI S ++ KG GFV FDSPE++ KAI
Sbjct: 13 TDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
Score = 33.4 bits (77), Expect = 0.016
Identities = 20/41 (48%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 192 SDKAITDDCAR-----GFVTFDSPESSDKAITEVNGTHVQG 227
S KAI D GFV FDSPE++ KAI +NG VQ
Sbjct: 29 STKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGRGVQA 69
>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 = 33.9 bits (77), Expect = 0.012
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 15/82 (18%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++++ LR FS G++ S + DK GFV + + + ++
Sbjct: 13 MTQDELRSLFSSIGEVESAKL---------------IRDKVAGHSLGYGFVNYVNAKDAE 57
Query: 215 KAITEVNGTHVQGVKLKVSLAR 236
+AI +NG +Q +KVS AR
Sbjct: 58 RAINTLNGLRLQSKTIKVSYAR 79
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding
protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or modifier
of damage tolerance Mdt1, a novel phosphothreonine
(pThr)-containing protein that specifically interacts
with the pThr-binding site of the Rad53 FHA1 domain. It
is encoded by gene MDT1 (YBL051C) from yeast
Saccharomyces cerevisiae. PIN4 is involved in normal
G2/M cell cycle progression in the absence of DNA damage
and functions as a novel target of checkpoint-dependent
cell cycle arrest pathways. It contains an N-terminal
RRM, a nuclear localization signal, a coiled coil, and a
total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein
1) and cip2 (Csx1-interacting protein 2) are novel
cytoplasmic RRM-containing proteins that counteract Csx1
function during oxidative stress. They are not essential
for viability in fission yeast Schizosaccharomyces
pombe. Both cip1 and cip2 contain one RRM. Like PIN4,
Cip2 also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 33.6 bits (77), Expect = 0.014
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 202 RG--FVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
RG F F SPE + + +NG + G +L+V R
Sbjct: 43 RGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79
>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 = 33.5 bits (77), Expect = 0.014
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 148 IFVQGAG--ISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKA 195
IFV G +EE +R++F FG I + + ++ +G F+TFDS E K
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57
>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 = 33.9 bits (77), Expect = 0.014
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + P+ ++KAI +NG +Q +KVS AR
Sbjct: 37 DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 80
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is
a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 75
Score = 33.6 bits (77), Expect = 0.015
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 6/48 (12%)
Query: 156 SEEFLRQHFSIFGKI--CSV----SMEVEKGRGFVTFDSPESSDKAIT 197
+ E LR++FS FG+I C V + + +G GFVTF P S DK +
Sbjct: 11 TAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLA 58
>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 = 33.9 bits (78), Expect = 0.015
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 140 EKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
E+P G T+FV G +EE +R+ F G+I ++ M +K + F + DKAI
Sbjct: 1 ERPPGCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMS-KKNFCHIRFAEEFAVDKAI 58
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing
factor Cwc2 and similar proteins. This subfamily
corresponds to the RRM of yeast protein Cwc2, also
termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and an intervening loop, also termed
RNA-binding loop or RB loop, between ZnF and RRM, all of
which are necessary and sufficient for RNA binding. The
ZnF is also responsible for mediating protein-protein
interaction. The C-terminal flexible region of Cwc2
interacts with the WD40 domain of Prp19.
Length = 78
Score = 33.4 bits (77), Expect = 0.016
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 6/47 (12%)
Query: 147 TIFVQGAGIS------EEFLRQHFSIFGKICSVSMEVEKGRGFVTFD 187
T++V G EE LR+HF +G I + + KG FV +
Sbjct: 3 TLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSKGIAFVRYK 49
>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 = 33.6 bits (76), Expect = 0.019
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
DK GFV + P+ ++KAI +NG +Q +KVS AR
Sbjct: 39 DKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR 82
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 33.0 bits (76), Expect = 0.019
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 151 QGAGISEEFLRQHFSIFGKICSVSM-EVEKGRGFVTFDSPESSDKAITDDC 200
SE+ LR+ FS +G + V + +KG V F S ++++ A+ ++C
Sbjct: 12 GNGDYSEDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVENEC 62
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 33.4 bits (77), Expect = 0.020
Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 25/93 (26%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICS----VSMEVEKGRGFVTFDSPESSDKAITDDC 200
T+FV G+S++F+R+ GK+ S K + F
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAF----------------- 44
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
GF F+ PE + +A+ +NG + G KL V
Sbjct: 45 --GFCEFEDPEGALRALRLLNGLELGGKKLLVK 75
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM2 of polypyrimidine tract-binding protein 1 (PTB or
hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2
or nPTB), regulator of differentiation 1 (Rod1),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), polypyrimidine tract-binding protein homolog
3 (PTBPH3), polypyrimidine tract-binding protein homolog
1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and
RRM3 of PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. Rod1 is a mammalian polypyrimidine tract
binding protein (PTB) homolog of a regulator of
differentiation in the fission yeast Schizosaccharomyces
pombe, where the nrd1 gene encodes an RNA binding
protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. .
Length = 85
Score = 33.3 bits (77), Expect = 0.021
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 21/86 (24%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++ + L Q FS +G VEK + F + +A V FDS ES++
Sbjct: 13 VTVDVLHQVFSPYG-------AVEK---ILIF-EKNTGVQA--------LVQFDSVESAE 53
Query: 215 KAITEVNGTHV--QGVKLKVSLARRQ 238
A +NG ++ L + +R +
Sbjct: 54 NAKKALNGRNIYDGCCTLDIQFSRLK 79
>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 = 33.1 bits (76), Expect = 0.022
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGR------GFVTFDSPESSDKAITD 198
I+E+ L++ F FG + V + + G GFV FD PE+ K + +
Sbjct: 14 DITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM1
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 74
Score = 32.9 bits (75), Expect = 0.024
Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++E+ L+Q F + G + +V + +K V + GFV + ++
Sbjct: 10 VTEDILKQIFQVGGPVQNVKIIPDKNNKGVNY----------------GFVEYHQSHDAE 53
Query: 215 KAITEVNGTHVQGVKLKVSLA 235
A+ +NG ++ +++V+ A
Sbjct: 54 IALQTLNGRQIENNEIRVNWA 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 = 32.7 bits (75), Expect = 0.027
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV F+ P +D A+ E+NG + G ++ V AR
Sbjct: 36 GFVEFEDPRDADDAVYELNGKELCGERVIVEHAR 69
Score = 28.1 bits (63), Expect = 1.0
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITD 198
E + + F +G+I ++++ G GFV F+ P +D A+ +
Sbjct: 10 RARERDVERFFKGYGRIREINLK--NGFGFVEFEDPRDADDAVYE 52
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 33.1 bits (75), Expect = 0.027
Identities = 29/101 (28%), Positives = 42/101 (41%), Gaps = 22/101 (21%)
Query: 140 EKPKGGNTIFVQGAGISEEF----LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
E P+G N + +EF L Q F FG + S + + DK
Sbjct: 3 EGPEGANLFIYH---LPQEFGDQDLLQMFMPFGNVVSAKVFI---------------DKQ 44
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV++D+P S+ AI +NG + +LKV L R
Sbjct: 45 TNLSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKR 85
>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 = 32.5 bits (75), Expect = 0.033
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 155 ISEEFLRQHFSIFGKICSVSM------EVEKGRGFVTFDSPESSDKAITDDC 200
I EE LR+HF G + +V + + KG G+V F + +S A+ +
Sbjct: 11 IEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62
>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 = 32.5 bits (75), Expect = 0.033
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 15/71 (21%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+EE +R F +G I V+ + + + D+ +S K CA FV F S E +
Sbjct: 11 ATEEDVRALFEEYGNIEEVT--IIRDK-----DTGQS--KG----CA--FVKFSSREEAQ 55
Query: 215 KAITEVNGTHV 225
KAI ++G
Sbjct: 56 KAIEALHGKVT 66
>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 = 32.7 bits (75), Expect = 0.033
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAITDDCARG 203
+S E L Q FS FG++ + V+ G G V F + AI C+ G
Sbjct: 11 VSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAI-KRCSEG 63
