RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15515
(242 letters)
>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 = 125 bits (317), Expect = 2e-37
Identities = 44/81 (54%), Positives = 64/81 (79%), Gaps = 1/81 (1%)
Query: 42 VPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQ 101
+P R+FVGGI TTE+EL + FS++G VK VKI+ DRAG+SKGYGF+TF+++E+A+++
Sbjct: 1 IPNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKIL 60
Query: 102 KDSDNIMFKEKRLNIAPAIKK 122
N+ F+ K+LNI PAI+K
Sbjct: 61 AM-GNLNFRGKKLNIGPAIRK 80
>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 = 114 bits (286), Expect = 6e-33
Identities = 43/81 (53%), Positives = 67/81 (82%)
Query: 42 VPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQ 101
+P R+FVGGI T E++L + FSQYG VK+VKIV DRAG+SKGYGF+TF+++E+A+++
Sbjct: 1 IPNRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKIL 60
Query: 102 KDSDNIMFKEKRLNIAPAIKK 122
++++ + F++K+LNI AI+K
Sbjct: 61 QEANRLCFRDKKLNIGQAIRK 81
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 87.3 bits (217), Expect = 1e-22
Identities = 28/73 (38%), Positives = 47/73 (64%), Gaps = 1/73 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
+FVG + TTE+EL ELFS++G V+ V++V D+ G SKG+ F+ F+SEE+A++ +
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 104 SDNIMFKEKRLNI 116
+ + L +
Sbjct: 61 LNGKELDGRPLKV 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 = 86.8 bits (215), Expect = 3e-22
Identities = 36/84 (42%), Positives = 55/84 (65%), Gaps = 2/84 (2%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
G ++P VFVGGI E E+ F++YG VK+VKI+ DR G+SKGYGF++F + + +
Sbjct: 1 GKIMPNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQ 60
Query: 99 RLQKDSDNIMFKEKRLNIAPAIKK 122
++ + I F K+L + PAI+K
Sbjct: 61 KIVESQ--INFHGKKLKLGPAIRK 82
>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 = 82.4 bits (204), Expect = 9e-21
Identities = 26/71 (36%), Positives = 47/71 (66%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+FVG + TTE++L ELFS++G ++ V+IV D+ G SKG+ F+ F+S E+A++ + +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 106 NIMFKEKRLNI 116
++L +
Sbjct: 61 GKELDGRKLKV 71
>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 = 78.0 bits (193), Expect = 4e-19
Identities = 24/69 (34%), Positives = 44/69 (63%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+FVG + TTE++L +LFS++G ++ ++IV D G SKG+ F+ F+ EE+A++ + +
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 106 NIMFKEKRL 114
+ L
Sbjct: 61 GKELGGREL 69
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 71.0 bits (175), Expect = 2e-16
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
++V + + TE++L E FS YG V+ V++V ++ +G+ F+ F S E+A+ K +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59
Query: 106 NIMFKEKRLN 115
++ + L
Sbjct: 60 GLVLDGRTLR 69
>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 = 70.9 bits (174), Expect = 3e-16
Identities = 24/75 (32%), Positives = 47/75 (62%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
++FV G+ + T++EL +LF ++G+VK V++V +R+G KG ++ +++E A +
Sbjct: 2 KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVL 61
Query: 103 DSDNIMFKEKRLNIA 117
D KEK +++A
Sbjct: 62 KMDGTEIKEKTISVA 76
>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 = 69.6 bits (171), Expect = 9e-16
Identities = 27/80 (33%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQ 101
++FV G+++ TTE EL LFS++G V++V ++ D G S+G+GF+TF+S E+A
Sbjct: 1 GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60
Query: 102 KDSDNIMFKEKRLNIAPAIK 121
+D + + + + + A +
Sbjct: 61 RDLNGKELEGRVIKVEKAKR 80
>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 = 66.6 bits (163), Expect = 1e-14
Identities = 25/57 (43%), Positives = 38/57 (66%), Gaps = 1/57 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
++FVGG+ TE+E E FSQ+G V +++ D G S+G+GF+TFDSE +R+
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERV 57
>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 = 65.8 bits (161), Expect = 2e-14
Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKD 103
R+FV + TTTE+EL ELF +G + +V + +D+ SKG+ F++F E A + +
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 104 SDNIMFKEKRLNI 116
D +F+ + L++
Sbjct: 61 LDGSIFQGRLLHV 73
>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 = 65.0 bits (159), Expect = 4e-14
Identities = 28/64 (43%), Positives = 45/64 (70%), Gaps = 4/64 (6%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDS 104
VF G++ TTE +L E+FS+YG +++V++V D + G S+G+GF+ F+S E+AK K+
Sbjct: 4 VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKE-AKER 60
Query: 105 DNIM 108
N M
Sbjct: 61 LNGM 64
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 68.8 bits (167), Expect = 1e-13
Identities = 26/75 (34%), Positives = 47/75 (62%), Gaps = 1/75 (1%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQ 101
+FVG + TE++L ELF ++G VK+V++V DR G S+G+ F+ F+SEE A++
Sbjct: 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAI 174
Query: 102 KDSDNIMFKEKRLNI 116
++ + + + L +
Sbjct: 175 EELNGKELEGRPLRV 189
>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 = 63.8 bits (156), Expect = 1e-13
Identities = 24/49 (48%), Positives = 35/49 (71%), Gaps = 1/49 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFD 92
++FVGG+ TE++L E FSQYG V+ V+IV D+ G +G+ F+TFD
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFD 49
>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 = 63.4 bits (155), Expect = 2e-13
Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 6/82 (7%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
+ VF+ + TE+EL ELFSQ+G VK +IV D+ G SKG F+ F ++E A++ +
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 103 DSDN-----IMFKEKRLNIAPA 119
+DN + +RL + A
Sbjct: 61 AADNAEDSGLSLDGRRLIVTLA 82
>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 = 62.4 bits (152), Expect = 4e-13
Identities = 25/69 (36%), Positives = 42/69 (60%), Gaps = 2/69 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGI-SKGYGFITFDSEEEAKR-LQ 101
K++FVGG+ TE +L + FSQ+G V +V ++ D +G+GFITF+SE+ + +
Sbjct: 3 KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62
Query: 102 KDSDNIMFK 110
+ +I K
Sbjct: 63 EHFHDINGK 71
>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 = 61.9 bits (151), Expect = 6e-13
Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKD 103
++VG + TE++L +LF Q+G V +++ DR G S+G+GF+ ++ EEA +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 104 SDNIMFKEKRLNIAPA 119
+ F + L + A
Sbjct: 61 LNGTDFGGRTLTVNEA 76
>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 = 61.3 bits (149), Expect = 9e-13
Identities = 21/56 (37%), Positives = 40/56 (71%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
++FVGG+++ TTED++ + FSQ+G V+ ++ D+ +G+GF+TF+SE+ +
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDK 56
>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 = 61.4 bits (150), Expect = 1e-12
Identities = 24/77 (31%), Positives = 44/77 (57%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
V+V + +++L ELF +YG + K++ D G SKG+GF+ F++ E A++ ++ +
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63
Query: 106 NIMFKEKRLNIAPAIKK 122
K+L + A KK
Sbjct: 64 GKEVNGKKLYVGRAQKK 80
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 60.6 bits (148), Expect = 1e-12
Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
+ VG +T +D L E+FS YG VK V + +DR + +GY ++ F+S E+A++ K
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP complex,
which is one of the key factors facilitating the
splicing of pre-mRNA via interaction at the 5' splice
site, and is involved in regulation of polyadenylation
of some viral and cellular genes, enhancing or
inhibiting efficient poly(A) site usage. U1-70K plays an
essential role in targeting the U1 snRNP to the 5'
splice site through protein-protein interactions with
regulatory RNA-binding splicing factors, such as the RS
protein ASF/SF2. Moreover, U1-70K protein can
specifically bind to stem-loop I of the U1 small nuclear
RNA (U1 snRNA) contained in the U1 snRNP complex. It
also mediates the binding of U1C, another U1-specific
protein, to the U1 snRNP complex. U1-70K contains a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by an adjacent glycine-rich region at the
N-terminal half, and two serine/arginine-rich (SR)
domains at the C-terminal half. The RRM is responsible
for the binding of stem-loop I of U1 snRNA molecule.
Additionally, the most prominent immunodominant region
that can be recognized by auto-antibodies from
autoimmune patients may be located within the RRM. The
SR domains are involved in protein-protein interaction
with SR proteins that mediate 5' splice site
recognition. For instance, the first SR domain is
necessary and sufficient for ASF/SF2 Binding. The family
also includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but its
SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 61.1 bits (149), Expect = 2e-12
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQK 102
K +FV + TTE +L F +YG +K++++V D+ G +GY FI F+ E + K K
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61
Query: 103 DSDNIMFKEKRL 114
+D +R+
Sbjct: 62 YADGKKIDGRRV 73
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the RRM
of SLIRP, a widely expressed small steroid receptor RNA
activator (SRA) binding protein, which binds to STR7, a
functional substructure of SRA. SLIRP is localized
predominantly to the mitochondria and plays a key role
in modulating several nuclear receptor (NR) pathways. It
functions as a co-repressor to repress SRA-mediated
nuclear receptor coactivation. It modulates SHARP- and
SKIP-mediated co-regulation of NR activity. SLIRP
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is required for SLIRP's corepression activities. .
Length = 73
Score = 60.4 bits (147), Expect = 2e-12
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEE-AKRLQK 102
++FVG + T EL E FSQ+G VK + D+ G+SKGYGF++F S + LQK
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 103 DS 104
Sbjct: 61 QK 62
>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 = 60.7 bits (148), Expect = 2e-12
Identities = 25/78 (32%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDS 104
+FV + TT+++L E FS+ G +K+ +V D+ +G+G++TF EE+AKR ++
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 105 DNIMFKEKRLNIAPAIKK 122
F +++++ A KK
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
>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 = 60.3 bits (147), Expect = 2e-12
Identities = 30/77 (38%), Positives = 49/77 (63%), Gaps = 2/77 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
++FVGG+ TT+D L + FSQ+G +++ ++ DR G S+GYGF+TF +E A+R K
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 103 DSDNIMFKEKRLNIAPA 119
D N + ++ N+ A
Sbjct: 61 DP-NPIIDGRKANVNLA 76
>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 = 60.0 bits (145), Expect = 4e-12
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGGI T E L + F QYG ++ ++I+ DR +G +G+ F+TFD + ++
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 58
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed in
all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. The family also
includes yeast ortholog mRNA 3'-end-processing protein
RNA15 and similar proteins. RNA15 is a core subunit of
cleavage factor IA (CFIA), an essential transcriptional
3'-end processing factor from Saccharomyces cerevisiae.
RNA recognition by CFIA is mediated by an N-terminal
RRM, which is contained in the RNA15 subunit of the
complex. The RRM of RNA15 has a strong preference for
GU-rich RNAs, mediated by a binding pocket that is
entirely conserved in both yeast and vertebrate RNA15
orthologs.
Length = 75
Score = 59.6 bits (145), Expect = 4e-12
Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
VFVG I TE++L E+FS+ G V ++V DR G KGYGF F+ E A ++
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 105 DNIMFKEKRLNIAPA 119
+ F + L + A
Sbjct: 61 NGYEFNGRALRVDFA 75
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 77
Score = 58.9 bits (143), Expect = 9e-12
Identities = 26/74 (35%), Positives = 47/74 (63%), Gaps = 1/74 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKD 103
+FVG ++ + +D+L E F + G V V+I D G SKG+G + F +EE A++ L+K
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60
Query: 104 SDNIMFKEKRLNIA 117
+ ++ +E R+++A
Sbjct: 61 GEELLGREIRVDLA 74
>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 = 58.1 bits (141), Expect = 2e-11
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 4/79 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKG----YGFITFDSEEEAKRL 100
R+++G + S TE L +LFS+YG +K+ + ++G KG Y F+TF+++EEA++
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 101 QKDSDNIMFKEKRLNIAPA 119
K + K+L + A
Sbjct: 61 LKSLNGKTALGKKLVVRWA 79
>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 = 57.7 bits (140), Expect = 2e-11
Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + + TE+E ELFS+YG V +V + + KG+GFI D+ A++ + +
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAEL 57
Query: 105 DNIMFKEKRLNI 116
D IM K ++L +
Sbjct: 58 DGIMRKGRQLRV 69
>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 = 62.9 bits (153), Expect = 2e-11
Identities = 35/151 (23%), Positives = 56/151 (37%), Gaps = 9/151 (5%)
Query: 54 TTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKR 113
T T+++L ELFS+ G + K+++D G+S+G+GF+ F + EEA R + M K
Sbjct: 296 TVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKP 355
Query: 114 LNIAPAIKKQGFTGTYDSL---PTVTSPVPPVPTSNMYYHNGLPYTYHNGMAFFPSN--- 167
L +A A +K+ P+ + PY F
Sbjct: 356 LYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLG 415
Query: 168 ---GQSMVPTSPPTVPTQVKILLPPGVLLCG 195
M P P + L P +
Sbjct: 416 WPRMSMMPTPMGPGGPLRPNGLAPMNAVRAP 446
Score = 47.1 bits (112), Expect = 3e-06
Identities = 16/54 (29%), Positives = 34/54 (62%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++V + + ED+L ELF+++G + ++ D +G S+G+ F+ F+ E+A +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAK 234
Score = 44.8 bits (106), Expect = 2e-05
Identities = 23/78 (29%), Positives = 41/78 (52%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+FV + + L + FS++G + K+ D G S+GYGF+ F+ EE AK + +
Sbjct: 91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVN 150
Query: 106 NIMFKEKRLNIAPAIKKQ 123
++ +K + + IKK
Sbjct: 151 GMLLNDKEVYVGRFIKKH 168
Score = 39.8 bits (93), Expect = 8e-04
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL--QK 102
++VG + TE +L +LF +G V V++ D S GYG++ F + +A+R
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 103 DSDNIMFKEKRL---NIAPAIKKQG 124
+ + K R+ P++++ G
Sbjct: 63 NFKRLGGKPIRIMWSQRDPSLRRSG 87
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 58.1 bits (141), Expect = 2e-11
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQ-YGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
+FVG +T + +L E FS+ Y K K+V+D+ G S+GYGF+ F E E KR +
Sbjct: 4 LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63
Query: 105 DNIM-FKEKRLNIAPAIKK 122
K + ++ AI K
Sbjct: 64 QGASGLGGKPIRVSLAIPK 82
>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 = 57.9 bits (140), Expect = 2e-11
Identities = 22/55 (40%), Positives = 40/55 (72%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
++F+GG++ T E L ++FS+YG + +V +V DR S+G+GF+TF++ ++AK
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAK 56
>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 = 57.8 bits (140), Expect = 2e-11
Identities = 24/77 (31%), Positives = 48/77 (62%), Gaps = 1/77 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQK 102
R+FV + + ED+L +LFS++G + +V + +D ++G SKG+ ++ F E+A + K
Sbjct: 3 GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62
Query: 103 DSDNIMFKEKRLNIAPA 119
+ D +F+ + ++I P
Sbjct: 63 ELDGKVFQGRLIHILPG 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 = 57.8 bits (140), Expect = 2e-11
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGIS-KGYGFITFDSEEEAKRLQKDS 104
+FVG + TEDEL E F ++G V +V+I G +GF+ FD E +++ +
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65
Query: 105 DNIMFKEKRLNIAP 118
+ RLN+
Sbjct: 66 PIYFRGDHRLNVEE 79
>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 = 57.2 bits (139), Expect = 3e-11
Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 5/52 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
V+VG + TE+EL FS +G +++V++ D KGY F+ FD+ E A
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAA 49
>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 = 57.3 bits (139), Expect = 3e-11
Identities = 23/59 (38%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKD 103
VFV + + EDEL +LFS+ G + V++V + G SKGY ++ F++EE + L+ D
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLD 60
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 57.7 bits (140), Expect = 4e-11
Identities = 24/72 (33%), Positives = 45/72 (62%), Gaps = 1/72 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQK 102
+FVG ++ TTE+ L E+FS+YG ++++++V D G SKGY F+ ++ E +A R +
Sbjct: 4 LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63
Query: 103 DSDNIMFKEKRL 114
D+ ++ +
Sbjct: 64 DAHKLVIDGSEI 75
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a transcription
coactivator of LEF-1 and AML-1 for the TCRalpha enhancer
function. In addition, THOC4 specifically binds to
rhesus (RH) promoter in erythroid, and might be a novel
transcription cofactor for erythroid-specific genes.