>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 = 32.8 bits (75), Expect = 0.034
Identities = 16/44 (36%), Positives = 22/44 (50%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
SEE LR+ FG I + + EK FV F S ++ K +T
Sbjct: 14 SYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVT 57
>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 = 32.6 bits (75), Expect = 0.034
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 2/33 (6%)
Query: 202 RGF--VTFDSPESSDKAITEVNGTHVQGVKLKV 232
+GF V F+SPE + +AI NG ++G +L+V
Sbjct: 39 KGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71
Score = 26.5 bits (59), Expect = 4.1
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 160 LRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAI 196
L+ F G + ++ + KG G V F+SPE + +AI
Sbjct: 15 LKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAI 56
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 32.8 bits (75), Expect = 0.038
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 147 TIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
+ F+ G + E +R +F FGK SV + GFV F++ E+++K
Sbjct: 4 SFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAKCGFVRFETREAAEKF 54
>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 = 32.4 bits (74), Expect = 0.039
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 23/81 (28%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVE----KGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
+EE L + FS +G + V + ++ K +GF FVT+ PE
Sbjct: 15 TEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGF-------------------AFVTYMIPE 55
Query: 212 SSDKAITEVNGTHVQGVKLKV 232
+ KA E++GT QG L +
Sbjct: 56 HAVKAFAELDGTVFQGRLLHL 76
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an N-terminal
C4C4 type RING finger motif, followed by a RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The RING
fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 32.5 bits (75), Expect = 0.060
Identities = 21/95 (22%), Positives = 35/95 (36%), Gaps = 17/95 (17%)
Query: 146 NTIFVQGAGIS---EEFLRQH--FSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDC 200
N ++V G EE L++ F +GKI + +
Sbjct: 6 NLVYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNG------------SQGPS 53
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
A +VT+ E + + I V+G ++ G LK S
Sbjct: 54 ASAYVTYSRKEDALRCIQAVDGFYLDGRLLKASFG 88
>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 = 32.0 bits (73), Expect = 0.063
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 156 SEEFLRQHFSIFGKI--CSV----SMEVEKGRGFVTFDSPESSDKAITD 198
+++ L+ +FS +G+I C V + + +G GFVTF S D A+
Sbjct: 12 TDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 32.2 bits (73), Expect = 0.065
Identities = 27/91 (29%), Positives = 39/91 (42%), Gaps = 9/91 (9%)
Query: 146 NTIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
NTIFVQG G ++ E + +F G I + K G + +D+
Sbjct: 3 NTIFVQGLGEDVTIESVADYFKQIGII-----KTNKKTGQPMINL--YTDRETGKLKGEA 55
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
V+FD P S+ AI +G G +KVS
Sbjct: 56 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 86
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 31.2 bits (71), Expect = 0.072
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 152 GAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
SE +R+ FS +G + V M FV F+S ES+ +A D G V ++P
Sbjct: 8 PPDTSESAIREIFSPYGAVKEVKMI--SNFAFVEFESLESAIRAK--DSVHGKVLNNNP 62
Score = 29.7 bits (67), Expect = 0.32
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
FV F+S ES+ +A V+G + L V+
Sbjct: 36 AFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67
>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 = 31.5 bits (72), Expect = 0.074
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 147 TIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAI 196
T+FV ++ L + F G++ V + + KG G V F + E + KA+
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL 57
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis. TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 31.6 bits (72), Expect = 0.079
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 23/72 (31%)
Query: 155 ISEEFLRQHFSIFGKICSV----SMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
I E LR F+ FG+I M+ K +G+ GFV+F
Sbjct: 11 IDTETLRAAFAPFGEISDARVVKDMQTGKSKGY-------------------GFVSFVKK 51
Query: 211 ESSDKAITEVNG 222
E ++ AI +NG
Sbjct: 52 EDAENAIQSMNG 63
>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 = 0.083
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 153 AGISEEFLRQHFSIFGKICSVSMEVEKGR---GFVTFDSPESSDKAI 196
+ LRQ F FG+I +++ GFVT+ + +AI
Sbjct: 12 IDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAI 58
>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 = 31.6 bits (72), Expect = 0.084
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 154 GISEEFLRQHFSIFGKICSVSM------EVEKGRGFVTFDSPESSDKAI 196
+ E L HF G SV + KG FV FD+ E+ KA+
Sbjct: 11 DTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL 59
>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 = 31.5 bits (72), Expect = 0.085
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 15/73 (20%)
Query: 160 LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITE 219
L+Q FS +GK+ V ++ SP + C GFVT S E + K I
Sbjct: 16 LKQLFSKYGKV--VGAKI-----VTNARSPGAR-------CF-GFVTMASVEEAAKCIQH 60
Query: 220 VNGTHVQGVKLKV 232
++ T + G + V
Sbjct: 61 LHRTELHGRVISV 73
>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 = 33.8 bits (77), Expect = 0.094
Identities = 16/34 (47%), Positives = 20/34 (58%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F S S +AI +NG V+ +LKVS AR
Sbjct: 152 AFVDFGSEADSQRAIKNLNGITVRNKRLKVSYAR 185
>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 = 31.6 bits (72), Expect = 0.098
Identities = 26/93 (27%), Positives = 39/93 (41%), Gaps = 15/93 (16%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPE---SSDKAITDDCAR 202
+FV +E+ L +HF G I +++K G P+ DK +
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGII-----KIDKKTG-----KPKIWLYKDKDTGEPKGE 50
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
VT+D P ++ AI N G +KVSLA
Sbjct: 51 ATVTYDDPHAASAAIEWFNNKDFMGNTIKVSLA 83
>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 = 31.4 bits (71), Expect = 0.099
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKAI 196
+FV G + E L +HFS FG + + +K G GFV F + +S+DKA
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 31.2 bits (70), Expect = 0.10
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 23/82 (28%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++EE L + FS FGK+ V K + D FV F+ +++
Sbjct: 13 VTEEILEKSFSEFGKLERV--------------------KKLKD---YAFVHFEERDAAV 49
Query: 215 KAITEVNGTHVQGVKLKVSLAR 236
+A+ E+NG ++G ++++ LA+
Sbjct: 50 RAMDEMNGKEIEGEEIEIVLAK 71
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 31.1 bits (71), Expect = 0.13
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
D A FVTF S E KA+ ++G +G L LA+
Sbjct: 42 QDFA--FVTFRSEEERQKALEILDGFKWKGRVLSARLAK 78
>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 = 31.1 bits (70), Expect = 0.13
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 157 EEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITD 198
E + + F +GKI V +++ G GFV FD +D A+ +
Sbjct: 13 ERDVERFFKGYGKILEV--DLKNGYGFVEFDDLRDADDAVYE 52
Score = 28.8 bits (64), Expect = 0.72
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
GFV FD +D A+ E+NG + G ++ V
Sbjct: 36 GFVEFDDLRDADDAVYELNGKDLCGERVIV 65
>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 = 30.7 bits (70), Expect = 0.16
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 23/89 (25%)
Query: 148 IFVQGAGISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPESSDKAITDDCARG 203
+F +E LR+ FS +G I V + + G RGF G
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGF-------------------G 44
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKV 232
FV F+S E + +A +NG + G +++V
Sbjct: 45 FVYFESVEDAKEAKERLNGMEIDGRRIRV 73
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 30.8 bits (70), Expect = 0.17
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 147 TIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAIT 197
T++V+ + E+L+ FS +G + VS+ K G F+ F++PE + KA
Sbjct: 1 TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 30.6 bits (70), Expect = 0.18
Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 23/83 (27%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVEKGR----GFVTFDSPESSDKAITDDCARGFVTFDSPE 211
+EE + + FS G I + M +++ GF C FV + + E
Sbjct: 11 TEEQIYELFSRCGDIKRIIMGLDRFTKTPCGF----------------C---FVEYYTRE 51
Query: 212 SSDKAITEVNGTHVQGVKLKVSL 234
++ A+ +NGT + ++V
Sbjct: 52 DAENAVKYLNGTKLDDRIIRVDW 74
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma
Protein (EWS). This subgroup corresponds to the RRM of
EWS, also termed Ewing sarcoma breakpoint region 1
protein, a member of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the FET
family, EWS contains an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U RNA.
It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor gene.
.
Length = 84
Score = 30.6 bits (69), Expect = 0.18
Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 7/90 (7%)
Query: 146 NTIFVQGAGISEEFLRQHFSIFGKICS-VSMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
+TI+VQG +++ + + F K C V + G+ V + + + K D
Sbjct: 1 STIYVQG--LNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGD----AT 54
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
V+++ P S+ A+ +G QG KLKVSL
Sbjct: 55 VSYEDPPSAKAAVEWFDGKDFQGSKLKVSL 84
>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 = 0.19
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 157 EEFLRQHFSIFGKICSV-----SMEVEKGRGFVTFDSPESSDKAITD 198
E+ L +G++ S S +G GF +S E + I+
Sbjct: 14 EQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISK 60
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in the
system using SV40 DNA. MSSP-2 is identical with Scr3, a
human protein which complements the defect of cdc2
kinase in Schizosaccharomyces pombe. MSSP-2 has been
implied in regulating DNA replication, transcription,
apoptosis induction, and cell-cycle movement, via the
interaction with C-MYC, the product of protooncogene
c-myc. MSSP-2 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 75
Score = 30.5 bits (68), Expect = 0.19
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 192 SDKAITDDCAR-----GFVTFDSPESSDKAITEVNGTHVQG 227
S KAI D GFV FDSP ++ KA+T + + VQ
Sbjct: 30 STKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA 70
Score = 30.5 bits (68), Expect = 0.21
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKAITDDCARG 203
G +++ L + +GKI S ++K G GFV FDSP ++ KA+T A G
Sbjct: 12 GTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASG 67
>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 = 30.3 bits (69), Expect = 0.20
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
GFV F + D+A+TE+NG + ++VS A
Sbjct: 47 GFVRFGDEDERDRALTEMNGVYCSSRPMRVSPA 79
>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 = 30.3 bits (69), Expect = 0.20
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
GFV + E ++ AI +NG G ++ V
Sbjct: 36 GFVHMEEEEDAEDAIKALNGYEFMGKRINV 65
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 30.7 bits (70), Expect = 0.21
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 184 VTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
+ F+ P +S D+ R FV F+ ES+ KA+ ++NG G +K S
Sbjct: 38 LIFEIPGASPD---DEAVRIFVEFERVESAIKAVVDLNGRFFGGRTVKAS 84
>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 = 30.6 bits (69), Expect = 0.23
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 16/78 (20%)
Query: 158 EFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAI 217
L++ F +GK+ ++ ++G C FVT ++++ A+
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRGGKL----------------CGFAFVTMKKRKNAEIAL 59
Query: 218 TEVNGTHVQGVKLKVSLA 235
NG + G + V A
Sbjct: 60 ENTNGLEIDGRPVAVDWA 77
>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 = 30.0 bits (68), Expect = 0.24
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAIT 197
+E+ L+ +FS FG++ V ++ + KG GFV F E K ++
Sbjct: 11 TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS 59
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 32.7 bits (74), Expect = 0.24
Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 15/92 (16%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+ E+ +R+ F FG I S++M S D A FV ++ PE++
Sbjct: 119 LREDTIRRAFDPFGPIKSINM---------------SWDPATGKHKGFAFVEYEVPEAAQ 163
Query: 215 KAITEVNGTHVQGVKLKVSLARRQLKVAPIND 246
A+ ++NG + G +KV + PI D
Sbjct: 164 LALEQMNGQMLGGRNIKVGRPSNMPQAQPIID 195
Score = 27.7 bits (61), Expect = 9.3
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 140 EKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSV------SMEVEKGRGFVTFDSPES 191
E+ K N I+V +SE ++ F FG+I + KG GF+ +++ +S
Sbjct: 199 EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQS 258
Query: 192 SDKAIT 197
+AI
Sbjct: 259 QSEAIA 264
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 30.7 bits (70), Expect = 0.24
Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 19/97 (19%)
Query: 147 TIFVQG---AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA------IT 197
T+FV G ++ L++ F FG I SV R V + K
Sbjct: 2 TVFV-GNLPLTTKKKDLKKLFKQFGPIESVRF-----RS-VPVKEKKLPKKVAAIKKKFH 54
Query: 198 D--DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
D D +V F ES++KA+ ++NGT +G ++V
Sbjct: 55 DKKDNVNAYVVFKEEESAEKAL-KLNGTEFEGHHIRV 90
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 84
Score = 30.4 bits (69), Expect = 0.25
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
+ F SPE ++K + ++NG + KL V L
Sbjct: 49 AYAEFSSPEQAEKVVKDLNGKVFKNRKLFVKL 80
>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 = 30.0 bits (67), Expect = 0.26
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 156 SEEFLRQHFSIFGKI--CSV----SMEVEKGRGFVTFDSPESSDKAI 196
S + LR +FS FG+I C V + + +G GFVTF P S DK +
Sbjct: 12 SPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58
>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 = 29.9 bits (68), Expect = 0.27
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 154 GISEEFLRQHFSIFGKICSVSME------VEKGRGFVTFDSPE 190
G E LR++FS FG + + + KG FV F+SPE
Sbjct: 10 GFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE 52
>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 = 30.0 bits (68), Expect = 0.27
Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 18/93 (19%)
Query: 148 IFVQGAG--ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG-- 203
I++ G ++E+ L + F G I + +K + K TD
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGII-----KRDK-------RTWPPMIKIYTDKETEPKG 48
Query: 204 --FVTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
VT+D P ++ AI NG +G K+KVSL
Sbjct: 49 EATVTYDDPSAAQAAIEWFNGYEFRGNKIKVSL 81
>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 = 30.0 bits (67), Expect = 0.30
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 156 SEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAI 196
S++ L+ +F+ FG++ C++ M+ GR GF+ F S +K +
Sbjct: 12 SKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVL 58
>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 = 29.7 bits (67), Expect = 0.30
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAITDDCARGF 204
+EE LR+ F FG I VS+ + KG G+V F P + A+ ++C + F
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL-ENCDKSF 66
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 30.0 bits (67), Expect = 0.32
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F S E + A+ +NGT ++G ++V+LA+