SKAR shows high sequence homology with THOC4 and
possesses one RRM as well. SKAR is widely expressed and
localizes to the nucleus. It may be a critical player in
the function of S6K1 in cell and organism growth control
by binding the activated, hyperphosphorylated form of
S6K1 but not S6K2. Furthermore, SKAR functions as a
protein partner of the p50 subunit of DNA polymerase
delta. In addition, SKAR may have particular importance
in pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 56.8 bits (138), Expect = 4e-11
Identities = 24/58 (41%), Positives = 36/58 (62%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQK 102
R+ V + TE++L ELF + G VK+VKI DR+G S+G + F+ E+A+R K
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIK 59
>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 = 56.5 bits (137), Expect = 6e-11
Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDN 106
+V + + ++ L E FS +G + K++ D G SKG+GF+ F S EEA + + +
Sbjct: 5 YVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNG 64
Query: 107 IMFKEKRLNIAPA 119
+ K L +A A
Sbjct: 65 RIIGGKPLYVALA 77
>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 = 56.1 bits (136), Expect = 8e-11
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSD 105
F+GG++ TTE+ L E FS+YG V I+ D G S+G+GF+TF ++
Sbjct: 2 FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61
Query: 106 NI 107
++
Sbjct: 62 HV 63
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 56.0 bits (136), Expect = 9e-11
Identities = 23/63 (36%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
++FVG + T TE+++ LF +YG +++V I+ D+ G SKG F+ F S EEA++ +
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 104 SDN 106
Sbjct: 61 LHG 63
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM1 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 76
Score = 55.5 bits (134), Expect = 2e-10
Identities = 18/56 (32%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
+FVG ++ + ++ L F ++G V +++ DR G S+G+G++ F+S E+AK+
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKK 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 = 54.5 bits (132), Expect = 3e-10
Identities = 22/55 (40%), Positives = 32/55 (58%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
R+ V + TED L E F G V VK++ R G S+ +GF+ F SEE+A++
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQ 56
>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 = 54.7 bits (132), Expect = 3e-10
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 51 ITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMF 109
+ T++EL LF G ++ KIV DR G S GYGF+ + E +A++ +
Sbjct: 8 LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67
Query: 110 KEKRLNIAPA 119
+ KRL ++ A
Sbjct: 68 RNKRLKVSYA 77
>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 = 54.1 bits (131), Expect = 3e-10
Identities = 15/60 (25%), Positives = 34/60 (56%), Gaps = 4/60 (6%)
Query: 60 LCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPA 119
L +LFS +G V+++K++ G+ F+ F +EE A++ + + ++F + L + +
Sbjct: 1 LYKLFSPFGNVEKIKLLKK----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>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 = 54.2 bits (131), Expect = 4e-10
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
++VFVG +T TE++L + FSQ+G V V I + + F+TF E A+ L +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP----FRAFAFVTFADPEVAQSLCGE 56
Query: 104 SDNIMFKEKRLNIAPA 119
I K ++++ A
Sbjct: 57 DHII--KGVSVHVSNA 70
>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 = 54.1 bits (131), Expect = 4e-10
Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+F+ + + L + FS +G + K+ D G SKGYGF+ F++EE A R + +
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64
Query: 106 NIMFKEKRLNIAP 118
++ +K++ + P
Sbjct: 65 GMLLNDKKVFVGP 77
>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 = 54.2 bits (131), Expect = 5e-10
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQ-YGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
+FVG + T+ L E F Y V+ K+V+D G SKGYGF+ F E+E R +
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Query: 104 SDNIMFKEKRLNIAPAI 120
+ + + + ++PA
Sbjct: 64 MNGVYCSSRPMRVSPAT 80
>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 = 53.4 bits (129), Expect = 7e-10
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++FVG + TT +EL LF +YG V + +V K YGF+ + EE+A+ K
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVV-------KNYGFVHMEEEEDAEDAIKAL 53
Query: 105 DNIMFKEKRLNI 116
+ F KR+N+
Sbjct: 54 NGYEFMGKRINV 65
>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 = 53.5 bits (129), Expect = 7e-10
Identities = 21/59 (35%), Positives = 42/59 (71%), Gaps = 1/59 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
++FVGG++ TTE+++ E F ++G + ++++ +D+ +G+ FITFDSEE K++ +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILE 59
>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 = 53.7 bits (130), Expect = 8e-10
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEA-KRLQK 102
R+FVGG++ + TE +L E FS++G V V+I+ + AG +G+ +I + E K+ +
Sbjct: 1 RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60
Query: 103 DSDNIMFKEKRLNIAPA 119
+ +K L I A
Sbjct: 61 TLNGTKWKGSVLKIEEA 77
>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 = 53.7 bits (129), Expect = 8e-10
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDS 104
+FV + + T+++L + FS +K +V D G S+GYGF+TF E+A+
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 105 DNIMFKEKRLNI 116
N + L +
Sbjct: 62 KNKKLHGRILRL 73
>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 = 53.2 bits (127), Expect = 1e-09
Identities = 25/62 (40%), Positives = 39/62 (62%), Gaps = 3/62 (4%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR--L 100
K++FVGGI T E L + F +YG + ++I+ DR +G +G+GF+TFD + + L
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60
Query: 101 QK 102
QK
Sbjct: 61 QK 62
>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 = 57.7 bits (139), Expect = 1e-09
Identities = 39/126 (30%), Positives = 56/126 (44%), Gaps = 17/126 (13%)
Query: 6 PSEGSSNPSSPSSTQNNAFF-------NYQAAVNNNAPKYG-------TVVPKR---VFV 48
+GS T + A Y N KYG V P R VFV
Sbjct: 4 EKQGSKVQEGTKGTPDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFV 63
Query: 49 GGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIM 108
G I EDEL LF + G + ++++++D +G ++GY F+TF +EEAK K +N
Sbjct: 64 GKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYE 123
Query: 109 FKEKRL 114
+ RL
Sbjct: 124 IRPGRL 129
>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 = 53.0 bits (128), Expect = 1e-09
Identities = 20/69 (28%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSD 105
FV + TT+++L +FS++G +K +++ D+ G S Y FI F+++E+ + D
Sbjct: 7 FVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMD 66
Query: 106 NIMFKEKRL 114
N++ ++R+
Sbjct: 67 NVLIDDRRI 75
>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 = 53.2 bits (128), Expect = 1e-09
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDN 106
V G+ TTE +L + FS +G + V++ D G SKG+GF+ F E+ ++
Sbjct: 4 VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHM 63
Query: 107 IMFKEKRLNIAPAIKK 122
I + ++ K
Sbjct: 64 I--DGRWCDVKIPNSK 77
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 52.6 bits (126), Expect = 1e-09
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++FVG +++T T DEL LF ++G V + V K Y F+ + EEEA +
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMEREEEALAAIEAL 54
Query: 105 DNIMFKEKRLNI 116
+ K +R+N+
Sbjct: 55 NGKEVKGRRINV 66
>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 = 52.6 bits (127), Expect = 1e-09
Identities = 25/53 (47%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEA 97
V+VG + TE+ L ELF Q G V V I DR +GYGF+ F SEE+A
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDA 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 = 52.6 bits (127), Expect = 2e-09
Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 2/58 (3%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR-LQK 102
+VG + TED+L +F +G ++ V++ D G SKGYGFI F E+AK+ L++
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59
>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 = 52.6 bits (126), Expect = 2e-09
Identities = 19/56 (33%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
++FVGG+ E +L E FSQ+G V++ +++ D+ G +G+GF+ F + + A +
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADK 56
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM2 of FCA, a gene
controlling flowering time in Arabidopsis, which
encodes a flowering time control protein that functions
in the posttranscriptional regulation of transcripts
involved in the flowering process. The flowering time
control protein FCA contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 52.5 bits (126), Expect = 2e-09
Identities = 19/53 (35%), Positives = 32/53 (60%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
++FVG + TE E+ E+FS YG V+ + ++ D S+G F+ + S+E A
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMA 53
>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 = 52.2 bits (126), Expect = 2e-09
Identities = 18/46 (39%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 55 TTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
ED+L ELF +G + +V + D+ G S+G+ F+TF + E+A+R
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAER 56
>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 = 51.9 bits (125), Expect = 3e-09
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
V++ G+ TT+++L +L +G + K ++D+ KGYGF+ FDS E A
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAAL 56
>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 = 51.5 bits (124), Expect = 3e-09
Identities = 29/75 (38%), Positives = 45/75 (60%), Gaps = 12/75 (16%)
Query: 45 RVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGIS--KGYGFITFDSEEEAKRLQ 101
RVFVG + T ++++L E+FS+YG KI+ GIS KGYGF+ FD+EE+A+
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYG-----KIL----GISLHKGYGFVQFDNEEDARAAV 52
Query: 102 KDSDNIMFKEKRLNI 116
+ ++L+I
Sbjct: 53 AGENGREIAGQKLDI 67
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is the ubiquitously expressed Hu family member. It
has a variety of biological functions mostly related to
the regulation of cellular response to DNA damage and
other types of stress. Hu proteins perform their
cytoplasmic and nuclear molecular functions by
coordinately regulating functionally related mRNAs. In
the cytoplasm, Hu proteins recognize and bind to
AU-rich RNA elements (AREs) in the 3' untranslated
regions (UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. Also included
in this subfamily is the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 51.9 bits (124), Expect = 4e-09
Identities = 24/54 (44%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
++V G+ T T+ EL +LFSQYG + +I+ D+ G+S+G GFI FD EA+
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAE 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 = 51.7 bits (124), Expect = 4e-09
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDS 104
+++G + E EL + FSQ+G VK V++ + G SK YGFI F + E A K
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 105 DNIMFKEKRLNI 116
+N + K L +
Sbjct: 62 NNYLLMGKVLQV 73
>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 = 55.3 bits (133), Expect = 7e-09
Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 5/110 (4%)
Query: 26 NYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISK 84
N A + P +++VG + TE EL ++F +G ++ V++ D G SK
Sbjct: 170 NRAAKAATHQPGDIPN-FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSK 228
Query: 85 GYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQGFTGTYDSLPT 134
G+GFI F EEAK + + + + + A Q T D+ T
Sbjct: 229 GFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYA---QDSTYLLDAANT 275
Score = 36.8 bits (85), Expect = 0.008
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEE 95
VFV + E +L E FS+ G V+ V+ + DR + SKG ++ F E
Sbjct: 92 VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVE 142
>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 = 50.9 bits (122), Expect = 9e-09
Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
KR+ V I + +L ++F Q+G + V+I+ + G SKG+GF+TF + +A R
Sbjct: 1 KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADR 55
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 50.7 bits (121), Expect = 9e-09
Identities = 23/69 (33%), Positives = 40/69 (57%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
VFVG I EDEL +F G + ++++++D G ++GY F+ + + EAKR ++ +
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63
Query: 106 NIMFKEKRL 114
N + RL
Sbjct: 64 NYEIRPGRL 72
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 50.6 bits (122), Expect = 9e-09
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVK-QVKIVVDRAGISKGYGFITFDSEEEAKR-LQKD 103
V + G+ + TE+++ + FS I + IV D G G ++ F S E+A+R L+K
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61
Query: 104 SDNIM 108
++ +
Sbjct: 62 NNKMG 66
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 50.4 bits (121), Expect = 9e-09
Identities = 24/71 (33%), Positives = 35/71 (49%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+FVG + + TE+ L ELF Q G ++ VKI D G K + F+TF E + +
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63
Query: 106 NIMFKEKRLNI 116
I + L I
Sbjct: 64 GIRLFGRELRI 74
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 50.7 bits (122), Expect = 1e-08
Identities = 16/54 (29%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
+FV G+ E+++ + F+++G +K + + +DR G KGY I +++++EA+
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQ 62
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 50.7 bits (122), Expect = 1e-08
Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIV------VDRAGISKGYGFITFDSEEEA-- 97
+FV + TTE+ L + F + G V+ V I +S GYGF+ F S+E A
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 98 --KRLQ 101
KRLQ
Sbjct: 63 ALKRLQ 68
>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 = 50.4 bits (121), Expect = 1e-08
Identities = 22/71 (30%), Positives = 43/71 (60%), Gaps = 1/71 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+FVG ++ T++EL E FS++G + +V + + RA + + FI F+ E+ A R + +
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNL-IKRANHTNAFAFIKFEREQAAARAVESEN 64
Query: 106 NIMFKEKRLNI 116
+ M K K +++
Sbjct: 65 HSMLKNKTMHV 75
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 50.3 bits (121), Expect = 1e-08
Identities = 21/54 (38%), Positives = 38/54 (70%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
VFVG I EDEL LF + G + ++++++D +G+++GY F+T+ ++E A+R
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQR 57
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 49.9 bits (120), Expect = 1e-08
Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 57 EDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
E EL + FSQ+G V ++++ + G SKGY F+ F+S E AK + + +N + E+ L
Sbjct: 13 EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLL 71
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM2 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 73
Score = 49.9 bits (120), Expect = 2e-08
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITF-DSEEEAKRLQKD 103
VFVG + E+EL + F G V+ V+IV DR GI KG+G++ F + A L+
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL- 60
Query: 104 SDNIMFKEKRLNI 116
+ I K +++ +
Sbjct: 61 -NGIKLKGRKIRV 72
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 50.0 bits (119), Expect = 2e-08
Identities = 24/76 (31%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDN 106
V G++ TTE +L E+FS+YG + V +V D R G S+G+ F+ F+ +++K + ++
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63
Query: 107 IMFKEKRLNIAPAIKK 122
+ +R+ + +I K
Sbjct: 64 MELDGRRIRVDYSITK 79
>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 = 50.2 bits (120), Expect = 2e-08
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 46 VFVGGITSTTTEDELCELF-SQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKD 103
+FVG ++ E +L LF S++ K KI+ D G+S+GYGF+ F E + +R +
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63
Query: 104 SDNIMFKEKRLNIAPA 119
+ + + I+ A
Sbjct: 64 MQGVYCGGRPMRISTA 79
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDS 104
+F+ + + T+ +L +LF+ +G V K+ VD+ G SK +GF+++D+ E A+ K
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 105 DNIMFKEKRL 114
+ KRL
Sbjct: 61 NGFQVGGKRL 70
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation
factor 64 kDa subunit (CstF64), is the vertebrate
conterpart of yeast mRNA 3'-end-processing protein
RNA15. It is expressed in all somatic tissues and is
one of three cleavage stimulatory factor (CstF)
subunits required for polyadenylation. CstF64 contains
an N-terminal RNA recognition motif (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a CstF77-binding domain, a repeated MEARA
helical region and a conserved C-terminal domain
reported to bind the transcription factor PC-4. During
polyadenylation, CstF interacts with the pre-mRNA
through the RRM of CstF64 at U- or GU-rich sequences
within 10 to 30 nucleotides downstream of the cleavage
site. CSTF2T, also termed tauCstF64, is a paralog of
the X-linked cleavage stimulation factor CstF64 protein
that supports polyadenylation in most somatic cells. It
is expressed during meiosis and subsequent haploid
differentiation in a more limited set of tissues and
cell types, largely in meiotic and postmeiotic male
germ cells, and to a lesser extent in brain. The loss
of CSTF2T will cause male infertility, as it is
necessary for spermatogenesis and fertilization.
Moreover, CSTF2T is required for expression of genes
involved in morphological differentiation of
spermatids, as well as for genes having products that
function during interaction of motile spermatozoa with
eggs. It promotes germ cell-specific patterns of
polyadenylation by using its RRM to bind to different
sequence elements downstream of polyadenylation sites
than does CstF64. .
Length = 75
Score = 49.8 bits (119), Expect = 2e-08
Identities = 23/53 (43%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEA 97
VFVG I TE++L ++FS+ G V ++V DR G KGYGF + +E A
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETA 53
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 49.9 bits (120), Expect = 2e-08
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKRL 100
+ + G+ TTE+++ + S +K V+++ D+ G S+G+ F+ F S E+A +
Sbjct: 3 NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQW 62
>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 = 49.5 bits (119), Expect = 2e-08
Identities = 20/54 (37%), Positives = 34/54 (62%), Gaps = 7/54 (12%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
K ++V + +TTE++L ELFS+YG V++VK + D Y F+ F+ ++A
Sbjct: 2 KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDA 48
>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 = 49.6 bits (119), Expect = 2e-08
Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
++V G+ T T+ EL LFS YG + +I+ D G+S+G GFI FD EA+R
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAER 57
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 49.7 bits (118), Expect = 2e-08
Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQK 102
++V G+ T T+ EL +LFSQYG + +I+VD+ G+S+G GFI FD EA+ K
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 77
Score = 49.2 bits (118), Expect = 3e-08
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQ-YGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
R+ V + ++ TE EL E FS+ G + VK++ G S+ FI + +EEEA++ +
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDY 61
Query: 104 SDNIMFKEKRLNI 116
+N ++++
Sbjct: 62 FNNTYINTSKISV 74
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living cells.
RRM2/3 are implicated in ACF interaction with APOBEC-1.
.