Sbjct: 41 FVHFTSREDAVHAMNNLNGTELEGSCIEVTLAK 73
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 29.7 bits (67), Expect = 0.33
Identities = 18/41 (43%), Positives = 25/41 (60%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+EE LR FS +G+I SV+ EK FV F + ++ KAI
Sbjct: 16 TEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAI 56
>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 = 30.0 bits (68), Expect = 0.33
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 156 SEEFLRQHFSIFGKI------CSVSMEVEKGRGFVTFDSPESSDKAITD 198
+++ L FS +G+I C + +G GF+ FD +++AI
Sbjct: 13 TQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61
Score = 26.9 bits (60), Expect = 4.3
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQG 227
GF+ FD +++AI +NGT G
Sbjct: 45 GFIRFDKRIEAERAIKALNGTIPPG 69
>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 = 29.8 bits (68), Expect = 0.34
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 23/72 (31%)
Query: 155 ISEEFLRQHFSIFGKICSV----SMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
E+ LR+ F FG I V E + RGF FVTF +
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGF-------------------AFVTFHTR 51
Query: 211 ESSDKAITEVNG 222
E +++AI ++NG
Sbjct: 52 EDAERAIEKLNG 63
>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 = 29.5 bits (66), Expect = 0.38
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 6/48 (12%)
Query: 156 SEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAIT 197
+++ LR++F FG++ C+V + GR GF+TF P+S ++ +
Sbjct: 11 TDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMK 58
>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 = 29.5 bits (66), Expect = 0.39
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 23/82 (28%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+ E+ +++ F +GK+ +E++ G+ GFV F+ +D
Sbjct: 11 VREKDIQRFFGGYGKL----LEIDLKNGY-------------------GFVEFEDSRDAD 47
Query: 215 KAITEVNGTHVQGVKLKVSLAR 236
A+ E+NG + G ++ V AR
Sbjct: 48 DAVYELNGKDLCGERVIVEHAR 69
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 29.4 bits (66), Expect = 0.41
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
GFVTF E + +A+ ++ + G L++ +A R+
Sbjct: 44 GFVTFAMLEDAQEALAKLKNKKLHGRILRLDIAERR 79
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 29.5 bits (66), Expect = 0.46
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
G V F+SPE +++A +NG + G ++ V + R
Sbjct: 42 GVVRFESPEVAERACRMMNGYKLNGREIDVRIDR 75
>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa
MCM3-associated protein (Map80) and similar proteins.
This subfamily corresponds to the RRM of Map80, also
termed germinal center-associated nuclear protein
(GANP), involved in the nuclear localization pathway of
MCM3, a protein necessary for the initiation of DNA
replication and also involves in controls that ensure
DNA replication is initiated once per cell cycle. Map80
contains one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 73
Score = 29.3 bits (66), Expect = 0.49
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 158 EFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
++L +HF FGK+ V K V F S+ A
Sbjct: 16 DWLERHFGKFGKVARVYCNPRKKSAVVHFFDHASAALA 53
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 29.2 bits (65), Expect = 0.49
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 23/82 (28%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++EE L + F FGK+ V K + D F+ FD + +
Sbjct: 13 VTEEILEKAFGQFGKLERV--------------------KKLKD---YAFIHFDERDGAV 49
Query: 215 KAITEVNGTHVQGVKLKVSLAR 236
KA+ E+NG ++G +++ A+
Sbjct: 50 KAMEEMNGKELEGENIEIVFAK 71
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 84
Score = 29.4 bits (66), Expect = 0.55
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV F + E + A+ ++G + G L V + R
Sbjct: 50 GFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFSHR 84
>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 = 29.3 bits (66), Expect = 0.55
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 15/72 (20%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDK 215
E+ L + FS FG++ V + ++K S +S A +V F PE + K
Sbjct: 15 KEDDLEKLFSKFGELSEVHVAIDK-------KSGKSKGFA--------YVLFLDPEDAVK 59
Query: 216 AITEVNGTHVQG 227
A E++G QG
Sbjct: 60 AYKELDGKVFQG 71
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 29.0 bits (65), Expect = 0.57
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 23/72 (31%)
Query: 155 ISEEFLRQHFSIFGKICSV----SMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
+++ L FS F M+ + RG+ GFV+F S
Sbjct: 11 VTDATLFAAFSAFPSCSDARVMWDMKSGRSRGY-------------------GFVSFRSQ 51
Query: 211 ESSDKAITEVNG 222
+ ++ AI E+NG
Sbjct: 52 QDAENAINEMNG 63
>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 = 29.2 bits (66), Expect = 0.64
Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 19/88 (21%)
Query: 147 TIFVQ--GAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
+IFV +++E L + FS GKI V++ +++ F F
Sbjct: 5 SIFVGQLSPDVTKEELNERFSRHGKILEVNL-IKRANHTNAF----------------AF 47
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKV 232
+ F+ +++ +A+ N + ++ + V
Sbjct: 48 IKFEREQAAARAVESENHSMLKNKTMHV 75
>gnl|CDD|225524 COG2977, EntD, Phosphopantetheinyl transferase component of
siderophore synthetase [Secondary metabolites
biosynthesis, transport, and catabolism].
Length = 228
Score = 30.8 bits (70), Expect = 0.73
Identities = 23/93 (24%), Positives = 36/93 (38%), Gaps = 8/93 (8%)
Query: 19 PEPERTQASSTLKRPIEAKDAREVARKLLK--SGAINPIVRPPKRCEQEGFKRPRGLERK 76
PE A + KR E R AR+ L+ A PI+R R P G+
Sbjct: 38 PEEPPLIARAVPKRKAEFLAGRICARQALRELGVADVPILRGEDRAPL----WPAGVVGS 93
Query: 77 LTETDRSTVSAYQPFSAIQPE--DSEPVDSKPK 107
++ D + ++ ++ D EP +S P
Sbjct: 94 ISHCDGTALAVVARRGRVRSIGIDIEPHESLPT 126
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 28.6 bits (64), Expect = 0.76
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 164 FSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
F FG I + ++G FV D+ E + AI
Sbjct: 21 FQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAI 53
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 28.6 bits (64), Expect = 0.76
Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 19/84 (22%)
Query: 149 FVQGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFD 208
F + +EE + ++F FG + V + ++ R F GFVTF+
Sbjct: 5 FPADSRFTEEDVSEYFGQFGPVLDVRIPYQQKRMF-------------------GFVTFE 45
Query: 209 SPESSDKAITEVNGTHVQGVKLKV 232
+ E+ + +++ N + G +++V
Sbjct: 46 NAETVKRILSKGNPHFICGSRVRV 69
>gnl|CDD|145308 pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29).