Length = 78
Score = 49.6 bits (118), Expect = 3e-08
Identities = 22/69 (31%), Positives = 41/69 (59%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+F+G + EDEL L + G + ++++++D G ++GY F+TF +++EAK K +
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63
Query: 106 NIMFKEKRL 114
N + RL
Sbjct: 64 NYEIRNGRL 72
>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 = 49.1 bits (117), Expect = 3e-08
Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 8/71 (11%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDS 104
+F+GG+ TT+D L E F Q+G V ++ D A G S+G+GF+TF K
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKP-------KSV 53
Query: 105 DNIMFKEKRLN 115
+ +M KE L+
Sbjct: 54 NEVMKKEHILD 64
>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 = 49.2 bits (117), Expect = 3e-08
Identities = 20/58 (34%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGGI T E L + F +YG ++ ++++ DR +G +G+ F+TFD + ++
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKI 58
>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 = 48.7 bits (116), Expect = 4e-08
Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + TE+E+ +LF +YG ++ I D KG+GFI ++ A+ + +
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD-----KGFGFIRLETRTLAEIAKAEL 57
Query: 105 DNIMFKEKRLNI 116
DN+ + K+L +
Sbjct: 58 DNMPLRGKQLRV 69
>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 = 49.0 bits (117), Expect = 4e-08
Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
++FVGG+ T++ L F++YG + + ++VD S+G+GFITF S +EA
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEA 57
>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 = 48.4 bits (116), Expect = 5e-08
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+FVG + TT +EL E F G + ++ I+ D+ G KG+ +I F ++ +
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFL-DKSSVENALLL 60
Query: 105 DNIMFKEKRLNI 116
+ F+ +++ +
Sbjct: 61 NESEFRGRQIKV 72
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 48.8 bits (116), Expect = 5e-08
Identities = 24/54 (44%), Positives = 37/54 (68%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
++V G+ T ++ E+ +LFSQYG + +I+VD+ GIS+G GFI FD EA+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAE 57
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 48.5 bits (116), Expect = 6e-08
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKD 103
++F+GG++ TT+D L FSQ+G + ++ D S+G+GF+TF S E
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
>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 = 48.5 bits (116), Expect = 6e-08
Identities = 18/72 (25%), Positives = 38/72 (52%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+ V + ED+L +LF +G + V++ + G + +GF+ + +EEEA++ K
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHF 61
Query: 105 DNIMFKEKRLNI 116
+N ++ +
Sbjct: 62 NNSFIDTSKITV 73
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate
nucleolin. This subfamily corresponds to the RRM4 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 78
Score = 48.0 bits (114), Expect = 8e-08
Identities = 27/56 (48%), Positives = 36/56 (64%), Gaps = 4/56 (7%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
K +FV G++ TTE+ L E F G + +IV DR G SKG+GF+ F SEE+AK
Sbjct: 1 KTLFVKGLSEDTTEETLKESFD--GSIA-ARIVTDRDTGSSKGFGFVDFSSEEDAK 53
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 90
Score = 48.6 bits (115), Expect = 8e-08
Identities = 26/58 (44%), Positives = 38/58 (65%), Gaps = 1/58 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQK 102
++V G+ T T+ EL +LFSQYG + +I+VD+ G+S+G GFI FD EA+ K
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65
>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 = 47.7 bits (114), Expect = 1e-07
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEA 97
+FV + E L +LFS +G V VK++ D KGYGF+T + EEA
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEA 56
>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 = 47.7 bits (114), Expect = 1e-07
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYG-IVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKD 103
+F+G + E L + FS +G I++ KI+ D G SKG+ FI++DS E + +
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 104 SDNIMFKEKRLNIAPAIKK 122
+ + + ++ A KK
Sbjct: 64 MNGQYLCNRPITVSYAFKK 82
>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 = 47.3 bits (113), Expect = 1e-07
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDN 106
V +T TT D+L +F +YG V V I DR S+G+ F+ F + +A+ D
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 107 IMFKEKRLNIA 117
+ L +
Sbjct: 63 KELDGRELRVQ 73
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 2 (Musashi-2) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 79
Score = 47.4 bits (112), Expect = 1e-07
Identities = 17/58 (29%), Positives = 40/58 (68%), Gaps = 1/58 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
K++FVGG+++ T +++ + F Q+G V+ ++ D+ +G+GF+TF++E+ +++
Sbjct: 4 KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 16/78 (20%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR----AGISKGYGFITFDSEEEAKR-L 100
++V + ED+L +FS++G V+ ++I + ++ G+ F+TF A+ L
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62
Query: 101 QKDSDNIMFKEKRLNIAP 118
Q + ++++++
Sbjct: 63 QL--NGTELGGRKISVSL 78
>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 = 47.3 bits (112), Expect = 2e-07
Identities = 24/76 (31%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG-ISKGYGFITFDSEEEAKRLQKDSDN 106
V G++ TTE +L E+FS+YG + V IV D+ S+G+ F+ F++ ++AK ++ ++
Sbjct: 14 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73
Query: 107 IMFKEKRLNIAPAIKK 122
+ +R+ + +I K
Sbjct: 74 MELDGRRIRVDFSITK 89
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1,
or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3,
or CUG-BP2, or NAPOR) belong to the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family
of RNA-binding proteins that have been implicated in
regulation of pre-mRNA splicing, and control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. The
human CELF-1 is a nuclear and cytoplasmic RNA-binding
protein that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for onset
of type 1 myotonic dystrophy (DM1), a neuromuscular
disease associated with an unstable CUG triplet
expansion in the 3'-UTR (3'-untranslated region) of the
DMPK (myotonic dystrophy protein kinase) gene; it
preferentially targets UGU-rich mRNA elements. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contain three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains): two consecutive RRMs (RRM1
and RRM2) situated in the N-terminal region followed by
a linker region and the third RRM (RRM3) close to the
C-terminus of the protein. The two N-terminal RRMs of
EDEN-BP are necessary for the interaction with EDEN as
well as a part of the linker region (between RRM2 and
RRM3). Oligomerization of EDEN-BP is required for
specific mRNA deadenylation and binding. CELF-2 is
expressed in all tissues at some level, but highest in
brain, heart, and thymus. It has been implicated in the
regulation of nuclear and cytoplasmic RNA processing
events, including alternative splicing, RNA editing,
stability and translation. CELF-2 shares high sequence
identity with CELF-1, but shows different binding
specificity; it binds preferentially to sequences with
UG repeats and UGUU motifs. It has been shown to bind to
a Bruno response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to the
3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2
of CELF-2, can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. This subgroup also
includes Drosophila melanogaster Bruno protein, which
plays a central role in regulation of Oskar (Osk)
expression in flies. It mediates repression by binding
to regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 84
Score = 47.1 bits (112), Expect = 2e-07
Identities = 25/66 (37%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA---GISKGYGFITFDSEEEAKRLQ 101
++FVG I + +E +L ELF QYG V Q+ ++ DR+ SKG F+TF + + A Q
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62
Query: 102 KDSDNI 107
N+
Sbjct: 63 NALHNM 68
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. Structurally related CFIm68 and
CFIm59, also termed cleavage and polyadenylation
specificity factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59), are functionally redundant. Both contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. Their N-terminal RRM mediates the interaction
with CFIm25, and also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 76
Score = 46.9 bits (112), Expect = 2e-07
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYG--IVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
++VG +T TT+++L ++ G VK +K +A G SKG+ ++ F SE A +++
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 103 DSDNIMFKEKRLNIAP 118
+ F K+ +
Sbjct: 61 KLEGREFNGKKCVVTY 76
>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 = 47.0 bits (112), Expect = 2e-07
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 54 TTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
T+DE+ LFS G ++ K++ D+ G S GYGF+ + E+A++
Sbjct: 12 NMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEK 58
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEAKRLQKDSD 105
VG + T+++ EL S +G V++ +V + G SKGYGF+ + S+ A + + D
Sbjct: 3 CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62
Query: 106 NIMFKEKRLNI 116
++L +
Sbjct: 63 GKQIGGRKLQV 73
>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 = 46.6 bits (111), Expect = 2e-07
Identities = 23/53 (43%), Positives = 35/53 (66%), Gaps = 1/53 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR 99
V G++STT +L +LFS+YG V KIV + R+ ++ +GF+T S EEA +
Sbjct: 4 VSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAK 56
>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 = 46.8 bits (112), Expect = 2e-07
Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITF-DSEEEAK 98
R+FVG + + T++ L FS+Y ++ K+V D R G SKGYGF++F D + K
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLK 63
>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 = 46.5 bits (111), Expect = 3e-07
Identities = 17/45 (37%), Positives = 28/45 (62%)
Query: 54 TTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
T+ EL ELFS +G VK V++ G +G+ F+ F +++EA+
Sbjct: 11 EATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQ 55
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to
the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 46.6 bits (111), Expect = 3e-07
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEAKR 99
V+VGGI +TEDE+ FS G ++++ ++ G +G FITF +EE AKR
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKR 55
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 46.5 bits (111), Expect = 3e-07
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDN 106
+VGG+ TE +L + F Q+G ++ + +V + F+TF + E A++ + N
Sbjct: 5 YVGGLGERVTEKDLRDHFYQFGEIRSITVVP-----RQQCAFVTFTTREAAEKAAERLFN 59
Query: 107 -IMFKEKRLNI 116
++ +RL +
Sbjct: 60 KLIINGRRLKL 70
>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 = 46.4 bits (111), Expect = 3e-07
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
++VGG+ E L F +G +K ++I +D +G+ F+ F+ E+A
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAA 54
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 48.1 bits (114), Expect = 3e-07
Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKD 103
++F+GG++ T + L + F+ +G V K++VDR G S+G+GF+ F+ E A +
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
Query: 104 SDNIMFKEKRLNIAPA 119
D + + + PA
Sbjct: 96 MDGKELNGRHIRVNPA 111
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 46.4 bits (110), Expect = 3e-07
Identities = 20/61 (32%), Positives = 38/61 (62%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
VFVG I EDEL LF + G + + +++++ +G ++GY F+ + ++EEA+ + +
Sbjct: 4 VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILN 63
Query: 106 N 106
N
Sbjct: 64 N 64
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 107
Score = 47.2 bits (112), Expect = 3e-07
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
+FV + TE+ L FS++G V+ V+D++ G +KG GF+ F +
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN 57
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 46.5 bits (111), Expect = 3e-07
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
+G + E + F++ G V VKI+ ++ G S GYGF+ F + E A++
Sbjct: 4 MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQ 56
>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 = 46.2 bits (110), Expect = 4e-07
Identities = 25/67 (37%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 54 TTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDSDNIMFKEK 112
T T++E LF G VK KIV D+ G S G+GF+ + S E+A+R + + + + K
Sbjct: 11 TLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNK 70
Query: 113 RLNIAPA 119
R+ +A A
Sbjct: 71 RIKVAYA 77
>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 = 45.8 bits (109), Expect = 5e-07
Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
+FVG ++ ED + E F +YG + V++ D +G KG+G++ F S+E A+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQ 54
>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 = 45.5 bits (108), Expect = 6e-07
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEAKRLQKD 103
+FVG ++ TTEDEL F + G +++V+++ + +G KG+ F+ F+ E A K
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKG 59
>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 = 45.7 bits (109), Expect = 6e-07
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 10/79 (12%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIV-------VDRAGISKGYGFITFDSEEEAK 98
++VG + TE+ LC+ F ++G + VKI+ R GF+ F + +A+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC---GFVAFMNRADAE 60
Query: 99 RLQKDSDNIMFKEKRLNIA 117
R + D L +
Sbjct: 61 RALDELDGKDVMGYELKLG 79
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 45.7 bits (108), Expect = 7e-07
Identities = 21/66 (31%), Positives = 42/66 (63%), Gaps = 2/66 (3%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR-LQ 101
K++FVGG+ TE+++ E F ++G ++ +++ +D + +G+ FITF E+ K+ L+
Sbjct: 5 KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64
Query: 102 KDSDNI 107
K N+
Sbjct: 65 KKFHNV 70
>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 = 45.4 bits (107), Expect = 7e-07
Identities = 18/57 (31%), Positives = 38/57 (66%), Gaps = 1/57 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
++FVGG++ TT +++ + F Q+G V ++ D+ +G+GF+TF+SE+ +++
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
>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 = 45.1 bits (107), Expect = 9e-07
Identities = 23/76 (30%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKD 103
R+F+ + T TE++L +LFS+YG + +V + +D+ KG+ F+T+ E A + +
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63
Query: 104 SDNIMFKEKRLNIAPA 119
D +F+ + L++ P+
Sbjct: 64 LDGTVFQGRLLHLLPS 79
>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 = 44.7 bits (106), Expect = 1e-06
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R++V T+E + E+FS YG VK+VK++ + F+ F+S E A R +
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSV 53
Query: 105 DNIMF 109
+
Sbjct: 54 HGKVL 58
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 77
Score = 44.9 bits (107), Expect = 1e-06
Identities = 18/48 (37%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITF 91
++F+GG+ + +ED++ EL +G +K +V D A G+SKGY F +
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEY 49
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a highly acidic carboxyl-terminal half. The family
also includes CUS2, a yeast homolog of human Tat-SF1.
CUS2 interacts with U2 RNA in splicing extracts and
functions as a splicing factor that aids assembly of
the splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the
conserved splicing factor SF3a. Like Tat-SF1, CUS2
contains two RRMs as well. .
Length = 92
Score = 45.2 bits (108), Expect = 1e-06
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVK--------QVKIVVDRAGISKGYGFITFDSEE 95
V+V G+ T +E E+FS+ GI+K ++K+ D G KG + EE
Sbjct: 4 VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYLKEE 61
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment
factor B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described
functions in transcriptional repression, RNA splicing
and metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1
has been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
nuclear localization signal (NLS). The C-terminus of
SAFB1 contains Glu/Arg- and Gly-rich regions that might
be involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously
coexpressed and share very high sequence similarity,
suggesting that they might function in a similar
manner. However, unlike SAFB1, exclusively existing in
the nucleus, SAFB2 is also present in the cytoplasm.
The additional cytoplasmic localization of SAFB2
implies that it could play additional roles in the
cytoplasmic compartment which are distinct from the
nuclear functions shared with SAFB1.
Length = 76
Score = 45.1 bits (106), Expect = 1e-06
Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR 99
+ ++V G++STT +L LFS+YG V K+V + R+ ++ YGF+T + EEA +
Sbjct: 2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATK 58
>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 = 48.0 bits (114), Expect = 1e-06
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
++V G+ T T+ EL +FS +G + +I+ D G+SKG GFI FD +EA R
Sbjct: 92 LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADR 146
Score = 42.2 bits (99), Expect = 1e-04
Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 5/98 (5%)
Query: 1 MSGAHPSEGSSNPSSPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDEL 60
A + ++ +SP +T + AA A +FV ++ T E L
Sbjct: 231 QQHAVAQQHAAQRASPPAT--DGQTAGLAAGAQIA--ASDGAGYCIFVYNLSPDTDETVL 286
Query: 61 CELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
+LF +G V+ VKI+ D KGYGF++ + +EA
Sbjct: 287 WQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEA 324
Score = 38.0 bits (88), Expect = 0.003
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 54 TTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
T T++E+ LF+ G ++ K+V D+ G S GYGF+ + E+A++
Sbjct: 14 TMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60
>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 = 44.6 bits (105), Expect = 1e-06
Identities = 18/57 (31%), Positives = 38/57 (66%), Gaps = 1/57 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRL 100
+VFVGG++ TTE+++ E F +G ++ +++ +D + +G+ F+T+ EE ++L
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKL 57
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 44.6 bits (105), Expect = 2e-06
Identities = 22/75 (29%), Positives = 45/75 (60%), Gaps = 2/75 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR-LQK 102
++FVGG++ T E+++ E F +G V+ +++ +D + +G+ FITF EE K+ ++K
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 103 DSDNIMFKEKRLNIA 117
N+ + + +A
Sbjct: 61 KYHNVGLSKCEIKVA 75
>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 = 44.1 bits (104), Expect = 2e-06
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 7/53 (13%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
++FVG + TE E+ LF QYG V + I+ K YGF+ D + A
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDII-------KNYGFVHMDDKTAA 47
>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 = 44.6 bits (106), Expect = 2e-06
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQ--------VKIVVDRAGISKGYGFITFDSEEEA 97
+++ G+ TED L ELF GI+K+ +KI D+ KG +T+D A
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60
Query: 98 K 98
+
Sbjct: 61 Q 61
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with wild
type of survival motor neuron (SMN) proteins directly,
further providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, and in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; it binds RNA
through its RRM domains. .
Length = 79
Score = 44.6 bits (105), Expect = 2e-06
Identities = 25/62 (40%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
VFVG I EDEL LF + G + +++++D +G ++GY FITF +E A+ K
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63
Query: 105 DN 106
DN
Sbjct: 64 DN 65
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 44.4 bits (106), Expect = 2e-06
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+VG + TE L E+FS G V +++ D S GY ++ F + +A+R
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAER 56
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 44.2 bits (104), Expect = 2e-06
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + + TE++ +LF +YG +V I DR G+GFI +S A+ + +
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR-----GFGFIRLESRTLAEIAKAEL 57
Query: 105 DNIMFKEKRLNI 116
D + K + L I
Sbjct: 58 DGTILKNRPLRI 69
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM1 of FCA, a gene
controlling flowering time in Arabidopsis, encoding a
flowering time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains),
and a WW protein interaction domain. .
Length = 80
Score = 44.2 bits (104), Expect = 2e-06
Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR 99
++FVG + T TE E+ +F ++G V +V I+ D R G +G F+ + + +EA R
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADR 56
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM3 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B) and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and is a
novel component of the NXF1 pathway. It binds to NXF1
and serves as receptor for the RNA export element RTE.
It also possess mRNA export activity and can facilitate
the access of DEAD-box protein DBP5 to mRNA at the
nuclear pore complex (NPC). RNA-binding protein 15B
(RBM15B), also termed one twenty-two 3 (OTT3), is a
paralog of RBM15 and therefore has post-transcriptional
regulatory activity. It is a nuclear protein sharing
with RBM15 the association with the splicing factor
compartment and the nuclear envelope as well as the
binding to mRNA export factors NXF1 and Aly/REF.
Members in this family belong to the Spen (split end)
protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 72
Score = 43.7 bits (104), Expect = 2e-06
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++VGG+ T+ EL F ++G ++++ D + Y +I ++S E A+
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRID--YDP---GRNYAYIEYESIEAAQA 49
>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 = 44.2 bits (105), Expect = 2e-06
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 44 KRV-FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+RV +VG I TT EL + F +G ++++ + G + YGF+T+ +A R
Sbjct: 2 RRVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN--YGFVTYRYACDAFR 56
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 43.5 bits (102), Expect = 3e-06
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++ VG I+S+ T EL F +YG V + IV D Y F+ + E+A +
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRGL 54
Query: 105 DNIMFKEKRLNI 116
DN F+ KR+++
Sbjct: 55 DNTEFQGKRMHV 66
>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 = 43.6 bits (103), Expect = 3e-06
Identities = 18/47 (38%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGI-SKGYGFITFD 92
F+GG++ TT + L E FS++G +K+ ++ D S+G+GF+TF
Sbjct: 2 FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFS 48
>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 = 43.1 bits (102), Expect = 4e-06
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
VFVGG+ TEDEL LF +G + VKI KG GF+ F A+
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP-----GKGCGFVQFVHRAAAEA 52
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 43.3 bits (102), Expect = 4e-06
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+ VF G + E+ LF +YG VDR + G+ F+ + E +A+ +
Sbjct: 1 RPVFCGNFEYDARQSEIERLFGKYG-------RVDRVDMKSGFAFVYMEDERDAEDAIRG 53
Query: 104 SDNIMFKEKR 113
DN F +R
Sbjct: 54 LDNFEFGRQR 63
>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 = 43.1 bits (102), Expect = 5e-06
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+FVG ++ + L F+ +G + ++V D G SKGYGF++F +E+A+
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAEN 56
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 43.0 bits (102), Expect = 5e-06
Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
V+V G T D++ E F ++G V +++ D KG F+ F +EE+AK+ +
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEKEK 61
Query: 106 NIMFKEKRLNI 116
+ +KEK L +
Sbjct: 62 -LKYKEKELTV 71
>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 = 43.4 bits (103), Expect = 5e-06
Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 43 PKRVFVGGITSTTTE-DELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQ 101
+ +FV + T + L +LFSQ G ++ + G +G+ F+ + + E+A+ Q
Sbjct: 2 SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQ 61
Query: 102 KDSDNIMFKEKRLNIA 117
+ + + + ++
Sbjct: 62 QALNGHSLQGSPIRVS 77
>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 = 42.6 bits (101), Expect = 6e-06
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
R++V + +ED++ +F +G +K + D G KGYGFI +++ + A+
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQ 56
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated
apoptosis.TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 42.7 bits (101), Expect = 6e-06
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF 91
++VG + T TED L ELFSQ G +K K++ + Y F+ +
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEY 44
>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 = 42.6 bits (100), Expect = 6e-06
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEE 95
+ +FVG + E+ L ELF Q G + +V I D+ G K +GF+ F E
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSE 53
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 43.1 bits (101), Expect = 6e-06
Identities = 22/62 (35%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+FVG I EDEL LF + G + +++++D G+++GY F+TF ++E A+ K
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63
Query: 105 DN 106
+N
Sbjct: 64 NN 65
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to the
RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contain
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. On the other
hand, both RRM1 and RRM2 of CELF-4 can activate cardiac
troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in
brain, is also known as bruno-like protein 5 (BRUNOL-5),
or CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, strongly
expressed in kidney, brain, and testis, is also known as
bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in an muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In additiona to three highly conserved RRMs,
CELF-6 also possesses numerous potential phosphorylation
sites, a potential nuclear localization signal (NLS) at
the C terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 43.2 bits (102), Expect = 6e-06
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQK 102
++FVG I E +L LF Q+G + ++ ++ D+ G+ KG F+T+ + E A + Q
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQS 65
>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 = 42.5 bits (100), Expect = 7e-06
Identities = 17/55 (30%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR 99
+FVG ++ T+ L FS + +++ D ++G S+GYGF++F S+++A+
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAEN 56
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 42.7 bits (101), Expect = 8e-06
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 1/77 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQK 102
++V + T D+L LF +YG + V I +D +G+ ++ F+ +A+
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60
Query: 103 DSDNIMFKEKRLNIAPA 119
D F + + I A
Sbjct: 61 YLDRTRFLGREIEIQFA 77
>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 = 42.3 bits (100), Expect = 8e-06
Identities = 19/54 (35%), Positives = 32/54 (59%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+FV + + T +L +LF + G V + + D G SKG+G + F+S E+A+R
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQR 54
>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 = 42.2 bits (100), Expect = 8e-06
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 55 TTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
TE +L +LFS +G V +V I G KG+ F+ F S+ +A
Sbjct: 11 CTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADA 53
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate
nucleolin. This subfamily corresponds to the RRM2 of
ubiquitously expressed protein nucleolin, also termed
protein C23, a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines.RRM2,
together with RRM1, binds specifically to RNA
stem-loops containing the sequence (U/G)CCCG(A/G) in
the loop. .
Length = 77
Score = 42.5 bits (100), Expect = 9e-06
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+FV + T DEL E+F +++ + G SKG +I F +E EA++
Sbjct: 6 LFVKNLPYNITVDELKEVFED---AVDIRLPSGKDGSSKGIAYIEFKTEAEAEK 56
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 42.2 bits (99), Expect = 9e-06
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 9/72 (12%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITF-DSEEEAKRLQKD 103
+FVGG++ TT+ +L E FS++G V I +D G S+G+GF+ F D+ K L +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQ- 59
Query: 104 SDNIMFKEKRLN 115
KE +L+
Sbjct: 60 ------KEHKLD 65
>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 = 42.1 bits (99), Expect = 1e-05
Identities = 17/54 (31%), Positives = 29/54 (53%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++VG + TED L ++F G V+ VKI+ D+ YGF+ + +A+
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEI 54
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions
as a translational regulator that activates translation
in an mRNA-specific manner. DAZAP1 was initially
identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 82
Score = 42.5 bits (100), Expect = 1e-05
Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITF 91
++FVGG++ TT++ L FSQYG V I+ D+ S+G+GF+ F
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48
>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 = 42.1 bits (99), Expect = 1e-05
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
V+VG I TT+ +L LF +G + + + DR G+ F+ D+ E+A
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDR-----GFAFVKLDTHEQA 49
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 42.2 bits (100), Expect = 1e-05
Identities = 16/47 (34%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITF 91
+++GG+ TE ++ +FSQYG + + +V D+ G SKG+ F+ +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAY 58
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate
RNA-binding protein 7 (RBM7). This subfamily
corresponds to the RRM of RBM7, a ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. RBM7 interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20. It may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM7 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
.
Length = 75
Score = 41.8 bits (98), Expect = 1e-05
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEE 95
+ +FVG + TE+ + ELF Q G V +VKI D+ G K + F+ F E
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEV 53
>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 = 41.8 bits (99), Expect = 1e-05
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+V+VG + T+ EL + F +YG ++ V + A G+ F+ F+ +A+
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWV----ARNPPGFAFVEFEDPRDAED 51
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 42.0 bits (98), Expect = 1e-05
Identities = 18/54 (33%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEE 96
+++F+GG++ TT+D L E F ++G + ++ D + S+G+GF+T+ EE
Sbjct: 3 RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEE 56
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing
protein 1 (RDM1) and similar proteins. This subfamily
corresponds to the RRM of RDM1, also termed RAD52
homolog B, a novel factor involved in the cellular
response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 42.0 bits (99), Expect = 2e-05
Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 44 KRVFVGGITSTTTEDE----LCELFSQYGIVKQVKIVVDRAGISKG-YGFITFDSEEEAK 98
K ++V GI+ TE+E LC FSQ+G++ VK+ + A + G Y F+ F S A
Sbjct: 1 KTLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAAS 60
Query: 99 RLQKDSD 105
R QK +
Sbjct: 61 RAQKACN 67
>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 = 41.7 bits (98), Expect = 2e-05
Identities = 15/54 (27%), Positives = 35/54 (64%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+++FVG ++ E+++ +F+ +G +++ ++ D+ G S+G F+TF S + A
Sbjct: 2 RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCA 55
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 80
Score = 41.6 bits (97), Expect = 2e-05
Identities = 20/54 (37%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAK 98
VFVG ++ T D++ F+ +G + ++V D A G SKGYGF++F ++ +A+
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 57
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 41.2 bits (97), Expect = 2e-05
Identities = 25/63 (39%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 46 VFVGGITSTTTEDE----LCELFSQYGIVKQVKIVVDRA-GISKGYGFITF---DSEEEA 97
+FV G S+ ED+ L E FS G + +V I DR G SKG+ +I F D E+A
Sbjct: 2 IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61
Query: 98 KRL 100
L
Sbjct: 62 LEL 64
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 86
Score = 41.6 bits (98), Expect = 2e-05
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 46 VFVGGITSTTTEDELC----ELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQ 101
VFV + ++ ++DEL E FS+YG + VK++ D + Y F+ F ++++AK
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQ--RPYAFVQFTNDDDAKNAL 62
Query: 102 KDSDNIMFKEKRLNIAPA 119
+ + + A
Sbjct: 63 AKGQGTILDGRHIRCERA 80
>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 = 41.0 bits (97), Expect = 2e-05
Identities = 19/66 (28%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISK---GYGFITFDSEEEAKRLQK 102
++VG ++ TTE+++ ELFS+ G +K++ + +DR +K G+ F+ + + E+A+ K
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDR--FTKTPCGFCFVEYYTREDAENAVK 58
Query: 103 DSDNIM 108
+
Sbjct: 59 YLNGTK 64
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. It functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 41.2 bits (97), Expect = 2e-05
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+FV + +L E+F G V + I D+ G S+G G + F+ EA +Q S
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEA--VQAIS- 57
Query: 106 NIMFKEKRL 114
MF + L
Sbjct: 58 --MFNGQML 64
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 41.1 bits (96), Expect = 3e-05
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+FVG + + TEDE +LF++YG +V I KG+GFI +S A+ + +
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFI-----NKGKGFGFIKLESRALAEIAKAEL 57
Query: 105 DNIMFKEKRLNI 116
D+ + ++L +
Sbjct: 58 DDTPMRGRQLRV 69
>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 = 41.3 bits (97), Expect = 3e-05
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 27/78 (34%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
+ V++G + + +E+EL E ++G + Q+KIV + K F+ F
Sbjct: 4 RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHF------------ 46
Query: 104 SDNIMFKEKRLNIAPAIK 121
L+IA AIK
Sbjct: 47 ----------LSIANAIK 54
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM2 of the sex-lethal protein (SXL)
which governs sexual differentiation and X chromosome
dosage compensation in Drosophila melanogaster. It
induces female-specific alternative splicing of the
transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 41.0 bits (96), Expect = 3e-05
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
++V + TEDEL ++F YG + Q ++ D+ G+ +G F+ +D EEA+
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQ 56
>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 = 41.1 bits (96), Expect = 3e-05
Identities = 24/72 (33%), Positives = 44/72 (61%), Gaps = 7/72 (9%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKD 103
++FVGG++ T++ +L + F+++G V I +D G S+G+GFI F ++A ++K
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILF---KDASSVEKV 57
Query: 104 SDNIMFKEKRLN 115
+ KE RL+
Sbjct: 58 LEQ---KEHRLD 66
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM2 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 41.2 bits (96), Expect = 3e-05
Identities = 18/59 (30%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
+++ G+ T T+ ++ ++FS++G + +++VD+A G+S+G FI FD EA+
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM1 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). Musashi-1 has
been implicated in the maintenance of the stem-cell
state, differentiation, and tumorigenesis. It
translationally regulates the expression of a mammalian
numb gene by binding to the 3'-untranslated region of
mRNA of Numb, encoding a membrane-associated inhibitor
of Notch signaling, and further influences neural
development. Moreover, it represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 77
Score = 41.1 bits (96), Expect = 3e-05
Identities = 19/48 (39%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITF 91
++F+GG++ TT++ L E F Q+G VK+ ++ D S+G+GF+TF
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM2 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contains three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains): two consecutive RRMs
(RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The two
N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including
alternative splicing, RNA editing, stability and
translation. CELF-2 shares high sequence identity with
CELF-1, but shows different binding specificity; it
preferentially binds to sequences with UG repeats and
UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 40.8 bits (95), Expect = 3e-05
Identities = 14/55 (25%), Positives = 35/55 (63%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+++F+G ++ E+++ +FS +G +++ +I+ G+S+G F+TF + A+
Sbjct: 2 RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQ 56
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 40.8 bits (96), Expect = 3e-05
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R++VG + E ++ +LF +YG +K + + R G + F+ F+ +A+ +
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRG--PPFAFVEFEDPRDAEDAVRGR 58
Query: 105 DNIMFKEKRLNI 116
D F RL +
Sbjct: 59 DGYDFDGYRLRV 70
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 40.7 bits (95), Expect = 3e-05
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 7/71 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+F+GG++ TT+ +L + FS++G V + +D G S+G+GF+ F E ++
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV---- 56
Query: 105 DNIMFKEKRLN 115
+ KE +LN
Sbjct: 57 --MDQKEHKLN 65
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM1 of hnRNP A2/B1 which is an RNA trafficking
response element-binding protein that interacts with
the hnRNP A2 response element (A2RE). Many mRNAs, such
as myelin basic protein (MBP), myelin-associated
oligodendrocytic basic protein (MOBP), carboxyanhydrase
II (CAII), microtubule-associated protein tau, and
amyloid precursor protein (APP) are trafficked by hnRNP
A2/B1. hnRNP A2/B1 also functions as a splicing factor
that regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Moreover, the overexpression of hnRNP A2/B1 has been
described in many cancers. It functions as a nuclear
matrix protein involving in RNA synthesis and the
regulation of cellular migration through alternatively
splicing pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 81
Score = 40.9 bits (95), Expect = 3e-05
Identities = 18/54 (33%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGI-SKGYGFITFDSEEE 96
+++F+GG++ TTE+ L + Q+G + ++ D A S+G+GF+TF E
Sbjct: 3 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNE 56
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM2 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal, highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 80
Score = 40.8 bits (95), Expect = 3e-05
Identities = 18/54 (33%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAK 98
VFVG ++ T +++ F+ +G + ++V D G SKGYGF++F ++ +A+
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAE 57
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 41.0 bits (97), Expect = 4e-05
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 19/80 (23%)
Query: 54 TTTEDELCELFSQY---------GIVKQVKIVVDRAGI-------SKGYGFITFDSEEEA 97
+ E +L ELF + +KQVKI+ D + SKGYGF+ F + E A
Sbjct: 11 SVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHA 70
Query: 98 KR-LQKDSDN--IMFKEKRL 114
+ L+ ++N I +KR
Sbjct: 71 LKALRALNNNPEIFGPDKRP 90
>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 = 40.4 bits (95), Expect = 4e-05
Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
RV++G + E ++ F YG ++++ + G+GF+ F+ +A
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREIN-------LKNGFGFVEFEDPRDA 46
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
being highly expressed throughout the brain and in
glandular tissues, moderately expressed in heart,
skeletal muscle, and liver, is also known as bruno-like
protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor
4. Like CELF-3, CELF-4 also contain three highly
conserved RRMs. The splicing activation or repression
activity of CELF-4 on some specific substrates is
mediated by its RRM1/RRM2. On the other hand, both RRM1
and RRM2 of CELF-4 can activate cardiac troponin T
(cTNT) exon 5 inclusion. CELF-5, expressed in brain, is
also known as bruno-like protein 5 (BRUNOL-5), or
CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, being strongly
expressed in kidney, brain, and testis, is also known
as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in a muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In addition to three highly conserved RRMs,
CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 40.5 bits (95), Expect = 5e-05
Identities = 19/54 (35%), Positives = 32/54 (59%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+++FVG ++ TED++ LF +G +++ I+ G SKG F+ F S EA
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEA 55
>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 = 40.4 bits (94), Expect = 5e-05
Identities = 18/54 (33%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEE 96
+++F+GG++ TT++ L F Q+G + ++ D S+G+GF+T+ S EE
Sbjct: 3 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEE 56
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of
RBM23 remains unclear, it shows high sequence homology
to RBM39 and contains two RRMs. It may possibly
function as a pre-mRNA splicing factor. .
Length = 73
Score = 39.9 bits (94), Expect = 5e-05
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEA 97
VFV ++ E +L E FS+ G V+ V+I+ DR + SKG ++ F EE
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54
>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 = 40.0 bits (93), Expect = 6e-05
Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 5/52 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
V+ GG+TS TE + + FS +G + +V++ D KGY F+ F+S E A
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD-----KGYSFVRFNSHESA 49
>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 = 40.3 bits (95), Expect = 7e-05
Identities = 19/46 (41%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 63 LFSQYGIVKQVKIV--VDRAGISKGYGFITFDSEEEAKRLQKDSDN 106
+FS++G+ K V I VD G +KGY F+ F + EEAK K +
Sbjct: 27 IFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNG 72
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 42.2 bits (99), Expect = 1e-04
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 15 SPSSTQNNAFFNYQAAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVK 74
+P +Q N N + R+++G + ED++ EL +G +K
Sbjct: 267 TPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFN 326
Query: 75 IVVDRA-GISKGYGFITF 91
++ D A G+SKGY F +
Sbjct: 327 LIKDIATGLSKGYAFCEY 344
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 39.2 bits (91), Expect = 1e-04
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRL 100
++F+GG++ T++ +L E S++G V I D G S+G+GF+ F ++
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKV 57
>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 = 39.3 bits (91), Expect = 1e-04
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+ V + T+DEL LFS G V+ K++ D+ AG S GYGF+ + + ++A+R
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63
Query: 105 DNIMFKEKRLNIAPA 119
+ + + K + ++ A
Sbjct: 64 NGLRLQSKTIKVSYA 78
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 39.1 bits (91), Expect = 1e-04
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++FVG + + EL E F QYG V +++I + G +GF+ FD E +++ +
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRI--NSGGKLPNFGFVVFDDSEPVQKILSNR 62
Query: 105 DNIMFK-EKRLNI 116
IMF+ + RLN+
Sbjct: 63 P-IMFRGDVRLNV 74
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 81
Score = 38.9 bits (91), Expect = 2e-04
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIV-KQVKIVVDR-AGISKGYGFITFDSEEEAKR---L 100
+ + G+ + TE+++ +G+ K V+++ + G S+G+ F+ F S EEA R L
Sbjct: 5 IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMEL 64
Query: 101 QKDSDNIMFKEKRL 114
+ + + L
Sbjct: 65 NQGKLQLQDYKITL 78
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 38.8 bits (91), Expect = 2e-04
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
V++ G+ + TE L FS+YG V V +V+DR +G + FD E A+ +
Sbjct: 10 VWLDGLDESVTEQYLTRHFSRYGPV--VHVVIDR---QRGQALVFFDKVEAAQAAVNEMK 64
Query: 106 NIMFKEKRLNI 116
++L +
Sbjct: 65 GRKLGGRKLQV 75
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 38.8 bits (90), Expect = 2e-04
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGIS-KGYGFITFDSEEEAKRLQKD 103
++FVG + E EL E F +G V +++I G +GF+ FD E +R+
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILG- 65
Query: 104 SDNIMFK-EKRLNI 116
+ IMF+ E RLN+
Sbjct: 66 AKPIMFRGEVRLNV 79
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM2 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B), and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possess mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also termed one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 38.9 bits (91), Expect = 2e-04
Identities = 20/53 (37%), Positives = 28/53 (52%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
FVG + T TE+EL F +YG+V+ V I G Y F+ F + + A R
Sbjct: 6 FVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHR 58
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 38.9 bits (91), Expect = 2e-04
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+ VGGI + +ED+L E FS G V +V++ DR ++ + F+ F E A
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESA 53
>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 = 38.5 bits (90), Expect = 2e-04
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 45 RVFVGGITS-TTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
R+F+ + + TED+L E F+ +G ++ + +V D+ SKG ++ F A R
Sbjct: 5 RLFI--VCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAAR 59
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 38.1 bits (89), Expect = 2e-04
Identities = 20/48 (41%), Positives = 32/48 (66%), Gaps = 2/48 (4%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITF 91
R+FV I + TE++L E F ++G ++ V IV D+ G SKG+G++ F
Sbjct: 3 RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type
and RNA-binding motif-containing protein 1 (ZCRB1) and
similar proteins. This subfamily corresponds to the RRM
of ZCRB1, also termed MADP-1, or U11/U12 small nuclear
ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or
U11/U12-31K), a novel multi-functional nuclear factor,
which may be involved in morphine dependence, cold/heat
stress, and hepatocarcinoma. It is located in the
nucleoplasm, but outside the nucleolus. ZCRB1 is one of
the components of U11/U12 snRNPs that bind to U12-type
pre-mRNAs and form a di-snRNP complex, simultaneously
recognizing the 5' splice site and branchpoint sequence.
ZCRB1 is characterized by an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 38.5 bits (90), Expect = 2e-04
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
V+V + + T ++L ++FS+YG V +V IV D+ SKG FI F E+A + K
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63
Query: 105 DN-IMFKEK 112
+N +F
Sbjct: 64 NNKELFGRT 72
>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 = 38.1 bits (89), Expect = 3e-04
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEE---EAKRLQ 101
+FVG + TT ++L F G V+++ D+ G SKG F+ FD+ E +A +L
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 102 KDSDNIMFKEKRLNI 116
K +++N+
Sbjct: 63 HTL----LKGRKINV 73
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM1
of U1A/U2B"/SNF protein family which contains Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs), connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. Moreover,
U2B" does not require an auxiliary protein for binding
to RNA, and its nuclear transport is independent of U2
snRNA binding. .