Length = 404
Score = 31.1 bits (71), Expect = 0.80
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 33 PIEAKD-AREVARKLLKSGAINPIVR 57
P+EA R + + ++GA N +V
Sbjct: 31 PVEAAPLVRALVEEAYEAGAKNVVVE 56
>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 = 28.8 bits (64), Expect = 0.82
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 8/55 (14%)
Query: 148 IFVQGAGISE--EFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDK 194
IFV G ++ E ++Q+F FGK+ + +K G GFVTF+S + +K
Sbjct: 2 IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK 56
>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 = 28.9 bits (64), Expect = 0.89
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 157 EEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
E LR +F +GKI ++ + ++ G FVTFD + DK +
Sbjct: 14 EHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIV 59
>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 = 28.6 bits (64), Expect = 0.91
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 155 ISEEFLRQHFSIFGKI--CSVSME---VEKGRGFVTFDSPESSDKAI 196
+E +R F+ FG I C+V + +G FVTF S + + AI
Sbjct: 13 CNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAI 59
>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 = 28.4 bits (64), Expect = 0.98
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
GFV + S S+ KA +++G + G KL+V
Sbjct: 44 GFVEYASKASALKAKNQLDGKQIGGRKLQV 73
Score = 27.2 bits (61), Expect = 2.8
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 156 SEEFLRQHFSIFGKIC------SVSMEVEKGRGFVTFDSPESSDKA 195
++E R+ S FG + S S KG GFV + S S+ KA
Sbjct: 12 TDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57
>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 = 28.2 bits (63), Expect = 1.1
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAITD 198
+E+ LR HF G+I V M KG FV F+ E + A+
Sbjct: 10 TTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKG 59
>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 = 28.4 bits (63), Expect = 1.1
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAI 196
IFV G E LR +F +GKI ++ + ++ G FVTFD ++ DK +
Sbjct: 3 IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIV 59
>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 = 28.3 bits (63), Expect = 1.2
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 153 AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
I+EE +R+ F +GK + + +KG GF+ ++ ++ A
Sbjct: 11 PDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIA 53
>gnl|CDD|184091 PRK13500, PRK13500, transcriptional activator RhaR; Provisional.
Length = 312
Score = 30.1 bits (67), Expect = 1.2
Identities = 18/51 (35%), Positives = 23/51 (45%)
Query: 114 RETNDDRTPVDKKVYGESLLTRLAPNEKPKGGNTIFVQGAGISEEFLRQHF 164
R T+D P + + L+TRLA + K F A SE LRQ F
Sbjct: 193 RYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQF 243
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM2 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 28.4 bits (63), Expect = 1.3
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAITDDCARG 203
+S E L + FS+FG++ + V+ G+G V F S+ KA+ D C+ G
Sbjct: 11 VSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKAL-DRCSDG 63
>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 = 28.4 bits (64), Expect = 1.3
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 10/48 (20%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVEKGR--------GFVTFDSPESSDKA 195
++E L FS FGKI S EV + + F+ F++ E ++A
Sbjct: 16 TDEDLEIIFSRFGKIKSC--EVIRDKKTGDSLQYAFIEFETKEDCEEA 61
>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome
proliferator-activated receptor gamma
coactivator-related protein 1 (PRC) and similar
proteins. This subgroup corresponds to the RRM of PRC,
also termed PGC-1-related coactivator, one of the
members of PGC-1 transcriptional coactivators family,
including peroxisome proliferator-activated receptor
gamma coactivators PGC-1alpha and PGC-1beta. Unlike
PGC-1alpha and PGC-1beta, PRC is ubiquitous and more
abundantly expressed in proliferating cells than in
growth-arrested cells. PRC has been implicated in the
regulation of several metabolic pathways, mitochondrial
biogenesis, and cell growth. It functions as a
growth-regulated transcriptional cofactor activating
many nuclear genes specifying mitochondrial respiratory
function. PRC directly interacts with nuclear
transcriptional factors implicated in respiratory chain
expression including nuclear respiratory factors 1 and 2
(NRF-1 and NRF-2), CREB (cAMP-response element-binding
protein), and estrogen-related receptor alpha
(ERRalpha). It interacts indirectly with the NRF-2beta
subunit through host cell factor (HCF), a cellular
protein involved in herpes simplex virus (HSV) infection
and cell cycle regulation. Furthermore, like PGC-1alpha
and PGC-1beta, PRC can transactivate a number of
NRF-dependent nuclear genes required for mitochondrial
respiratory function, including those encoding
cytochrome c, 5-aminolevulinate synthase, Tfam, and
TFB1M, and TFB2M. Further research indicates that PRC
may also act as a sensor of metabolic stress that
orchestrates a redox-sensitive program of inflammatory
gene expression. PRC is a multi-domain protein
containing an N-terminal activation domain, an LXXLL
coactivator signature, a central proline-rich region, a
tetrapeptide motif (DHDY) responsible for HCF binding, a
C-terminal arginine/serine-rich (SR) domain, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 91
Score = 28.3 bits (63), Expect = 1.3
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 160 LRQHFSIFGKI--CSVSMEVE-KGRGFVTFDSPESSDKAI 196
L+ FS+FG+I C++ E GFVT+ E + AI
Sbjct: 19 LKDRFSVFGEIEECTIHFRSEGDNYGFVTYRYTEEAFAAI 58
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 27.9 bits (63), Expect = 1.4
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKAI 196
++EE L + F G + +V + ++ G GFV F S E +D AI
Sbjct: 10 VTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAI 57
Score = 27.6 bits (62), Expect = 2.2
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
GFV F S E +D AI +N + G ++V+
Sbjct: 43 GFVEFLSEEDADYAIKIMNMIKLYGKPIRVN 73
>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 = 28.2 bits (63), Expect = 1.5
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 146 NTIFVQGAGIS--EEFLRQHFSIFGKICSVSM-----EVEKGRGFVTF 186
NT+FV G I E +R F+ +G + V + V KG GFV+F
Sbjct: 6 NTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSF 53
>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 = 27.9 bits (62), Expect = 1.6
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 10/80 (12%)
Query: 164 FSIFGKICSVSMEVEKGRGFVTFDSPESSDKA---ITD---DCAR--GFVTFDSPESSDK 215
+SIF + +S EV + F S S K+ +TD +R GFV F +
Sbjct: 2 YSIF--VGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQR 59
Query: 216 AITEVNGTHVQGVKLKVSLA 235
A+ E+ G + G +++S A
Sbjct: 60 ALIEMQGVYCGGRPMRISTA 79
>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 = 27.5 bits (61), Expect = 1.6
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+E+ +R F +GK+ + ++ K GFV D ++D+AI
Sbjct: 13 TEQEIRSLFEQYGKV--LECDIIKNYGFVHMDDKTAADEAI 51
>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 = 1.8
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
G++E L + S FG I V+M +K + V F+ + +
Sbjct: 13 GVTEADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVN 56
>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 = 27.6 bits (62), Expect = 1.8
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 147 TIFVQGAGIS--EEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAITDD 199
T+FV S E+ LR+ FS G+I V + KG +V F++ ES +A+ D
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLD 60
>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 = 27.5 bits (62), Expect = 1.8
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESS 192
++E L S FGK+ +V + K + V DS ES+
Sbjct: 10 DVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESA 48
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 30.0 bits (67), Expect = 1.9
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F+ E + KA+ E+NG ++G +++V+LA+
Sbjct: 273 FVHFEDREDAVKAMDELNGKELEGSEIEVTLAK 305
>gnl|CDD|223279 COG0201, SecY, Preprotein translocase subunit SecY [Intracellular
trafficking and secretion].