Length = 78
Score = 37.9 bits (89), Expect = 3e-04
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 2/57 (3%)
Query: 60 LCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNI 116
L LFSQ+G V + IV + +G F+ F E A + F +K + I
Sbjct: 20 LYALFSQFGPV--LDIVASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRI 74
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 76
Score = 37.8 bits (88), Expect = 3e-04
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEA 97
RV+VG I+ ED + + FS +G +K + + D KG+ F+ ++ E A
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAA 55
>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 = 37.7 bits (88), Expect = 4e-04
Identities = 20/78 (25%), Positives = 43/78 (55%), Gaps = 7/78 (8%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDS 104
+++G ++ TE++L LF +YG ++ + ++ R G ++ ++ ++A R LQK
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPR-----GCAYVCMETRQDAHRALQK-L 58
Query: 105 DNIMFKEKRLNIAPAIKK 122
N+ K++ +A A K
Sbjct: 59 RNVKLAGKKIKVAWAPNK 76
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers. hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 37.7 bits (87), Expect = 4e-04
Identities = 19/52 (36%), Positives = 29/52 (55%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
VFV + +L E+FS G+V + I+ D+ G S+G G +TF+ EA
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEA 54
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 37.6 bits (88), Expect = 5e-04
Identities = 16/72 (22%), Positives = 38/72 (52%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++ V + ++D++ ELF+++G +K+ + DR+G S G + F+ +A + K
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQY 61
Query: 105 DNIMFKEKRLNI 116
+ + + + I
Sbjct: 62 NGVPLDGRPMKI 73
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 37.5 bits (87), Expect = 5e-04
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
++FVG + T+++EL LF YG V ++ + + F+ E A R ++
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM-------RQFAFVHLRGEAAADRAIEEL 54
Query: 105 DNIMFKEKRL 114
+ ++L
Sbjct: 55 NGRELHGRKL 64
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of 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 functions 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 = 37.3 bits (86), Expect = 5e-04
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR--LQKD 103
++VG ++ TE + +LFSQ G K K+++D AG + Y F+ F A +
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAG-NDPYCFVEFFEHRHAAASLAAMN 60
Query: 104 SDNIMFKEKRLNIA 117
IM KE ++N A
Sbjct: 61 GRKIMGKEVKVNWA 74
>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 = 37.4 bits (86), Expect = 5e-04
Identities = 16/48 (33%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITF 91
++F+GG++ T+ D L + FS++G +++ ++ D S+G+GF+TF
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 37.5 bits (88), Expect = 5e-04
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 9/80 (11%)
Query: 44 KRVFVGGITSTTTEDELCELFSQY----GIVKQVKIVVDRAGISKG--YGFITFDSEEEA 97
+R++VG + TE+EL + F+Q G+ + V I+ + F+ F + EEA
Sbjct: 2 RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEA 61
Query: 98 KR-LQKDSDNIMFKEKRLNI 116
L D I+FK + L I
Sbjct: 62 TAALAL--DGIIFKGQPLKI 79
>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 = 37.4 bits (87), Expect = 5e-04
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 45 RVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
R+F+G + T ++++L +FS YG + Q+ + YGF+ FDS E
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVL-------KNAYGFVQFDSPESCANAINC 53
Query: 104 SDNIMFKEKRL 114
M + ++L
Sbjct: 54 EQGKMIRGRKL 64
>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin.
This subfamily corresponds to the RRM1 of ubiquitously
expressed protein nucleolin, also termed protein C23.
Nucleolin is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. RRM1,
together with RRM2, binds specifically to RNA stem-loops
containing the sequence (U/G)CCCG(A/G) in the loop. .
Length = 75
Score = 37.1 bits (86), Expect = 6e-04
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEE-AKRLQKDS 104
+FVG + DEL S++ K + + R G SK +G++ F+S E+ K L+
Sbjct: 3 LFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKALELTG 62
Query: 105 DNIMFKEKRLNIA 117
++ E +L A
Sbjct: 63 KKLLGNEIKLEKA 75
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor and component of
the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RBM15 belongs to the Spen (split
end) protein family, which contain three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralog and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 37.6 bits (87), Expect = 6e-04
Identities = 17/56 (30%), Positives = 32/56 (57%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+ +F+G + T TE +L F ++G++ +V I G + YGF+ F++ + A R
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHR 63
>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 = 37.5 bits (88), Expect = 7e-04
Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 12/85 (14%)
Query: 41 VVPKR-VFVGGITSTTTEDELC---ELFSQYGIVKQVKIVVDRAGISKGYG------FIT 90
V+ + V+V G+ ++E+ E F QYG +K KIV++R G ++T
Sbjct: 2 VIQRNLVYVVGLPPRLADEEVLKKPEYFGQYGKIK--KIVINRNTSYNGSQGPSASAYVT 59
Query: 91 FDSEEEAKRLQKDSDNIMFKEKRLN 115
+ +E+A R + D + L
Sbjct: 60 YSRKEDALRCIQAVDGFYLDGRLLK 84
>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 = 39.6 bits (92), Expect = 8e-04
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 56 TEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRL 114
T+ EL LF G + +I+ D + G S GY F+ F SE +++R K+ + I + KRL
Sbjct: 120 TDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL 179
Query: 115 NIAPA 119
++ A
Sbjct: 180 KVSYA 184
Score = 35.8 bits (82), Expect = 0.013
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAK 98
++V + T T+D+L +F +YG + Q I+ D+ G +G F+ F+ EEA+
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQ 249
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 36.7 bits (85), Expect = 8e-04
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDS 104
V+VG + T +EL F G V +V I+ D+ G KG+ +I F S++E+ R
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVRTALAL 60
Query: 105 DNIMFKEKRLNIAP 118
D +F+ +++ + P
Sbjct: 61 DESLFRGRQIKVMP 74
>gnl|CDD|241167 cd12723, RRM1_CPEB1, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding
protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 100
Score = 37.4 bits (87), Expect = 0.001
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 13/64 (20%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAG--------ISKGYGFITFDSEEE 96
+VF+GG+ TE L F +G V V+ G KGY ++ F+SE+
Sbjct: 4 KVFLGGVPWDITEAGLINTFKPFGSVS-----VEWPGKDGKHPRHPPKGYVYLIFESEKS 58
Query: 97 AKRL 100
K L
Sbjct: 59 VKAL 62
>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 = 36.6 bits (85), Expect = 0.001
Identities = 15/56 (26%), Positives = 25/56 (44%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKE 111
E +L + YG V +I+ D G S+G GF +S E+ + + + K
Sbjct: 13 DEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFNGKYLKG 68
>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 = 37.2 bits (86), Expect = 0.001
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
V++G I S T EL + FS +G +++ I G YGF+T+ EEA
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEG--DNYGFVTYRYTEEA 54
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a
specific inhibitory effect on oestrogen action, SLTM is
shown to exert a generalized inhibitory effect on gene
expression associated with induction of apoptosis in a
wide range of cell lines. .
Length = 74
Score = 36.6 bits (84), Expect = 0.001
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKR 99
++V G++S T +L LF +YG V K+V + R+ +K YG +T S E R
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVAR 56
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 36.6 bits (84), Expect = 0.001
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQKDS 104
+FV ++ E L +LF +G V VK++ D KG+GF+T + +EA
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 105 DNIMFKEKRLNIAPAIKKQ 123
+ ++ L ++ KQ
Sbjct: 64 NGYRLGDRVLQVSFKTSKQ 82
>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 = 36.3 bits (83), Expect = 0.001
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+++ G+ TT+ +L +L YG + K ++D+ KGYGF+ FDS A++
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 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 = 36.2 bits (83), Expect = 0.001
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 7/56 (12%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
K +FV + +T TE+ L + FS++G +++VK + D Y F+ F+ + A R
Sbjct: 2 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVR 50
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 36.0 bits (83), Expect = 0.002
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
V+VG + +T +EL FS G + +V I+ D+ +G KGY +I F ++
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFA-TRDSVEAAVAL 60
Query: 105 DNIMFKEKRLNIAP 118
D F+ + + + P
Sbjct: 61 DESSFRGRVIKVLP 74
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 35.9 bits (83), Expect = 0.002
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
V+VG + E E+ +LF +YG + + + + GY FI F+ +A+ +
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPR--PPGYAFIEFEDARDAEDAIRGR 58
Query: 105 DNIMFKEKRLNI 116
D F +RL +
Sbjct: 59 DGYDFDGQRLRV 70
>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 = 36.3 bits (83), Expect = 0.002
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+++ G+ TT+ +L +L YG + K ++D+ KGYGF+ FDS A++
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQK 64
>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 = 36.1 bits (84), Expect = 0.002
Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 15/86 (17%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKI---VVDRAGISKGYGFITFDSEEEAKRLQK 102
VFVG + TT + +L +LF Q+G ++ V+ V + K I K+
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIK-------KKFHD 55
Query: 103 DSDN----IMFKEKRLNIAPAIKKQG 124
DN ++FKE+ A+K G
Sbjct: 56 KKDNVNAYVVFKEEES-AEKALKLNG 80
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 35.8 bits (83), Expect = 0.002
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 58 DELCELFSQYGIVKQVKIVVDRAGI---SKGYGFITFDSEEEAKRLQKDSDNIMFKEK 112
E E F + K KI +D G +G +ITF+ E+A R D + F +
Sbjct: 10 KEEEEYF--GEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGR 65
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells. And it also regulates the neurite elongation and
morphological differentiation. HuD specifically bound
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 36.2 bits (83), Expect = 0.002
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
+FV ++ + E L +LF +G V VK++ D KG+GF+T + +EA
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEA 58
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 36.1 bits (83), Expect = 0.002
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKG--YGFITFDSEEEAKR 99
+ +F+G + +E EL F +YGI+++V V+ R +G Y F+ F + + A R
Sbjct: 9 RNLFIGNLDHNVSEVELRRAFDKYGIIEEV--VIKRPARGQGGAYAFLKFQNLDMAHR 64
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2
of PHIP1. A. thaliana PHIP1 and its homologs represent
a novel class of plant-specific RNA-binding proteins
that may play a unique role in the polarized mRNA
transport to the vicinity of the cell plate. The family
members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 35.4 bits (82), Expect = 0.002
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEE 95
V++G + TED++ E F + V++ D+ G KG+G + F EE
Sbjct: 1 TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEE 51
>gnl|CDD|240876 cd12430, RRM_LARP4_5_like, RNA recognition motif in La-related
protein 4 (LARP4), La-related protein 5 (LARP5 or
LARP4B) and similar proteins. This subfamily
corresponds to the RRM of LARP4 and LARP5. LARP4 is a
cytoplasmic factor that can bind poly(A) RNA and
interact with poly(A) binding protein (PABP). It may
play a role in promoting translation by stabilizing
mRNA. LARP5 is a cytosolic protein that co-sediments
with polysomes and accumulates upon stress induction in
cellular stress granules. It can interact with the
cytosolic poly(A) binding protein 1 (PABPC1) and the
receptor for activated C Kinase (RACK1), a component of
the 40S ribosomal subunit. LARP5 may function as a
stimulatory factor of translation through bridging mRNA
factors of the 3' end with initiating ribosomes. Both,
LARP4 and LARP5, are structurally related to the La
autoantigen. Like other La-related proteins (LARPs)
family members, LARP4 and LARP5 contain a La motif
(LAM) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 76
Score = 35.4 bits (82), Expect = 0.002
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 51 ITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
I +T E+E+ LFS K R I+ + F+TF++EE+A+
Sbjct: 8 IPESTPEEEVKALFSGQNCPKFTSC---RFDINNSW-FVTFETEEDAQE 52
>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 = 35.5 bits (82), Expect = 0.003
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA-KRLQKDS 104
V++G I + TE++L FSQYG ++ V + + K F+ F + A K +
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLRE-----KNCAFVNFTNISNAIKAIDGVK 60
Query: 105 DNIMFKEKRLNIAP 118
+ +FK+ +++
Sbjct: 61 SHPLFKKFKISYGK 74
>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 = 35.6 bits (81), Expect = 0.003
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKR 99
+++ G+ TT+ +L +L YG + K ++D+ KGYGF+ FDS A++
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQK 61
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 35.4 bits (82), Expect = 0.003
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISK--GYGFITFDSEEEAKR 99
T EL ELFS +G +K V++ G G+GF+ F ++++AKR
Sbjct: 13 TVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKR 58
>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 = 35.4 bits (81), Expect = 0.003
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
V+ GGI S TE + + FS +G + ++++ + KGY FI F + E A
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESA 49
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 35.3 bits (82), Expect = 0.003
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF-DSEEEAKRLQKDS 104
++VG + TTT D+L E FSQ G VK V++ D Y F+ F + L+
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD-ETQPTRYAFVEFAEQTSVINALK--L 63
Query: 105 DNIMFKEKRLNI 116
+ MF + L +
Sbjct: 64 NGAMFGGRPLKV 75
>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 = 34.9 bits (80), Expect = 0.003
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 7/75 (9%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
RVF+G + E ++ F YG ++ + + +G+GF+ FD +A +
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDID-------LKRGFGFVEFDDPRDADDAVYEL 53
Query: 105 DNIMFKEKRLNIAPA 119
D +R+ I A
Sbjct: 54 DGKELCNERVTIEHA 68
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 35.0 bits (80), Expect = 0.003
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+FV + +L E+FS G VK+ I D+ G S+G G +TF+ EA
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEA 54
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 35.4 bits (81), Expect = 0.003
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+F+ + T+ +L + F +G V K+ +D+ +SK +GF+++D+ + A+ +
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66
Query: 105 DNIMFKEKRLNI 116
+ KRL +
Sbjct: 67 NGFQIGTKRLKV 78
>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 = 35.0 bits (81), Expect = 0.004
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYG-FITFDSEEEAKR 99
+++ + I ++L L S YG VK + V + S+ +T++S E+A++
Sbjct: 1 RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTK---SETATVNVTYESPEQAQQ 54
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM2 of U1A/U2B"/SNF protein family,
containing Drosophila sex determination protein SNF and
its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs) connected by a variable, flexible linker.
SNF is an RNA-binding protein found in the U1 and U2
snRNPs of Drosophila where it is essential in sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). U1A is an RNA-binding protein associated with
the U1 snRNP, a small RNA-protein complex involved in
pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA and its nuclear
transport is independent on U2 snRNA binding. .
Length = 72
Score = 34.9 bits (81), Expect = 0.004
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
K +F+ + TT++ L LF+Q+ K+V++V R G F+ F++EE+A
Sbjct: 3 KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRR-----GIAFVEFETEEQA 51
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly
development. Cabeza contains one RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 35.1 bits (81), Expect = 0.004
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVK--------IVVDRA-GISKGYGFITFD 92
VFV + TTE +L E F GI+K K + D+ G KG +T+D
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYD 56
>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 = 34.7 bits (80), Expect = 0.004
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEE 95
VFV G T+E++L + FS +G V V + D+ Y + FDS+E
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKG----VYAIVEFDSKE 50
>gnl|CDD|241121 cd12677, RRM4_Nop4p, RNA recognition motif 4 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM4 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 156
Score = 36.5 bits (84), Expect = 0.005
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 4/34 (11%)
Query: 68 GIVKQVKIVVDR----AGISKGYGFITFDSEEEA 97
G+VKQ K+ ++ AG S+GYGF+ F S + A
Sbjct: 69 GVVKQAKVETEKAGSTAGRSRGYGFMEFISHKYA 102
>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 = 34.8 bits (80), Expect = 0.005
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKDS 104
+F+ + + EL ++F +G V K+ VDRA SK +GF++FD+ A+ +
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66
Query: 105 DNIMFKEKRLNI 116
+ KRL +
Sbjct: 67 NGFQIGMKRLKV 78
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM1 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding protein
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 34.5 bits (79), Expect = 0.005
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+FV + TE L LF YG V+ V IS+G + F +AKR ++
Sbjct: 4 LFVINVPRDVTESTLRRLFEVYGDVRG----VQTERISEGIVTVHFYDIRDAKRAVRELC 59
Query: 106 NIMFKEKRLNI 116
+++ L
Sbjct: 60 GRHMQQQALGG 70
>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 = 34.6 bits (80), Expect = 0.005
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 50 GITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRL 100
I T +++ +F+Q+G VK V G GY I F + E A++
Sbjct: 8 SIGPGVTREDIKAVFAQFGEVKYVDFT---EGADTGY--IRFKTPEAAQKA 53
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end)
protein family. This subfamily corresponds to the RRM1
domain in the Spen (split end) family which includes RNA
binding motif protein 15 (RBM15), putative RNA binding
motif protein 15B (RBM15B), and similar proteins found
in Metazoa. RBM15, also termed one-twenty two protein 1
(OTT1), conserved in eukaryotes, is a novel mRNA export
factor and component of the NXF1 pathway. It binds to
NXF1 and serves as receptor for the RNA export element
RTE. It also possesses mRNA export activity and can
facilitate the access of DEAD-box protein DBP5 to mRNA
at the nuclear pore complex (NPC). RNA-binding protein
15B (RBM15B), also known as one twenty-two 3 (OTT3), is
a paralog of RBM15 and therefore has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong- to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 34.5 bits (80), Expect = 0.006
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 57 EDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNI 116
ED L F ++G V + V G + ++ F E+A+ + ++ ++ LN+
Sbjct: 19 EDVLYHEFKKFG---DVSVRVLHDGEDERVAYVNFRHPEDAREAKHAKGRLVLFDRPLNV 75
Query: 117 AP 118
P
Sbjct: 76 EP 77
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 34.7 bits (79), Expect = 0.007
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
+F+ + E L ++F +G V VK++ D KG+GF+T + EEA
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEA 56
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 75
Score = 34.3 bits (79), Expect = 0.007
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF 91
++VG + E+ + E F +YG V+ VKI+ R F+ F
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDF 47
>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 = 34.2 bits (78), Expect = 0.007
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 7/54 (12%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
K +FV + +T TE+ L + F Q+G +++VK + D Y FI FD + A
Sbjct: 2 KVLFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGA 48
>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 = 34.2 bits (78), Expect = 0.007
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
RV++G ++ E ++ F YG + +V + GYGF+ FD +A
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDL-------KNGYGFVEFDDLRDA 46
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 34.5 bits (80), Expect = 0.007
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEAKRLQK 102
VFVG I ++D + +L + G V K V D G K +GF F+ E A R +
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60
Query: 103 DSDNIMFKEKRLNI 116
+ + K+L +
Sbjct: 61 LLNGLELGGKKLLV 74
>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage
factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar
proteins. This subgroup corresponds to the RRM of
CFIm59. Cleavage factor Im (CFIm) is a highly conserved
component of the eukaryotic mRNA 3' processing machinery
that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. The two separate genes,
CPSF6 and CPSF7, code for two isoforms of the large
subunit, CFIm68 and CFIm59. The family includes CFIm59,
also termed cleavage and polyadenylation specificity
factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59). CFIm59 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. The N-terminal
RRM of CFIm59 mediates the interaction with CFIm25. It
also serves to enhance RNA binding and facilitate RNA
looping. .
Length = 90
Score = 34.5 bits (79), Expect = 0.008
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQK 102
V+VG + TT+ +L ++ G+ V ++K +RA G SKGY + SE +L +
Sbjct: 4 VYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 63
Query: 103 DSDNIMFKEKRLNIAPAIKK 122
+ +++++ PA ++
Sbjct: 64 LLPGKVLNGEKVDVRPATRQ 83
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA
branch site protein p14 (SF3B14) and similar proteins.
This subfamily corresponds to the RRM of SF3B14 (also
termed p14), a 14 kDa protein subunit of SF3B which is
a multiprotein complex that is an integral part of the
U2 small nuclear ribonucleoprotein (snRNP) and the
U11/U12 di-snRNP. SF3B is essential for the accurate
excision of introns from pre-messenger RNA and has been
involved in the recognition of the pre-mRNA's branch
site within the major and minor spliceosomes. SF3B14
associates directly with another SF3B subunit called
SF3B155. It is also present in both U2- and
U12-dependent spliceosomes and may contribute to branch
site positioning in both the major and minor
spliceosome. Moreover, SF3B14 interacts directly with
the pre-mRNA branch adenosine early in spliceosome
assembly and within the fully assembled spliceosome.
SF3B14 contains one well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 77
Score = 34.1 bits (79), Expect = 0.008
Identities = 13/54 (24%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++V + + +EL +LF +YG ++Q++I + ++G F+ ++ +AK
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE--TRGTAFVVYEDIYDAKN 56
>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 = 33.7 bits (77), Expect = 0.010
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
RV++G ++ E ++ F YG + ++ + GYGF+ F+ +A
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEID-------LKNGYGFVEFEDSRDA 46
>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 = 34.1 bits (79), Expect = 0.010
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 57 EDELCELFSQYGIVKQVKIVVDRAGISKGY--GFITFDSEEEAKRLQKDSDNIMF 109
+DE+ E +YG V V + + + F+ F +EA + + + F
Sbjct: 20 KDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFF 74
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 33.8 bits (78), Expect = 0.010
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 8/60 (13%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF----DSEEEAKRLQK 102
FV I S ++EL LF Q+G ++ + A +G+ +++ + + LQ
Sbjct: 5 FVRNINSNVEDEELRALFEQFGDIRTLYT----ACKHRGFIMVSYYDIRAARRAKRALQG 60
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 33.4 bits (76), Expect = 0.012
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 45 RVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
RVF+G + T + ++ +FS+YG KIV + KG+ F+ + +E A+
Sbjct: 3 RVFIGNLNTLVVKKSDVEAIFSKYG-----KIV--GCSVHKGFAFVQYVNERNARAAVAG 55
Query: 104 SDNIMFKEKRLNI 116
D M + L+I
Sbjct: 56 EDGRMIAGQVLDI 68
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 86
Score = 33.5 bits (76), Expect = 0.014
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
+FV + E L ++F +G V VK++ D KG+GF+T + +EA
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEA 58
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 83
Score = 33.3 bits (76), Expect = 0.016
Identities = 14/67 (20%), Positives = 35/67 (52%)
Query: 59 ELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAP 118
+L ++F +YG V++ I R G G+ F+T + A+ ++++ + + + +
Sbjct: 17 KLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDW 76
Query: 119 AIKKQGF 125
A++K +
Sbjct: 77 AVQKNRW 83
>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 = 0.016
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+ V + T++EL LF G ++ K+V D+ G S GYGF+ + ++A++
Sbjct: 7 LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66
Query: 105 DNIMFKEKRLNIAPA 119
+ + + K + ++ A
Sbjct: 67 NGLRLQTKTIKVSYA 81
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 33.1 bits (76), Expect = 0.016
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGIS-KGYGFITFDSEEEA 97
V+V + T + L +FS+YG V V + + KG+ FI F++ EEA
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEA 54
>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 = 33.2 bits (76), Expect = 0.017
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
V+ G ++ ++ LF G V++V ++ + + FITF++ E A
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV---QPHAFITFENLEAA 50
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 33.2 bits (76), Expect = 0.017
Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
R++VG + S E +L +LF +YG ++ +++ R + + F+ F+ +A+
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVP--FAFVRFEDPRDAE 52
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 33.0 bits (75), Expect = 0.017
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKD 103
K + V ++ + +ED L E+F + ++ + G KGY F+ F+S E+AK
Sbjct: 2 KVLVVNNLSYSASEDSLQEVFEKATSIR----IPQNNGRPKGYAFVEFESAEDAKEALNS 57
Query: 104 SDN 106
+N
Sbjct: 58 CNN 60
>gnl|CDD|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage
factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar
proteins. This subgroup corresponds to the RRM of
CFIm68. Cleavage factor Im (CFIm) is a highly conserved
component of the eukaryotic mRNA 3' processing machinery
that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. The family includes CFIm68, also
termed cleavage and polyadenylation specificity factor
subunit 6 (CPSF6), or cleavage and polyadenylation
specificity factor 68 kDa subunit (CPSF68), or protein
HPBRII-4/7. CFIm68 contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a central
proline-rich region, and a C-terminal RS-like domain.
The N-terminal RRM of CFIm68 mediates the interaction
with CFIm25. It also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 77
Score = 33.2 bits (76), Expect = 0.018
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGI--VKQVKIVVDRA-GISKGYGFITFDSEEEAKRL 100
++VG +T TT+ +L E G+ + ++K +RA G SKG+ I SE +++L
Sbjct: 2 LYVGNLTWWTTDQDLTEAIQSIGVNDLLEIKFFENRANGQSKGFALIVLGSESSSRKL 59
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein (hnRNP) H protein family.
This subfamily corresponds to the RRM2 of hnRNP H
protein family which includes hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'),
hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation. hnRNP
H3 may be involved in the splicing arrest induced by
heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. .
Length = 77
Score = 33.1 bits (76), Expect = 0.018
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 50 GITSTTTEDELCELFSQYGIVKQ-VKIVVDRAGISKGYGFITFDSEEEAKR-LQKDSDNI 107
G+ +++E+ + FS IV + + +D G S G ++ F S+E A+R L K + I
Sbjct: 7 GLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERALGKHKEKI 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 = 33.0 bits (76), Expect = 0.022
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA-KRLQKDSDN 106
V ++ + + L + FSQ+G V++ ++VD G S G G + F + A +++ S+
Sbjct: 4 VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCSEG 63
Query: 107 IMF 109
Sbjct: 64 CFL 66
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 33.1 bits (76), Expect = 0.025
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 18/83 (21%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKG--YGFITFDSEEEAKRLQKD 103
+ G+ T+ +++ E FSQ+G VK V +G G++ F + E AK+
Sbjct: 4 LKFSGLNKPTSREDIKEAFSQHGEVKYV-------DFLEGDKEGYVRFKTPEAAKK---- 52
Query: 104 SDNIMFKEKRLNIAPAIKKQGFT 126
EK IK+ T
Sbjct: 53 -----ALEKATEAKLKIKEAEVT 70
>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 = 32.8 bits (74), Expect = 0.026
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+ V + T++E LF G ++ K+V D+ G S GYGF+ + +A +
Sbjct: 6 LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65
Query: 105 DNIMFKEKRLNIAPA 119
+ + + K + ++ A
Sbjct: 66 NGLKLQTKTIKVSYA 80
>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 = 32.0 bits (73), Expect = 0.036
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 53 STTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRL 100
S TE+++ E F Q+G V V+I + +GF+TF++ E KR+
Sbjct: 9 SRFTEEDVSEYFGQFGPVLDVRI---PYQQKRMFGFVTFENAETVKRI 53
>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM2 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 78
Score = 32.1 bits (73), Expect = 0.038
Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGI-VKQVKIVVDRAGISKGYGFITFDSEEEA 97
+F+ G+ + TED + + FS G+ V V + +R G++ G + F ++E+A
Sbjct: 2 LFLRGLPFSVTEDNVRDFFS--GLKVDGVIFLKNRRGLNNGNSMVKFATKEDA 52
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response element
(IGFRE). Moreover, PSF functions as a transcriptional
repressor interacting with Sin3A and mediating silencing
through the recruitment of histone deacetylases (HDACs)
to the DNA binding domain (DBD) of nuclear hormone
receptors. PSF is an essential pre-mRNA splicing factor
and is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. PSF
forms a heterodimer with the nuclear protein p54nrb,
also known as non-POU domain-containing octamer-binding
protein (NonO). The PSF/p54nrb complex displays a
variety of functions, such as DNA recombination and RNA
synthesis, processing, and transport. PSF contains two
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which are responsible for interactions with
RNA and for the localization of the protein in speckles.
It also contains an N-terminal region rich in proline,
glycine, and glutamine residues, which may play a role
in interactions recruiting other molecules. .
Length = 80
Score = 32.4 bits (73), Expect = 0.040
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDSDN 106
V ++ + + L E FSQ+G V++ ++VD G S G G + F S+ A++ ++ ++
Sbjct: 4 VRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCTEG 63
Query: 107 IMF 109
+
Sbjct: 64 VFL 66
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 32.0 bits (73), Expect = 0.042
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF 91
+ +F+G + TTT +L E F ++G + + I + + G + Y FI +
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEI--IDIDIKKQGGNPAYAFIQY 48
>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 = 31.9 bits (72), Expect = 0.044
Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++FV + T +L E FSQ G V +I ++ G SKG G + FDS E A++
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMEN-GKSKGCGTVRFDSPESAEK 54
>gnl|CDD|241007 cd12563, RRM2_RBM6, RNA recognition motif 2 in vertebrate
RNA-binding protein 6 (RBM6). This subgroup corresponds
to the RRM2 of RBM6, also termed lung cancer antigen
NY-LU-12, or protein G16, or RNA-binding protein DEF-3,
which has been predicted to be a nuclear factor based on
its nuclear localization signal. It shows high sequence
similarity to RNA-binding protein 5 (RBM5 or LUCA15 or
NY-REN-9). Both, RBM6 and RBM5, specifically bind
poly(G) RNA. They contain two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. In contrast to RBM5, RBM6 has two additional
unique domains: the decamer repeat occurring more than
20 times, and the POZ (poxvirus and zinc finger) domain.
The POZ domain may be involved in protein-protein
interactions and inhibit binding of target sequences by
zinc fingers. .
Length = 87
Score = 32.1 bits (73), Expect = 0.045
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIV--KQVKIVVDRAG-ISKGYGFITFDSEEEAKRL 100
K + + I +T + + + Y + V+I+ ++ G K +GFI DS EA RL
Sbjct: 3 KTIILKRIKRSTPPEVIVKALDPYVRLSTSNVRIIKNKPGPGGKTFGFIDLDSHAEALRL 62
Query: 101 QK 102
K
Sbjct: 63 VK 64
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 31.6 bits (72), Expect = 0.056
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
V+V I TE++L LFS G V ++ D + + + FI F EE A+
Sbjct: 5 VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLR-FAFIEFTDEEGAR 56
>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 = 31.4 bits (72), Expect = 0.059
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRL 100
+ + + TE +L L S +G K +++ R K + DS E AK +
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFG--KVTNVLLLR---GKNQALVEMDSVESAKSM 51
>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 = 31.4 bits (72), Expect = 0.062
Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIM 108
+L E FS++G + +++ + + F + EEAK+ + + +
Sbjct: 15 NITKLNEHFSKFGTIVNIQVNYNPES-----ALVQFSTSEEAKKAYRSPEAVF 62
>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 = 31.8 bits (72), Expect = 0.067
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVK--------QVKIVVDRA-GISKGYGFITFDSEEE 96
+FV G+ T + + + F Q GI+K + + DR G KG ++FD
Sbjct: 5 IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64
Query: 97 AK 98
AK
Sbjct: 65 AK 66
>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3). This subgroup corresponds to the RRM2 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators.
Unlike other MSSP proteins, RBMS3 is not a
transcriptional regulator. It binds with high affinity
to A/U-rich stretches of RNA, and to A/T-rich DNA
sequences, and functions as a regulator of cytoplasmic
activity. RBMS3 contain two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and its C-terminal
region is acidic and enriched in prolines, glutamines
and threonines. .
Length = 88
Score = 31.6 bits (71), Expect = 0.069
Identities = 15/56 (26%), Positives = 29/56 (51%)
Query: 43 PKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
P +++ + + E EL + +G V +I+ D G+S+G GF +S E+ +
Sbjct: 1 PTNLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCE 56
>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 = 31.4 bits (72), Expect = 0.070
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+ED+ +L +G V+++ R G K F TFD+E+ A
Sbjct: 12 SEDDKEDLLKHFGASS-VRVMSRR-GKLKNTAFATFDNEQAAS 52
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein
zinc fingers (zf-RanBP), and an asparagine-rich region.
It may possess RNA-binding and zinc ion binding
activities. Additional research had indicated that ARP
may function as a factor involved in the stress
response. .
Length = 88
Score = 31.7 bits (72), Expect = 0.071
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGI-------VKQVKIVVDRAGISKGYGFITFDSEEE 96
K +++ + TT+ EL F+QYG+ +K + GF F S EE
Sbjct: 1 KVLYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEE 60
Query: 97 AKR 99
A
Sbjct: 61 AME 63
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 and RRM4 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
and is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 82
Score = 31.4 bits (71), Expect = 0.073
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 12/79 (15%)
Query: 44 KRVFVGGIT-----STTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA- 97
+ V++G ++ E EL + +YG ++ ++I+ + K FI F + A
Sbjct: 3 RNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILRE-----KACAFINFMNIPNAI 57
Query: 98 KRLQK-DSDNIMFKEKRLN 115
LQ + R+N
Sbjct: 58 AALQTLNGKKPYDTIVRIN 76
>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 = 31.4 bits (71), Expect = 0.077
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVK--------QVKIVVDR-AGISKGYGFITFDSEEE 96
++V G+ T +EL + F G+VK V I D+ G KG ++++
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62
Query: 97 AKRLQKDSDNIMFKEKRLNIA 117
AK + D F+ +L ++
Sbjct: 63 AKAAVEWFDGKDFQGSKLKVS 83
>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 = 31.2 bits (70), Expect = 0.082
Identities = 15/52 (28%), Positives = 30/52 (57%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
V ++ + + L + FSQ+G V++ ++VD G G GF+ F ++ A++
Sbjct: 4 VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARK 55
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 31.4 bits (72), Expect = 0.084
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 44 KRVFVGGITSTTTEDELCELFSQY-----GIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
KR++V ++ TE++L +F ++ I + G KG F+TF SEE A
Sbjct: 2 KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61
Query: 99 RLQKDSDNIMFKEK 112
+ + + K K
Sbjct: 62 KALNLVNGYVLKGK 75
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in
yeast. Yra1p is associated with Pse1p and Kap123p, two
members of the beta-importin family, further mediating
transport of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission
yeast as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 31.2 bits (71), Expect = 0.086
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 45 RVFVGGITSTTTEDELCELF-SQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+V V + TE ++ E F SQ G +K+V + + G S G ITF +A +
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATK 56
>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 = 30.9 bits (70), Expect = 0.095
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 54 TTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
TT E+++ +LF +G +V R I K + F+ F+ E+A
Sbjct: 11 TTREEDIEKLFEPFG-----PLV--RCDIRKTFAFVEFEDSEDAT 48
>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 = 31.2 bits (71), Expect = 0.10
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
K F+ G+ E ++ + F Q+G K V IV RA GF+ F++ E A++
Sbjct: 3 KSFFLFGVEDDLPEYKIRDYFEQFGKSKSV-IVNHRAKC----GFVRFETREAAEK 53
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 31.2 bits (71), Expect = 0.11
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYG-IVKQVKIVVDRA-GISKGYGFITFDSEEEAKR 99
+++G + E+ + F+ G V VKI+ ++ G GY F+ F E A+R
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAER 57
>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 = 31.2 bits (71), Expect = 0.11
Identities = 18/78 (23%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIV------KQVKIVVDRAGISKGYGFITFDSEEEAK 98
RV++ ++ +++E++L E + V + V+ R G + F S E+A+
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 99 RLQKDSDNIMFKEKRLNI 116
++ KD + +FK ++L +
Sbjct: 61 KVVKDLNGKVFKNRKLFV 78
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family may share similar expression
patterns and functions. CPEB-2 is an RNA-binding protein
that is abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation; it directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a Zn-finger motif.
In addition, they do have conserved nuclear export
signals that are not present in CPEB-1. .
Length = 92
Score = 31.3 bits (71), Expect = 0.12
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 13/65 (20%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVD--RAGIS------KGYGFITFDSEE 95
++VFVGG+ EDE+ F ++G +VVD S KGY F+ F E
Sbjct: 1 RKVFVGGLPPDIDEDEITASFRRFG-----PLVVDWPHKAESKSYFPPKGYAFLLFQEES 55
Query: 96 EAKRL 100
+ L
Sbjct: 56 SVQAL 60
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate
RNA-binding Raly-like protein (RALYL). This subgroup
corresponds to the RRM of RALYL, also termed
heterogeneous nuclear ribonucleoprotein C-like 3, or
hnRNP core protein C-like 3, a putative RNA-binding
protein that shows high sequence homology with Raly, an
RNA-binding protein playing a critical role in
embryonic development. The biological role of RALYL
remains unclear. Like Raly, RALYL contains two distinct
domains, an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal auxiliary
domain. .
Length = 69
Score = 30.8 bits (69), Expect = 0.12
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 45 RVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
RVF+G + T+ + ++ +F++YG KIV + KGY F+ + SE A+
Sbjct: 3 RVFIGNLNTAIVKKADIEAIFAKYG-----KIV--GCSVHKGYAFVQYISERHAR 50
>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 = 30.9 bits (69), Expect = 0.12
Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDS 104
+ V + T++E LF G ++ K+V D+ G S GYGF+ + ++A++
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 105 DNIMFKEKRLNIAPA 119
+ + + K + ++ A
Sbjct: 65 NGLRLQTKTIKVSYA 79
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element
(TAR) RNA which is synthesized by cellular RNA
polymerase II at the viral long terminal repeat. NELF
is a heterotetrameric protein consisting of NELF A, B,
C or the splice variant D, and E. NELF-E contains an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). It
plays a role in the control of HIV transcription by
binding to TAR RNA. In addition, NELF-E is associated
with the NELF-B subunit, probably via a leucine zipper
motif. .
Length = 75
Score = 30.7 bits (70), Expect = 0.12
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 7/58 (12%)
Query: 42 VPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++V G TE+ L + FS +G + + I ++ K GF+TF+ E A R
Sbjct: 3 KGNTLYVHGYG--LTEEILKKAFSPFGNI--INISME---KEKNCGFVTFEKMESADR 53
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 30.7 bits (70), Expect = 0.13
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
V V + TTE+++ + F G +++VKIV G+ I F++E+EA
Sbjct: 3 VKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLV---AVIEFETEDEA 51
>gnl|CDD|237517 PRK13807, PRK13807, maltose phosphorylase; Provisional.
Length = 756
Score = 33.0 bits (76), Expect = 0.14
Identities = 26/82 (31%), Positives = 35/82 (42%), Gaps = 28/82 (34%)
Query: 110 KEKRLNIAPAIKKQGFTG------TY-DS----LPTVTSPVPPVPTSN--MYYHNGLPYT 156
++ RLNI P +GFTG TY D+ +P + P T N Y +N LP
Sbjct: 334 EDARLNIGP----KGFTGEKYGGATYWDTEAYCVPFYLATADPEVTRNLLKYRYNQLPGA 389
Query: 157 YHN----GM--AFFPSNGQSMV 172
N G+ A +P MV
Sbjct: 390 KENAKKQGLKGALYP-----MV 406
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM3 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). 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
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RRMs.