Length = 436
Score = 29.5 bits (67), Expect = 2.0
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 38 DAREVARKLLKSGAINPIVRPPKRCEQE 65
+ E+A L KSG P +RP K E+
Sbjct: 336 NPEEIAENLKKSGGFIPGIRPGKDTEKY 363
>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 = 27.6 bits (62), Expect = 2.0
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEK-----GRGFVTFDSPESSDKAI 196
++EE L + F G++ V + ++ G V F+ E +++AI
Sbjct: 11 DVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAI 58
>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 = 28.4 bits (63), Expect = 2.1
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 156 SEEFLRQHFSIFGKI------CSVSMEVEKGRGFVTFDSPESSDKAI 196
+EE L HFS FG + S KG GFV F + + +
Sbjct: 14 TEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60
>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 = 27.6 bits (62), Expect = 2.2
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 23/87 (26%)
Query: 153 AGISEEFLRQHFSIF-GKICSVSM---EVEKGRGFVTFDSPESSDKAITDDCARGFVTFD 208
A ++E L++HFS G+I V + E K R F+ +
Sbjct: 10 ASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRI-------------------AFIGYK 50
Query: 209 SPESSDKAITEVNGTHVQGVKLKVSLA 235
+ E + KA N T++ K+ V A
Sbjct: 51 TEEEAQKAKDYFNNTYINTSKISVEFA 77
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 27.7 bits (61), Expect = 2.3
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAITDDCARG 203
+S E L Q FS FG + + V+ G+GFV F + ++ KA+ + CA G
Sbjct: 11 VSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKAL-ERCADG 63
>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 = 27.3 bits (61), Expect = 2.3
Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 23/82 (28%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKG----RGFVTFDSPESSDKAITDDCARGFVTFDSP 210
+ + LR+ F +G++ V + ++ RGF FV F
Sbjct: 10 TTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGF-------------------AFVRFYDK 50
Query: 211 ESSDKAITEVNGTHVQGVKLKV 232
++ A+ ++G + G +L+V
Sbjct: 51 RDAEDAMDAMDGKELDGRELRV 72
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 80
Score = 27.5 bits (60), Expect = 2.3
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKAITDDCARG 203
G +++ L + +GKI S ++K G GFV FDSP ++ KA+ A G
Sbjct: 15 GTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASLKANG 70
Score = 27.1 bits (59), Expect = 3.6
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 192 SDKAI----TDDC-ARGFVTFDSPESSDKAITEVNGTHVQG 227
S KAI T+ C GFV FDSP ++ KA+ + VQ
Sbjct: 33 STKAILDKNTNQCKGYGFVDFDSPAAAQKAVASLKANGVQA 73
>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 = 27.3 bits (60), Expect = 2.3
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 148 IFVQGAG--ISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDK 194
+FV G +EE ++++F FG+I ++ + ++ +G FVT+ E K
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQK 56
>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 = 27.2 bits (61), Expect = 2.4
Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 24/86 (27%)
Query: 153 AGISEEFLRQHFSIFGKICSVSMEVEKG---RGFVTFDSPESSDKAITDDCARGFVTFDS 209
A E LR+ FS FG++ SV + + RGF FV F +
Sbjct: 12 ATKKE--LRELFSPFGQVKSVRLPKKFDGSHRGF-------------------AFVEFVT 50
Query: 210 PESSDKAITEVNGTHVQGVKLKVSLA 235
+ + A+ + TH+ G L + A
Sbjct: 51 KQEAQNAMEALKSTHLYGRHLVLEYA 76
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 27.2 bits (60), Expect = 2.4
Identities = 25/89 (28%), Positives = 36/89 (40%), Gaps = 18/89 (20%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
T+FV + EE L + F G + V++ +K E K+ GF
Sbjct: 3 TLFVGNLECRVREEILYELFLQAGPLTKVTICKDK----------EGKPKSF------GF 46
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVS 233
V F ES AI +NG + G +KV
Sbjct: 47 VCFKHSESVPYAIALLNGIRLYGRPIKVH 75
>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 = 27.3 bits (61), Expect = 2.4
Identities = 16/37 (43%), Positives = 24/37 (64%), Gaps = 6/37 (16%)
Query: 160 LRQHFSIFGKI--CSVSMEVE----KGRGFVTFDSPE 190
L+++FS FGK+ C+V + E KG GFV+F S +
Sbjct: 16 LKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD 52
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 27.0 bits (60), Expect = 2.5
Identities = 21/93 (22%), Positives = 34/93 (36%), Gaps = 26/93 (27%)
Query: 147 TIFVQG---AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
T+FV G EE + + F FG + + TF
Sbjct: 1 TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRK-------TF----------------A 37
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F+ E + KA+ ++G+ + G L V +
Sbjct: 38 FVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70
>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 = 27.3 bits (61), Expect = 2.6
Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 15/76 (19%)
Query: 160 LRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITE 219
L + FS +GK+ V++ +K ++ +S A F+ F E + K +
Sbjct: 18 LHKIFSKYGKVVKVTIVKDK-------ETRKSKGVA--------FILFLDREDAHKCVKA 62
Query: 220 VNGTHVQGVKLKVSLA 235
+N + G LK S+A
Sbjct: 63 LNNKELFGRTLKCSIA 78
>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 = 27.3 bits (61), Expect = 2.6
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 148 IFVQGA--GISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAI 196
IFV G + E L++HF G I +++ + KG ++ F S + A+
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL 58
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 27.2 bits (60), Expect = 2.7
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV FD P +D A+ E++G + ++ + AR
Sbjct: 36 GFVEFDDPRDADDAVYELDGKELCNERVTIEHAR 69
Score = 25.7 bits (56), Expect = 7.5
Identities = 13/40 (32%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 157 EEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
E+ + + F +G+I + ++++G GFV FD P +D A+
Sbjct: 13 EKDVERFFKGYGRIRDI--DLKRGFGFVEFDDPRDADDAV 50
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 27.4 bits (61), Expect = 2.8
Identities = 20/92 (21%), Positives = 43/92 (46%), Gaps = 18/92 (19%)
Query: 146 NTIFVQGAGIS--EEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
+ +FV G S +E L + F G + SV + VT S + A
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRL--------VTNRSGKPKGLA-------- 46
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
+V +++ S+ +A+ +++GT ++ + V+++
Sbjct: 47 YVEYENESSASQAVLKMDGTEIKEKTISVAIS 78
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 27.5 bits (60), Expect = 2.9
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 192 SDKAITDDCAR-----GFVTFDSPESSDKAITEVNGTHVQG 227
S KAI D GFV FDSP ++ KA++ + + VQ
Sbjct: 36 STKAILDKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQA 76
Score = 27.1 bits (59), Expect = 3.5
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 167 FGKICSVSMEVEK------GRGFVTFDSPESSDKAITDDCARG 203
+GKI S ++K G GFV FDSP ++ KA++ A G
Sbjct: 31 YGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSALKASG 73
>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 = 26.9 bits (60), Expect = 3.0
Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 21/83 (25%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESS 213
++EE L+ F +G+I S+ M +G CA +V ++ + +
Sbjct: 13 KVTEEDLKNLFEEYGEIQSIDMIPPRG-------------------CA--YVCMETRQDA 51
Query: 214 DKAITEVNGTHVQGVKLKVSLAR 236
+A+ ++ + G K+KV+ A
Sbjct: 52 HRALQKLRNVKLAGKKIKVAWAP 74
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily corresponds
to the RRM2 of La and LARP7. La is a highly abundant
nuclear phosphoprotein and well conserved in eukaryotes.
It specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. LARP7
is an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
of 7SK RNA. It is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP), intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. LARP7 plays an essential role in the inhibition
of positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
Both La and LARP7 contain an N-terminal La motif (LAM),
followed by two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 26.9 bits (60), Expect = 3.2
Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 21/84 (25%)
Query: 152 GAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
G G++ E ++ F+ FG++ +V F + G++ F +PE
Sbjct: 10 GPGVTREDIKAVFAQFGEV-----------KYVDFTEGADT----------GYIRFKTPE 48
Query: 212 SSDKAITEVNGTHVQGVKLKVSLA 235
++ KA + ++ L+
Sbjct: 49 AAQKAREAFVEKGEGLLGKEIKLS 72
>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 = 27.2 bits (60), Expect = 3.2
Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 20/82 (24%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+SE LR HF + ++ +S+ ++ FD +
Sbjct: 11 VSEGDLRSHFQKY-QVSVISL----------CKLSNYRYASLH---------FDRASDAL 50
Query: 215 KAITEVNGTHVQGVKLKVSLAR 236
A+ ++NG + G+ +KV + +
Sbjct: 51 LAVKKMNGGVLSGLSIKVRMVK 72
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 27.1 bits (61), Expect = 3.2
Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 22/80 (27%)
Query: 156 SEEFLRQHFSIFGKICSV---SMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPES 212
+ +R F +G+I S+ S+ K R F C +V F SPES
Sbjct: 13 DQSDIRDLFEQYGEILSIRFPSLRFNKTRRF----------------C---YVQFTSPES 53
Query: 213 SDKAITEVNGTHVQGVKLKV 232
+ A+ +NG +G KL V
Sbjct: 54 AAAAVALLNGKLGEGYKLVV 73
>gnl|CDD|241225 cd12781, RRM1_hnRPLL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). This subgroup corresponds to the RRM1 of
hnRNP-LL, which 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 heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 27.4 bits (60), Expect = 3.4
Identities = 14/43 (32%), Positives = 20/43 (46%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
+ E L + FG IC V M K + V F+ ES+ K +
Sbjct: 15 VVEADLVEALEKFGPICYVMMMPFKRQALVEFEMVESAKKCVA 57
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 26.8 bits (60), Expect = 3.6
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 146 NTIFVQ--GAGISEEFLRQHFSIFGKICSVSMEVEKGRG---FVTFDSPESSDKA 195
NT+FV G +EE LRQ FS + M KG G FV F+ + +A
Sbjct: 3 NTLFVANLGPNTTEEELRQLFSRQPGFRRLKM-HNKGGGPVCFVEFEDVSFATQA 56
>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 = 27.1 bits (60), Expect = 3.7
Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 23/83 (27%)
Query: 154 GISEEFLRQHFSIFGKICSV----SMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDS 209
G E+ L+++FS FG + +V S + + + GF+ F +
Sbjct: 10 GFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHY-------------------GFIQFLN 50
Query: 210 PESSDKAITEVNGTHVQGVKLKV 232
PE + A +N + G L+V
Sbjct: 51 PEVAAIAAKSMNNYLLMGKVLQV 73
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 26.6 bits (59), Expect = 3.8
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
G V F + +AI +++GT + G K+K+
Sbjct: 39 EGVVEFATYSDMKRAIEKLDGTELNGRKIKLI 70
>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 = 26.9 bits (60), Expect = 4.0
Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 19/84 (22%)
Query: 160 LRQHFSIFGKICSVSMEVEKGRG------FVTFDSPESSDKAITDDCARGFVTFDSPESS 213
+R HF FG+I ++++ G VTF + + A+
Sbjct: 15 IRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGD-PLRPSAAHEAAK----------- 62
Query: 214 DKAITEVNGTHVQGVKLKVSLARR 237
A+ +NG + G +++V L R
Sbjct: 63 -AAVDGLNGRRIGGKRVRVELDRD 85
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 26.4 bits (59), Expect = 4.1
Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 18/80 (22%)
Query: 153 AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPES 212
+SE+ FG SV + +G+ + A F TFD+ ++
Sbjct: 9 PELSEDDKEDLLKHFG-ASSVRVMSRRGKL---------------KNTA--FATFDNEQA 50
Query: 213 SDKAITEVNGTHVQGVKLKV 232
+ +A++ ++ + G +L V
Sbjct: 51 ASQALSRLHQLKILGKRLVV 70
>gnl|CDD|185358 PRK15461, PRK15461, NADH-dependent gamma-hydroxybutyrate
dehydrogenase; Provisional.
Length = 296
Score = 28.7 bits (64), Expect = 4.1
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 189 PESSDKAITDDCARGFVTFDSP--ESSDKAIT 218
P +DK I D A+GF D P +SD AIT
Sbjct: 99 PLQTDKLIADMQAKGFSMMDVPVGRTSDNAIT 130
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 26.8 bits (60), Expect = 4.3
Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 32/93 (34%)
Query: 145 GNTIFVQGAGISEE--------FLRQHFSIFGKICSVSM-----EVEKGRGFVTFDSPES 191
N + V G + E LR+ FS FG V + E K +G+
Sbjct: 1 DNVVVVDGLPVVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYA------- 53
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTH 224
FV F +PE + +A+ +NG
Sbjct: 54 ------------FVEFATPEEAKEAVKALNGYK 74
>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 = 26.5 bits (59), Expect = 4.4
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
FVTF S AI +NG + G +L++
Sbjct: 45 AFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 75
>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 = 26.8 bits (60), Expect = 4.5
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 203 GFVTFDSPESSDKAITEVNGTHVQG--VKLKVS 233
GFV+F P KA+ E+NG +V +KL+ S
Sbjct: 51 GFVSFSDPNDYLKAMKEMNGKYVGNRPIKLRKS 83
>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 = 26.5 bits (59), Expect = 4.7
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 150 VQGAGISEEFLRQHFSIFGKICSVSM------EVEKGRGFVTFDSPESSDKAI 196
V G ++E+ LR+ F+ FG+I + + + KG +V F S+ +A+
Sbjct: 9 VCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 91
Score = 26.8 bits (60), Expect = 5.0
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
V F PE +D+ I +NG G +L+
Sbjct: 55 VKFKEPEEADRCIEALNGRWFAGRQLEAER 84
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 28.5 bits (64), Expect = 5.9
Identities = 20/109 (18%), Positives = 33/109 (30%), Gaps = 4/109 (3%)
Query: 17 PRPEPERTQASSTLKRPIEAKDAREVARKLLKSGAINPIVRPPKRCEQEGFKRPRGLERK 76
P+ P+R A P + E S V+ K+ + E+K
Sbjct: 1271 PKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKK 1330
Query: 77 LTETDRSTVSAYQPFSAIQPEDSEPVDSKPKFLKVSKRETNDDRTPVDK 125
+S Q S + +P+ K +DD + VD
Sbjct: 1331 TARKKKSKTRVKQA----SASQSSRLLRRPRKKKSDSSSEDDDDSEVDD 1375
>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this
family for which functions are known are DNA-DNA
helicases used for the initiation of nucleotide excision
repair and transacription as part of the TFIIH
complex.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 732
Score = 28.2 bits (63), Expect = 6.0
Identities = 15/86 (17%), Positives = 29/86 (33%), Gaps = 3/86 (3%)
Query: 34 IEAKDAREVARKLLKSGAINPIVRPPKRCEQEGFKRPRGLERKLTETDRSTVSAYQPFSA 93
+E+ EV ++LLK I P E+E + P ++ ++ +
Sbjct: 118 VESPHP-EVLQRLLKDPVIAPCRI--DPTEEESLQTPTYGSKEDFIINKPGFTGGASAGQ 174
Query: 94 IQPEDSEPVDSKPKFLKVSKRETNDD 119
++ E K E +D
Sbjct: 175 LEANQGESAVPKDIADFYELEEEEED 200
>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of
Bacterial RNA polymerase. The bacterial alpha subunit
of RNA polymerase (RNAP) consists of two independently
folded domains: an amino-terminal domain (alphaNTD) and
a carboxy-terminal domain (alphaCTD). AlphaCTD is not
required for RNAP assembly but interacts with
transcription activators. AlphaNTD is essential in vivo
and in vitro for RNAP assembly and basal transcription.