Length = 71
Score = 30.2 bits (69), Expect = 0.16
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 46 VFVGGIT-STTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
+ V G+ D+L LF YG V ++K + + G + + A+R +
Sbjct: 2 LMVYGLDKDKMNCDKLFNLFCLYGNVLRIKFLKSK----PGTAMVQMGDPQAAERAIEYL 57
Query: 105 DNIMFKEKRLNIAP 118
+ ++ ++L +
Sbjct: 58 NGVVLFGQKLEVNF 71
>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM1 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 70
Score = 30.1 bits (68), Expect = 0.16
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDS 104
R+ + + + T+ E+ +L S Y VK VD+ SK +T + ++A R
Sbjct: 1 RIVIRNLPADVTKQEVHDLLSDYQ-VKYCD--VDK---SKRTAQVTLLNGDQASRAIAKL 54
Query: 105 DNIMFKEKRLNI 116
+KE+++++
Sbjct: 55 HQSSYKERKISV 66
>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 = 30.3 bits (68), Expect = 0.16
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 4/73 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
V VGG++ + +E +L F +Y QV ++ + Y + FD +A K +
Sbjct: 2 VHVGGLSPSVSEGDLRSHFQKY----QVSVISLCKLSNYRYASLHFDRASDALLAVKKMN 57
Query: 106 NIMFKEKRLNIAP 118
+ + +
Sbjct: 58 GGVLSGLSIKVRM 70
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 30.2 bits (68), Expect = 0.20
Identities = 14/68 (20%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
+++ ++S+ + EL + F +G +++ K+++ G + YGFIT+ E A
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRG--EKYGFITYRHSEHAALSLGKGA 62
Query: 106 NIMFKEKR 113
++ + +
Sbjct: 63 SLRKRNEP 70
>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 = 30.2 bits (69), Expect = 0.21
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 9/50 (18%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISKGYG---FITFDSEEEAKRLQK 102
T D L ++FS YG V+ KI++ K G + FDS E A+ +K
Sbjct: 14 TVDVLHQVFSPYGAVE--KILI----FEKNTGVQALVQFDSVESAENAKK 57
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM2 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 71
Score = 29.9 bits (68), Expect = 0.22
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 5/36 (13%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVK 74
GT++ VF S ++ EL LFSQ+G VK ++
Sbjct: 2 GTLL---VFNLD--SPISDQELRSLFSQFGEVKDIR 32
>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 = 29.9 bits (68), Expect = 0.24
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 49 GGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
GG+ + + +EL +F +YG V+ + + K Y F+++ S E+A
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVMP-----PGKPYCFVSYSSIEDAAA 54
>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 = 29.8 bits (67), Expect = 0.26
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 46 VFVGGITSTTTEDELCELFSQYG--IVKQVKIVVD--RAG--ISKGYGFITFDSEEEAKR 99
+FV + +TT L + F + +VK D R G +S G+GF+ F ++E+A+
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 100 LQKDSD 105
K D
Sbjct: 63 ALKAMD 68
>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM1 of the CPEB family of proteins
that bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate
their translation. CPEB proteins are well conserved in
both, vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins have been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bind to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The
second subfamily includes CPEB-2, CPEB-3, CPEB-4, and
related protiens. Due to high sequence similarity,
members in this subfamily may share similar expression
patterns and functions. CPEB-2 is an RNA-binding
protein that is abundantly expressed in testis and
localized in cytoplasm in transfected HeLa cells. It
preferentially binds to poly(U) RNA oligomers and may
regulate the translation of stored mRNAs during
spermiogenesis. CPEB-2 impedes target RNA translation
at elongation; it directly interacts with the
elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a Zn-finger motif. CPEB-2, -3, and -4 have
conserved nuclear export signals that are not present
in CPEB-1. .
Length = 112
Score = 30.3 bits (68), Expect = 0.29
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYG 68
++VFVGG+ TE ++ F ++G
Sbjct: 1 RKVFVGGLPWDITEADILNSFRRFG 25
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind
to cytoplasmic proteins. Raver-2 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. Raver-2 binds to PTB through the
SLLGEPP motif only, and binds to RNA through its RRMs.
.
Length = 77
Score = 29.5 bits (66), Expect = 0.30
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 54 TTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEAKR 99
+ T +E EL YG +++ +V + G SKGYGF+ + ++ A +
Sbjct: 10 SFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASK 56
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 3 in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologues exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 72
Score = 29.5 bits (67), Expect = 0.33
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 51 ITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+ TTE+EL ELF ++G + ++ + S+ + F +A++
Sbjct: 8 LPFGTTEEELRELFEKFGSLGRLLLPP-----SRTIALVEFLEPSDARK 51
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically bind mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone and play a key role in
cell growth and differentiation. DND1 is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two
RRMs. .
Length = 82
Score = 29.6 bits (67), Expect = 0.33
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGI-VKQVKI--VVDRAGISKGYGFITFDSEEEA 97
R+FVGGI T T++E+ E FS+ V V + D ++G+ F+ ++S A
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAA 58
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 77
Score = 29.5 bits (66), Expect = 0.35
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 48 VGGITSTTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEAKRLQKD 103
+ + T T+ + EL +G +++ +V + G SKGYGF+ + ++ A R + D
Sbjct: 4 IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSD 60
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and 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 = 81
Score = 29.7 bits (66), Expect = 0.37
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR--LQKD 103
++VG ++ TE + +LFSQ G K K++ + + Y F+ F +A +
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMN 60
Query: 104 SDNIMFKEKRLNIAPAIKKQ 123
I+ KE ++N A Q
Sbjct: 61 GRKILGKEVKVNWATTPSSQ 80
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 29.3 bits (66), Expect = 0.38
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 47 FVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++G ++S E +L +LF ++ I +V GY F+ + A +
Sbjct: 2 YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKG-----GYAFVDCPDQSWADK 49
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM5 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 29.4 bits (66), Expect = 0.42
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
T+ ++ LFS YG +K V++ ++G+ F+ F + +EA
Sbjct: 13 TKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEA 54
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT motif
responsible for docking many substrates to calcineurin,
and an unrecognized C-terminal TxxP motif of unknown
function. .
Length = 75
Score = 29.1 bits (66), Expect = 0.44
Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 9/77 (11%)
Query: 40 TVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
T VP VF T+ + L LFS YG + V S + F S EEA
Sbjct: 4 TNVPSEVF----TNAELKAALESLFSSYG--EIATFVYLP---SFRRARVVFSSPEEAAL 54
Query: 100 LQKDSDNIMFKEKRLNI 116
+ + +F+ L +
Sbjct: 55 ARIELHGTVFEGSVLRV 71
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 29.1 bits (65), Expect = 0.44
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSE 94
VFVG + E+ L +F + G ++ V+IV D + + KG+ ++ F E
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDE 51
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate
RNA-binding protein Raly. This subgroup corresponds to
the RRM of Raly, also termed autoantigen p542, or
heterogeneous nuclear ribonucleoprotein C-like 2, or
hnRNP core protein C-like 2, or hnRNP associated with
lethal yellow protein homolog, an RNA-binding protein
that may play a critical role in embryonic development.
It is encoded by Raly, a ubiquitously expressed gene of
unknown function. Raly shows a high degree of identity
with the 5' sequences of p542 gene encoding
autoantigen, which can cross-react with EBNA-1 of the
Epstein Barr virus. Raly contains two distinct domains,
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal auxiliary domain that
includes a unique glycine/serine-rich stretch. .
Length = 76
Score = 29.2 bits (65), Expect = 0.44
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 45 RVFVGGI-TSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
RVF+G + T+ + ++ +FS+YG V + KGY F+ + +E A+
Sbjct: 3 RVFIGNLNTAVVKKSDVETIFSKYGRVVG-------CSVHKGYAFVQYSNERHAR 50
>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 = 31.6 bits (71), Expect = 0.45
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEAKRLQKD 103
RV+VG I+ ED + F +G +K + + D A G KG+ F+ ++ E A+ +
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 104 SDNIMFKEKRLNI 116
+ M + + +
Sbjct: 169 MNGQMLGGRNIKV 181
Score = 28.9 bits (64), Expect = 2.8
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGIS-KGYGFITFD---SEEEA 97
R++V + +E ++ +F +G + + ++ G KGYGFI ++ S+ EA
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA 262
>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM2 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein
1 (RBMS1), or suppressor of CDC2 with RNA-binding motif
2 (SCR2). MSSP-1 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence CT(A/T)(A/T)T, and stimulates
DNA replication in the system using SV40 DNA. MSSP-1 is
identical with Scr2, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-1 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with c-MYC, the product
of protooncogene c-myc. MSSP-1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 85
Score = 29.3 bits (65), Expect = 0.47
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+++ + + E EL + +G V +I+ D +G S+G GF +S E+ +
Sbjct: 3 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCE 55
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell
surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or
ENOX) proteins. This subgroup corresponds to the
conserved RNA recognition motif (RRM) in ECTO-NOX
proteins (also termed ENOX), comprising a family of
plant and animal NAD(P)H oxidases exhibiting both,
oxidative and protein disulfide isomerase-like,
activities. They are growth-related and drive cell
enlargement, and may play roles in aging and
neurodegenerative diseases. ENOX proteins function as
terminal oxidases of plasma membrane electron transport
(PMET) through catalyzing electron transport from
plasma membrane quinones to extracellular oxygen,
forming water as a product. They are also hydroquinone
oxidases that oxidize externally supplied NADH, hence
NOX. ENOX proteins harbor a di-copper center that lack
flavin. ENOX proteins display protein disulfide
interchange activity that is also possessed by protein
disulfide isomerase. In contrast to the classic protein
disulfide isomerases, ENOX proteins lack the double
CXXC motif. This family includes two ENOX proteins,
ENOX1 and ENOX2. ENOX1, also termed candidate
growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous
and refractory to drugs. ENOX2, also termed APK1
antigen, or cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role
in cell proliferation and tumor progression. In
contrast to ENOX1, ENOX2 is drug-responsive and harbors
a drug binding site to which the cancer-specific
S-peptide tagged pan-ENOX2 recombinant (scFv) is
directed. Moreover, ENOX2 is specifically inhibited by
a variety of quinone site inhibitors that have
anticancer activity and is unique to the surface of
cancer cells. ENOX proteins contain many functional
motifs.
Length = 84
Score = 29.3 bits (66), Expect = 0.50
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 6/52 (11%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEE 95
K VFVGG+ TE+ + E+F Q G +I+ R K + I F E
Sbjct: 7 KTVFVGGLPENATEEIIREVFEQCG-----EIIAIRMS-KKNFCHIRFAEEF 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 = 29.3 bits (65), Expect = 0.57
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 57 EDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLN 115
+ +L ++F +G V K+ +D+ +SK +GF+++D+ A+ + + KRL
Sbjct: 21 DQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLK 80
Query: 116 I 116
+
Sbjct: 81 V 81
>gnl|CDD|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2
small nuclear ribonucleoprotein B" (U2B"). This
subgroup corresponds to the RRM1 of U2B" (also termed
U2 snRNP B"), a unique protein that comprises the U2
snRNP. It was initially identified to bind to stem-loop
IV (SLIV) at the 3' end of U2 snRNA. Additional
research indicates U2B" binds to U1 snRNA stem-loop II
(SLII) as well and shows no preference for SLIV or SLII
on the basis of binding affinity. U2B" does not require
an auxiliary protein for binding to RNA and its nuclear
transport is independent of U2 snRNA binding. U2B"
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). It also contains a nuclear localization
signal (NLS) in the central domain. However, nuclear
import of U2B'' does not depend on this NLS. The
N-terminal RRM is sufficient to direct U2B" to the
nucleus. .
Length = 80
Score = 28.8 bits (64), Expect = 0.61
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+F+ + T E L LF+Q+ K+V++V R I+ F+ F++E +A
Sbjct: 8 LFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIA----FVEFENEAQA 55
>gnl|CDD|240873 cd12427, RRM4_hnRNPL_like, RNA recognition motif 4 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM4 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 = 84
Score = 28.7 bits (65), Expect = 0.61
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 53 STTTEDELCELFSQYGIVKQVKIVV-DRAGISKGYGFITFDSEEEA 97
T TE++L ELF++ G KI + + G I F++ EA
Sbjct: 12 PTFTEEDLRELFAEKGAPPPSKIKIFPKKSERSSSGLIEFETVAEA 57
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B shows high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 28.6 bits (64), Expect = 0.68
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSD 105
VF+ G+ T E ++ E F V+ V + G + G + F + ++AK K
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGLD-VEDVIFLKRHNGRNNGNAIVKFATFQDAKEALKRHR 60
Query: 106 NIM 108
+M
Sbjct: 61 ELM 63
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for
growth. Srp1p is closely related to the SR protein
family found in metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. Some family members also contain another RRM
domain.
Length = 78
Score = 28.6 bits (64), Expect = 0.71
Identities = 13/54 (24%), Positives = 27/54 (50%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++V G + T +L F +YG + + I R S+ + F+ ++S +A+
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAED 55
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM2 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 28.3 bits (63), Expect = 0.76
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD-RAGISKGYGFITFDSEEEA 97
++V G T + TE+ L E F Q ++ + + D +G Y F+ F + A
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSA 53
>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 = 0.78
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 60 LCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
L E FS +G V++ ++VD G G G + F + A++
Sbjct: 16 LEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARK 55
>gnl|CDD|176509 cd08566, GDPD_AtGDE_like, Glycerophosphodiester phosphodiesterase
domain of Agrobacterium tumefaciens and similar
proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in Agrobacterium tumefaciens
glycerophosphodiester phosphodiesterase (AtGDE, EC
3.1.4.46) and its uncharacterized eukaryotic homolgoues.
Members in this family shows high sequence similarity to
Escherichia coli GP-GDE, which catalyzes the degradation
of glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols. AtGDE exists as a hexamer that is a trimer of
dimers, which is unique among current known GDPD family
members. However, it remains unclear if the hexamer
plays a physiological role in AtGDE enzymatic function.
Length = 240
Score = 30.0 bits (68), Expect = 0.89
Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 11/78 (14%)
Query: 67 YGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMF----------KEKRLNI 116
+ +V +V + G SEE+AK L+ + +M E+
Sbjct: 109 DADLDEVIALVKKHGAL-DQVIFKSYSEEQAKELRALAPEVMLMPIVRDAEDLDEEEARA 167
Query: 117 APAIKKQGFTGTYDSLPT 134
A+ F T+D L
Sbjct: 168 IDALNLLAFEITFDDLDL 185
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 27.8 bits (62), Expect = 1.0
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 13/68 (19%)
Query: 39 GTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF----DSE 94
GT+V VF + + + D+L ++F YG +K+++ ++ + + FI F +E
Sbjct: 2 GTLV---VF--NLDPSVSNDDLHQIFGAYGEIKEIRETPNK----RHHKFIEFYDVRSAE 52
Query: 95 EEAKRLQK 102
K L +
Sbjct: 53 AALKALNR 60
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46),
belonging to the Aly/REF family of RNA binding proteins
that have been implicated in coupling transcription
with pre-mRNA splicing and nucleo-cytoplasmic mRNA
transport. SKAR is widely expressed and localizes to
the nucleus. It may be a critical player in the
function of S6K1 in cell and organism growth control by
binding the activated, hyperphosphorylated form of S6K1
but not S6K2. Furthermore, SKAR functions as a protein
partner of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. SKAR contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain).
Length = 69
Score = 28.0 bits (63), Expect = 1.1
Identities = 15/53 (28%), Positives = 32/53 (60%), Gaps = 6/53 (11%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
R+ V + + TED++ ELFS G +K+ ++V R G+++ + + +++A
Sbjct: 2 RLVVSNLHPSVTEDDIVELFSAIGALKRARLV--RPGVAE----VVYVRKDDA 48
>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 = 28.0 bits (63), Expect = 1.1
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+EDEL ++FS+YG V V VV KG + F S++ A
Sbjct: 17 SEDELRKIFSKYGDVSDV--VVSSK--KKGSAIVEFASKKAA 54
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 28.1 bits (63), Expect = 1.1
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 55 TTEDELCELFSQYGIVKQ-VKIVVDRAGISKGYGFITFDSEEEAKR 99
T+ E+ F+ I +Q + I+ D+ G + G ++ F SEE+A R
Sbjct: 11 VTKGEVLAFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMR 56
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed
RNA-binding motif, single-stranded-interacting protein
4, an RNA-binding protein that is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. For instance, DND1
binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and
cell cycle regulator and tumor suppressor, LATS2 (large
tumor suppressor, homolog 2 of Drosophila). It helps
maintain their protein expression through blocking the
inhibitory function of microRNAs (miRNA) from these
transcripts. DND1 may also impose another level of
translational regulation to modulate expression of
critical factors in embryonic stem (ES) cells. DND1
interacts specifically with apolipoprotein B editing
complex 3 (APOBEC3), a multi-functional protein
inhibiting retroviral replication. The DND1-APOBEC3
interaction may play a role in maintaining viability of
germ cells and for preventing germ cell tumor
development. DND1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 78
Score = 27.8 bits (62), Expect = 1.2
Identities = 13/52 (25%), Positives = 27/52 (51%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
VF+G I ED L LF G + + ++++ +G+++G+ + + A
Sbjct: 4 VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGA 55
>gnl|CDD|241173 cd12729, RRM1_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM1 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical. Both of them
have been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 79
Score = 27.9 bits (62), Expect = 1.2
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 46 VFVGGITSTTTEDELCELFSQYGI---VKQVKIVVDRAGISKGYGFITFDSEEEAK-RLQ 101
V V G+ + + DE+ FS I + + R G G F+ +SEE+ K L+
Sbjct: 4 VKVRGLPWSCSVDEVQRFFSDCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALK 63
Query: 102 KDSDNI 107
KD + +
Sbjct: 64 KDRETM 69
>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 = 27.6 bits (61), Expect = 1.4
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
++FV + T L + F++ G V I ++ G SKG G + F+S E A+R
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVRFESPEVAER 54
>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM2 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein
2 (RBMS2), or suppressor of CDC2 with RNA-binding motif
3 (SCR3). MSSP-2 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence T(C/A)TT, and stimulates DNA
replication in the system using SV40 DNA. MSSP-2 is
identical with Scr3, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-2 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-2 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 86
Score = 28.1 bits (62), Expect = 1.4
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+++ + + E EL + +G V +I+ D +G S+G GF +S E+ +
Sbjct: 3 LYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCE 55
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase,
or COMPASS component SET1, or lysine
N-methyltransferase 2, or Set1 complex component, is
encoded by SET1 from the fission yeast S. pombe. It is
essential for the H3 lysine-4 methylation. in vivo, and
plays an important role in telomere maintenance and DNA
repair in an ATM kinase Rad3-dependent pathway. spSet1p
is the homology counterpart of Saccharomyces cerevisiae
Set1p (scSet1p). However, it is more closely related to
Set1 found in mammalian. Moreover, unlike scSet1p,
spSet1p is not required for heterochromatin assembly in
fission yeast. spSet1p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a conserved SET domain that may play a role in DNA
repair and telomere function. .
Length = 86
Score = 28.1 bits (63), Expect = 1.4
Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFD 92
+ + G++ TT ++ F +G +++ ++ +D G S G +TF
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFR 48
>gnl|CDD|152203 pfam11767, SET_assoc, Histone lysine methyltransferase SET
associated. SET domains are protein lysine
methyltransferase enzymes. SET domains appear to be
protein-protein interaction domains. A subset of SET
domains have been called PR domains. The SET domain
consists of two regions known as N-SET and SET-C. SET-C
forms an unusual and conserved knot-like structure of
probably functional importance. Additionally to SET-N
and SET-C, an insert region (SET-I) and flanking regions
of high structural variability form part of the overall
structure. This domain is found in fungi associated with
SET and N-SET domains.
Length = 66
Score = 27.2 bits (61), Expect = 1.5
Identities = 10/43 (23%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 74 KIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNI 116
+++ D+ G +I F+ +EA+R + D +F R+ +
Sbjct: 28 RVLDDKTGF-----YIVFNDSKEAERCFRAEDGTLFFNYRMQM 65
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its
median region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated
in protein shuttling and protein-protein interactions.
.
Length = 77
Score = 27.7 bits (61), Expect = 1.7
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
+V+VG + + + EL FS YG ++ V I + G+ F+ F+ +A+
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP----GFAFVEFEDPRDAE 50
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains).
The RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 27.2 bits (61), Expect = 1.8
Identities = 11/55 (20%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIV---VDRAGISKGYGFITFDSEEEA 97
V V ++ TE+++ LF G ++++++ D A + F+ ++ E+
Sbjct: 2 VQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDV 56
>gnl|CDD|223098 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 29.2 bits (66), Expect = 2.2
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 79 RAGISKGYGFITFDSEEEAKRLQK 102
+ G I DSEEE +RL
Sbjct: 112 AFALELGIKLINVDSEEELERLSA 135
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 27.3 bits (60), Expect = 2.3
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDR-AGISKGYGFITF 91
+ VF + + +L E FS G V+ V+++ DR + SKG ++ F
Sbjct: 2 RTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEF 50
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3
(PTBPH3). This subfamily corresponds to the RRM4 of
PTBPH3. Although its biological roles remain unclear,
PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. Like PTB, PTBPH3 contains four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 79
Score = 27.1 bits (60), Expect = 2.3
Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
K + V + S TE+++ +++G++ VK+ K + F +EE+A
Sbjct: 8 KMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESN---GKKQALVEFATEEQA 58
>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1
small nuclear ribonucleoprotein A (U1 snRNP A or U1-A
or U1A). This subgroup corresponds to the RRM2 of U1A
(also termed U1 snRNP A or U1-A), an RNA-binding
protein associated with the U1 snRNP, a small
RNA-protein complex involved in pre-mRNA splicing. U1A
binds with high affinity and specificity to stem-loop
II (SLII) of U1 snRNA. It is predominantly a nuclear
protein that shuttles between the nucleus and the
cytoplasm independently of interactions with U1 snRNA.
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins, including polypyrimidine tract binding
protein (PTB), polypyrimidine-tract binding
protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also
binds to a flavivirus NS5 protein and plays an
important role in virus replication. It contains two
RNA recognition motifs (RRMs); the N-terminal RRM
(RRM1) binds tightly and specifically to the U1 snRNA
SLII and its own 3'-UTR, while in contrast, the
C-terminal RRM (RRM2) does not appear to associate with
any RNA and it may be free for binding other proteins.
U1A also contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 80
Score = 27.4 bits (60), Expect = 2.3
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEA 97
+F+ + T E L LF+Q+ K+V++V R I+ F+ FD+E +A
Sbjct: 8 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIA----FVEFDNEVQA 55
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 29.0 bits (64), Expect = 2.4
Identities = 25/112 (22%), Positives = 50/112 (44%), Gaps = 12/112 (10%)
Query: 45 RVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITF--DSEEEAKRLQK 102
R+ VGG+ + D+L ++FS G V V+ V + + + +I F S +L
Sbjct: 12 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG---RSFAYIDFSPSSTNSLTKLFS 68
Query: 103 DSDNIMFKEKRLNIAPA-------IKKQGFTGTYDSLPTVTSPVPPVPTSNM 147
+ ++K RL + A +K++ + S T+ +P P +++
Sbjct: 69 TYNGCVWKGGRLRLEKAKEHYLARLKREWEAASSTSDNTIKAPSDSPPATHL 120
>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 = 27.2 bits (61), Expect = 2.5
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 47 FVGGITSTTTEDELCELFS 65
FV + TTE+EL +LFS
Sbjct: 6 FVANLGPNTTEEELRQLFS 24
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup
corresponds to the RRM1 of RBM5, also termed protein
G15, or putative tumor suppressor LUCA15, or renal
carcinoma antigen NY-REN-9, a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor. RBM5 shows high sequence
similarity to RNA-binding protein 6 (RBM6 or NY-LU-12
or g16 or DEF-3). Both, RBM5 and RBM6, specifically
bind poly(G) RNA. They contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), two C2H2-type zinc
fingers, a nuclear localization signal, and a
G-patch/D111 domain. .
Length = 87
Score = 27.3 bits (60), Expect = 2.5
Identities = 13/58 (22%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVK--QVKIVVDRAGISKGYGFITFDSEEEAKR 99
K + + G+ TE+++ EL + + V+++ + G+S+G+ F+ F ++A
Sbjct: 6 KTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDATS 63
>gnl|CDD|240888 cd12442, RRM_RBM48, RNA recognition motif in RNA-binding protein 48
(RBM48) and similar proteins. This subfamily
corresponds to the RRM of RBM48, a putative RNA-binding
protein of unknown function. It contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 100
Score = 27.3 bits (61), Expect = 3.0
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVD--RAGISKGYGFITFDSEEEAKRLQKD 103
+ V G+ + E EL ELF+ YG +++ +++ + ++ Y I F++ + A+ ++
Sbjct: 13 LLVQGVPALGVEKELLELFALYGTIEEYRLLDEYPCEEFTEVY-LIKFETIQSARFAKRK 71
Query: 104 SDNIMFKEKRLNI--AP 118
D F L++ AP
Sbjct: 72 LDERSFFGGLLHVCYAP 88
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 26.5 bits (59), Expect = 3.2
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 44 KRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRA-GISKGYGFITFDSEEEA 97
+R+FV ++ + T+++L LF ++ + D G SKG+ ++T+ + A
Sbjct: 1 QRLFVV-VSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASA 54
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein
19 (RBM19) and similar proteins. This subfamily
corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 72
Score = 26.6 bits (59), Expect = 3.6
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 50 GITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR-LQKDSDNI 107
G E + E FS V ++IV + G G+ F+ SEE+ K+ L+++ D +
Sbjct: 7 GAPFNVKEKHIREFFSPLKPVA-IRIVKNDHGRKTGFAFVDLKSEEDLKKALKRNKDYM 64
>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and
CTD-associated factor 4 (SCAF4) and similar proteins.
The CD corresponds to the RRM of SCAF4 (also termed
splicing factor, arginine/serine-rich 15 or SFR15, or
CTD-binding SR-like protein RA4) that belongs to a new
class of SCAFs (SR-like CTD-associated factors).
Although its biological function remains unclear, SCAF4
shows high sequence similarity to SCAF8 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) and may play a direct role
in coupling with both, transcription and pre-mRNA
processing, processes. SCAF4 and SCAF8 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and serine/arginine-rich motifs.
Length = 81
Score = 26.9 bits (59), Expect = 3.6
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 7/85 (8%)
Query: 40 TVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKR 99
+V ++VG + TT+ ++ L ++G ++ + ++ R G +I ++A R
Sbjct: 1 SVCSTTLWVGQLDKRTTQQDVTSLLEEFGPIESINMIPPR-----GCAYIVMVHRQDAYR 55
Query: 100 -LQKDSD-NIMFKEKRLNIAPAIKK 122
LQK S N+ +K + IA A+ K
Sbjct: 56 ALQKLSRGNVKVNQKSIKIAWALNK 80
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 28.2 bits (63), Expect = 4.2
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 4/64 (6%)
Query: 56 TEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLN 115
D L LF YG V++VK + ++ K I +A+ + + K L
Sbjct: 289 NCDRLFNLFCVYGNVERVKFMKNK----KETALIEMADPYQAQLALTHLNGVKLFGKPLR 344
Query: 116 IAPA 119
+ P+
Sbjct: 345 VCPS 348
>gnl|CDD|143430 cd07112, ALDH_GABALDH-PuuC, Escherichia coli NADP+-dependent
gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
PuuC-like. NADP+-dependent,
gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
(GABALDH) PuuC of Escherichia coli which catalyzes the
conversion of putrescine to 4-aminobutanoate and other
similar sequences are present in this CD.
Length = 462
Score = 28.3 bits (64), Expect = 4.2
Identities = 12/19 (63%), Positives = 12/19 (63%)
Query: 87 GFITFDSEEEAKRLQKDSD 105
ITFDSEEEA L DS
Sbjct: 375 SVITFDSEEEAVALANDSV 393
>gnl|CDD|219779 pfam08285, DPM3, Dolichol-phosphate mannosyltransferase subunit 3
(DPM3). This family corresponds to subunit 3 of
dolichol-phosphate mannosyltransferase, an enzyme which
generates mannosyl donors for
glycosylphosphatidylinositols, N-glycan and protein O-
and C-mannosylation. DPM3 is an integral membrane
protein and plays a role in stabilising the
dolichol-phosphate mannosyl transferase complex.
Length = 91
Score = 26.5 bits (59), Expect = 4.5
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 85 GYGFITF-DSEEEAKRLQKD 103
GYG +TF D E AK LQK+
Sbjct: 57 GYGLLTFNDCPEAAKELQKE 76
>gnl|CDD|214400 MTH00020, ND5, NADH dehydrogenase subunit 5; Reviewed.
Length = 610
Score = 28.1 bits (63), Expect = 4.6
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 174 TSPPTVPTQVKILLPPGVLLCGICLIFLITLALAPTIKRPS 214
T PP VP +K LLP + L GI L+ ++ + T + P
Sbjct: 480 TLPPIVPLSIK-LLPVFLSLGGIGLVIILYFYSSKTFRVPF 519
>gnl|CDD|233961 TIGR02644, Y_phosphoryl, pyrimidine-nucleoside phosphorylase. In
general, members of this protein family are designated
pyrimidine-nucleoside phosphorylase, enzyme family EC
2.4.2.2, as in Bacillus subtilis, and more narrowly as
the enzyme family EC 2.4.2.4, thymidine phosphorylase
(alternate name: pyrimidine phosphorylase), as in
Escherichia coli. The set of proteins encompassed by
this model is designated subfamily rather than equivalog
for this reason; the protein name from this model should
be used when TIGR02643 does not score above trusted
cutoff [Purines, pyrimidines, nucleosides, and
nucleotides, Other].
Length = 405
Score = 28.0 bits (63), Expect = 5.2
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 87 GFITFDSEEEA-KRLQKDSDNIMFKEKRLNIAPAIKK----QGFTGTYDSLPTVTS 137
GF T SE E + + K I+ + K ++APA KK + TGT DS+P + S
Sbjct: 127 GFRTELSEAEFIEIVNKVGLAIIGQTK--DLAPADKKLYALRDVTGTVDSIPLIAS 180
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 28.1 bits (62), Expect = 5.3
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 8/44 (18%)
Query: 62 ELFSQYGIVKQVKIVVDRAGIS-----KGYG-FITFDSEEEAKR 99
E F QYG +K KIVV++ S G +IT+ ++E+A R
Sbjct: 139 EYFGQYGKIK--KIVVNKKTSSLNSTASHAGVYITYSTKEDAAR 180
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM3 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 86
Score = 26.4 bits (59), Expect = 5.3
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 84 KGYGFITFDSEEEAKRLQKDSDN----IMFKEKRLNIAPAIKKQG 124
GY FI F + E A++ K + +K +I A + QG
Sbjct: 43 VGYAFINFVNPEYAEKFYKAFNGKKWKNFKSKKVCDITYA-RIQG 86
>gnl|CDD|238768 cd01491, Ube1_repeat1, Ubiquitin activating enzyme (E1), repeat 1.
E1, a highly conserved small protein present universally
in eukaryotic cells, is part of cascade to attach
ubiquitin (Ub) covalently to substrate proteins. This
cascade consists of activating (E1), conjugating (E2),
and/or ligating (E3) enzymes and then targets them for
degradation by the 26S proteasome. E1 activates
ubiquitin by C-terminal adenylation, and subsequently
forms a highly reactive thioester bond between its
catalytic cysteine and ubiquitin's C-terminus. E1 also
associates with E2 and promotes ubiquitin transfer to
the E2's catalytic cysteine. Ubiquitin-E1 is a
single-chain protein with a weakly conserved two-fold
repeat. This CD represents the first repeat of Ub-E1.
Length = 286
Score = 27.6 bits (62), Expect = 6.2
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 12/48 (25%)
Query: 32 NNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQY---GIVKQVKIV 76
N P+ V F G TS+ FS+Y GIV QVK+
Sbjct: 207 NGCEPRKIKVKGPYTFSIGDTSS---------FSEYIRGGIVTQVKLS 245
>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein
Vip1 and similar proteins. This subfamily corresponds
to Vip1, an RNA-binding protein encoded by gene vip1
from fission yeast Schizosaccharomyces pombe. Its
biological role remains unclear. Vip1 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 68
Score = 25.6 bits (56), Expect = 6.7
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 46 VFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAK 98
V+V I+ TTE ++ + FS G K + + G S+ ITF+ AK
Sbjct: 1 VYVSNISPKTTEKQISDFFSFCG--KISNLDLTNDGESQT-ATITFEKPSAAK 50
>gnl|CDD|237941 PRK15315, PRK15315, outer membrane protein RatA; Provisional.
Length = 1865
Score = 27.7 bits (61), Expect = 6.8
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 10/55 (18%)
Query: 118 PAIKKQGFTGTYDSLPTVTSPVPPV---------PTSNMYYHNGLPYTYHNGMAF 163
+K Q D+ PT TS +P V +NMY H +T NG F
Sbjct: 1401 IGLKNQLTANLNDT-PTATSSLPVVFTVLTSPDSDKANMYGHMPETFTASNGAEF 1454
>gnl|CDD|223971 COG1041, COG1041, Predicted DNA modification methylase [DNA
replication, recombination, and repair].
Length = 347
Score = 27.3 bits (61), Expect = 6.8
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 4/57 (7%)
Query: 69 IVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKRLNIAPAIKKQGF 125
I + +V+ A Y F +R ++D D EK I AI +G
Sbjct: 79 INEFTVLVLGEAVDWSEYKFEEEKGRVRIRRKEQDVD--KGLEKA--IGGAIPSEGL 131
>gnl|CDD|225343 COG2723, BglB,
Beta-glucosidase/6-phospho-beta-glucosidase/beta-
galactosidase [Carbohydrate transport and metabolism].
Length = 460
Score = 27.6 bits (62), Expect = 6.9
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 81 GISKGYGFITFDSEEEAKRLQKDS 104
G K YG + D + + +R K S
Sbjct: 419 GYKKRYGLVYVDYDTDLERTPKKS 442
>gnl|CDD|150740 pfam10100, DUF2338, Uncharacterized protein conserved in bacteria
(DUF2338). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 429
Score = 27.4 bits (61), Expect = 6.9
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 38 YGTVVPKRVFVGGITSTTTE-DELCELFSQYGI 69
T V K++++G S + E LC +F+Q GI
Sbjct: 162 LTTAVKKKLYLGSTHSGSAELSRLCAVFAQLGI 194
>gnl|CDD|235568 PRK05701, fliR, flagellar biosynthesis protein FliR; Reviewed.
Length = 242
Score = 27.4 bits (62), Expect = 7.1
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 11/42 (26%)
Query: 178 TVPTQVKILLPPGVLLCGICLIFLITLALAPTIKRPSLKPLN 219
++P +VK+ L +T A+AP + P + +
Sbjct: 29 SIPARVKLGL-----------ALALTFAVAPLLPVPDVPLFS 59
>gnl|CDD|183606 PRK12578, PRK12578, acetyl-CoA acetyltransferase; Provisional.
Length = 385
Score = 27.5 bits (61), Expect = 7.1
Identities = 30/107 (28%), Positives = 43/107 (40%), Gaps = 12/107 (11%)
Query: 29 AAVNNNAPKYGTVVPKRVFVGGITSTTTEDELCELFSQYGIVKQVKIVVDRAGISKGYGF 88
A V+ A KYG + PK F +T E+ L + I ++D IS G
Sbjct: 164 ALVSVKAHKYGAMNPKAHFQKPVT---VEEVLKSRAISWPIK-----LLDSCPISDGSAT 215
Query: 89 ITFDSEEEAKRLQKDS----DNIMFKEKRLNIAPAIKKQGFTGTYDS 131
F SEE+ K L+ DS I + +A + GF T +
Sbjct: 216 AIFASEEKVKELKIDSPVWITGIGYANDYAYVARRGEWVGFKATQLA 262
>gnl|CDD|233698 TIGR02049, gshA_ferroox, glutamate--cysteine ligase, T.
ferrooxidans family. This family consists of a rare
family of glutamate--cysteine ligases, demonstrated
first in Thiobacillus ferrooxidans and present in a few
other Proteobacteria. It is the first of two enzymes for
glutathione biosynthesis. It is also called
gamma-glutamylcysteine synthetase [Biosynthesis of
cofactors, prosthetic groups, and carriers, Glutathione
and analogs].
Length = 403
Score = 27.5 bits (61), Expect = 7.3
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 64 FSQYGIVKQVKIVVDRAGISKGYGFITFDSEEEAKRLQKDSDNIMFKEKR-LNIAPAIKK 122
+ +YGI Q ++V + G G +T S EE L + N M K K L ++ I +
Sbjct: 249 YEEYGIHTQPYVIVKADAGTYGMGIMTATSGEEVLGLNRKERNKMAKVKEGLEVSEVIIQ 308
Query: 123 QGFTGTYDSL-PTVTSPV 139
+G T++ V PV
Sbjct: 309 EGVY-TFEMFNEAVAEPV 325
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
0.315 0.132 0.386
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,240,870
Number of extensions: 1153019
Number of successful extensions: 1846
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1654
Number of HSP's successfully gapped: 385
Length of query: 242
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 148
Effective length of database: 6,768,326
Effective search space: 1001712248
Effective search space used: 1001712248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.2 bits)