It is similar to the eukaryotic RPB3/AC40/archaeal D
subunit, and contains two subdomains: one subdomain is
similar the eukaryotic Rpb11/AC19/archaeal L subunit
which is involved in dimerization; and the other is an
inserted beta sheet subdomain. The alphaNTDs of plant
plastid RNAP (PEP) are also included in this subfamily.
PEP is largely responsible for the transcription of
photosynthetic genes and is closely related to the
multi-subunit bacterial RNAP, which is a large
multi-subunit complex responsible for the synthesis of
all bacterial RNAs. The bacterial RNAP core enzyme
consists of four subunits (beta', beta, alpha and
omega). All residues in the alpha subunit that is
involved in dimerization or in the interaction with
other subunits are located within alphaNTD.
Length = 215
Score = 27.8 bits (63), Expect = 6.4
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 173 VSMEVEKGRGFVTFDSPESSDKAI 196
+ + +EKGRG+V + +S +K I
Sbjct: 129 MELRIEKGRGYVPAEENKSEEKPI 152
>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 = 26.0 bits (58), Expect = 6.4
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 203 GFVTFDSPESSDKAITEVNGTHV-QGVKLKVS 233
FV F++ E + A+ + G + G +K+S
Sbjct: 41 AFVEFETEEQATVALQALQGFKITPGHAMKIS 72
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 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 = 98
Score = 26.4 bits (58), Expect = 6.7
Identities = 9/39 (23%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 198 DDCARGF--VTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
C GF V +++ E +++ ++GT ++G ++++S
Sbjct: 40 GSCVGGFAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSF 78
>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 = 26.2 bits (58), Expect = 6.8
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAIT 197
E+ + + F +G+I SV + + KG G+V F S E++ A+
Sbjct: 10 ADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALD 58
>gnl|CDD|216804 pfam01949, DUF99, Protein of unknown function DUF99. The function
of this archaebacterial protein family is unknown.
Length = 185
Score = 27.6 bits (62), Expect = 6.9
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 132 LLTRLAPNEK-PKGGNTIFVQGAGISEEFLRQ---HFSIFGKI 170
++ +L P E P G +++Q AGI E ++ +I GKI
Sbjct: 123 IIRKLGPIEPLPTRGGPVYIQAAGIDPEEAKELIERTTIRGKI 165
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation step
of chromosome segregation. Not every bacterium has both
a topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 27.9 bits (62), Expect = 7.0
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 20 EPERTQASSTLKRPIEAKDAREVARK 45
E A + + I+A+DA+E A+K
Sbjct: 362 EENNNDAKLLIDKAIKARDAKEAAKK 387
>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 = 26.2 bits (57), Expect = 7.8
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 23/84 (27%)
Query: 156 SEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
+E LR+ FS +G I VS+ + + RGF FV F++ +
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGF-------------------AFVYFENVD 62
Query: 212 SSDKAITEVNGTHVQGVKLKVSLA 235
+ +A NG + G +++V +
Sbjct: 63 DAKEAKERANGMELDGRRIRVDFS 86
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 26.0 bits (58), Expect = 8.2
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 198 DDCARGFVTFDSPESSDKAITEVNG 222
DD R FV F + + KA+ +NG
Sbjct: 47 DDAVRIFVEFSDADEAIKAVRALNG 71
>gnl|CDD|226950 COG4584, COG4584, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 278
Score = 27.4 bits (61), Expect = 8.6
Identities = 12/38 (31%), Positives = 16/38 (42%)
Query: 23 RTQASSTLKRPIEAKDAREVARKLLKSGAINPIVRPPK 60
Q S+L ARE R+ L++ P RPP
Sbjct: 14 YRQGMSSLSIARATGVARETVRRYLQAKPPKPQRRPPV 51
>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 = 25.8 bits (56), Expect = 9.3
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 6/48 (12%)
Query: 156 SEEFLRQHFSIFGKI--CSV----SMEVEKGRGFVTFDSPESSDKAIT 197
++E LR HF +G + C V + + +G GFVT+ S E D A+
Sbjct: 15 TDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62
>gnl|CDD|233755 TIGR02165, cas_GSU0054, CRISPR-associated protein GSU0054/csb2,
Dpsyc system. This model represents a CRISPR-associated
protein from the Dpsyc subtype, named for Desulfotalea
psychrophila LSv54. CRISPR systems confer resistance in
prokaryotes to invasive DNA or RNA, including phage and
plasmids. CRISPR-associated proteins typically are found
near CRISPR repeats and other CRISPR-associated
proteins, have low levels of sequence identify, have
sequence relationships that suggest lateral transfer,
and show some sequence similarity to DNA-active proteins
such as helicases and repair proteins [Mobile and
extrachromosomal element functions, Other].
Length = 487
Score = 27.4 bits (61), Expect = 9.4
Identities = 21/84 (25%), Positives = 31/84 (36%), Gaps = 6/84 (7%)
Query: 9 KSLQAQKAPRPEPERTQASST---LKRPIEAKDAREVARKLLKSGAINPIVRPPKRCEQE 65
+SL Q+ P P P R A+ T L R + + V R ++ A VR K +
Sbjct: 364 RSLDPQRWPAPSPARIWATVTPVVLPRRPKKRGDGHVFRDEFETEAAG-QVR--KALRRA 420
Query: 66 GFKRPRGLERKLTETDRSTVSAYQ 89
G P ++ AY
Sbjct: 421 GLPEPAAIQPLAASLVAGAPRAYV 444
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 0.129 0.366
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,710,176
Number of extensions: 1362940
Number of successful extensions: 1474
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1332
Number of HSP's successfully gapped: 252
Length of query: 298
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 202
Effective length of database: 6,679,618
Effective search space: 1349282836
Effective search space used: 1349282836
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: 59 (26.4 bits)