RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8001
(172 letters)
>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 = 134 bits (339), Expect = 7e-42
Identities = 45/76 (59%), Positives = 60/76 (78%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
LYVGNLTWWTT+ D+++AI+SIGV D +++KFFEN +NGQSKGF + LGSE S +M+
Sbjct: 2 LYVGNLTWWTTDQDLTEAIQSIGVNDLLEIKFFENRANGQSKGFALIVLGSESSSRKLMD 61
Query: 133 RLPTLELHGRKPMVAY 148
+LP ELHG+ P+V
Sbjct: 62 KLPKKELHGQNPVVTP 77
>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 = 108 bits (271), Expect = 2e-31
Identities = 37/76 (48%), Positives = 50/76 (65%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
LYVGNLTWWTT+ D+ A+ GV D +KFFE+ +NG+SKGF V SE + + V E
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 133 RLPTLELHGRKPMVAY 148
+L E +G+K +V Y
Sbjct: 61 KLEGREFNGKKCVVTY 76
>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 = 101 bits (253), Expect = 1e-28
Identities = 42/87 (48%), Positives = 57/87 (65%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
+YVGN +WWTT+ + IRS+GV D +++KF EN +NGQSKG+ V + SE S+ ++E
Sbjct: 4 VYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 63
Query: 133 RLPTLELHGRKPMVAYPTRNVLYQFEA 159
LP L+G K V TR L QFEA
Sbjct: 64 LLPGKVLNGEKVDVRPATRQNLSQFEA 90
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 62.6 bits (153), Expect = 8e-14
Identities = 25/72 (34%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
L+VGNL TTE ++ + G V+ + G+SKGF V SEE +
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFG--KVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58
Query: 132 ERLPTLELHGRK 143
E L EL GR
Sbjct: 59 EALNGKELDGRP 70
>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 = 50.7 bits (122), Expect = 2e-09
Identities = 25/71 (35%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+VGNL TTE D+ D G ++ + G+SKGF V EE +E
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFG--PIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALE 57
Query: 133 RLPTLELHGRK 143
L EL GR+
Sbjct: 58 ALNGKELGGRE 68
>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 = 50.0 bits (120), Expect = 5e-09
Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+VGNL TTE D+ + G + V+ + +G+SKGF V S E +E
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFG--EIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALE 57
Query: 133 RLPTLELHGRK 143
L EL GRK
Sbjct: 58 ALNGKELDGRK 68
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 53.0 bits (126), Expect = 8e-09
Identities = 28/119 (23%), Positives = 46/119 (38%), Gaps = 2/119 (1%)
Query: 25 STEHDDIDLYDDVTLQPFPEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTE 84
S ++ + + +T S Q + + L+VGNL + TE
Sbjct: 70 SERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTE 129
Query: 85 ADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRK 143
D+ + + G + + + G+S+GF V SEES +E L EL GR
Sbjct: 130 EDLRELFKKFGPVKRVRLVR--DRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRP 186
>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 = 47.6 bits (114), Expect = 5e-08
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
NLYVGNL + TE D+ D G + + + G+S+GF V + + E + +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFG--EVTSARVITDRETGRSRGFGFVEMETAEEANAAI 58
Query: 132 ERLPTLELHGRK 143
E+L + GR
Sbjct: 59 EKLNGTDFGGRT 70
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 46.4 bits (111), Expect = 1e-07
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
LYV NL TE D+ + G + + + + + +GF V S E ++
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVR----NKDRPRGFAFVEFASPEDAEAALK 56
Query: 133 RLPTLELHGRK 143
+L L L GR
Sbjct: 57 KLNGLVLDGRT 67
>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 = 43.9 bits (104), Expect = 1e-06
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
L+VGNL+W + + G + + + G+S+GF V S E +
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFG--TVVGARVITDRETGRSRGFGYVDFESPEDAKKAI 58
Query: 132 ERLPTLELHGR 142
E + EL GR
Sbjct: 59 EAMDGKELDGR 69
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Although the
cellular function of RBM23 remains unclear, it shows
high sequence homology to RBM39 and contains two RRMs.
It may possibly function as a pre-mRNA splicing factor.
.
Length = 73
Score = 42.2 bits (100), Expect = 4e-06
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
LYVGNL + TE D+ G +F+ ++ + G+SKG+ + E +E
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQ--RDPETGRSKGYGFIQFADAEDAKKALE 58
Query: 133 RLPTLELHGRKPM 145
+L EL GR P+
Sbjct: 59 QLNGFELAGR-PI 70
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 43.9 bits (103), Expect = 4e-06
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L++G L+W T +A + DA G D +D K + G+S+GF V E + + +
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFG--DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94
Query: 133 RLPTLELHGRK 143
+ EL+GR
Sbjct: 95 EMDGKELNGRH 105
>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 = 39.7 bits (93), Expect = 4e-05
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
+L V L W TTE D+ D + G + VK ++ GQSKGF V E V+
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVK--KDPKTGQSKGFGFVRFADYEDQVKVL 58
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. hnRNP M functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 37.6 bits (88), Expect = 3e-04
Identities = 24/71 (33%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++V NL + T D+ D R G DVK + G+SKGF TV S E +E
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND---GRSKGFGTVLFESPEDAQRAIE 57
Query: 133 RLPTLELHGRK 143
+L GR+
Sbjct: 58 MFNGYDLEGRE 68
>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 = 37.3 bits (87), Expect = 4e-04
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
L+VGNL+W + D+ + + G + +DV+ ++ +G+SKGF V +EE
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECG--EVVDVRIAQDD-DGRSKGFGHVEFATEEG 52
>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 = 36.6 bits (85), Expect = 5e-04
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 13/64 (20%)
Query: 74 YVGNLTWWTTEADMSD-----AIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMS 128
Y+GNL W TE D+ + I S V+ + G+ KGF V EES+
Sbjct: 3 YIGNLAWDITEDDVREFFKGCEITS--------VRLATDKETGEFKGFGHVDFADEESLD 54
Query: 129 LVME 132
++
Sbjct: 55 AALK 58
>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 = 36.5 bits (84), Expect = 6e-04
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
+++G L+W TT+ D+ D G + +D + G+S+GF V ES+ VM+
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFG--EVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 58
Query: 133 R 133
+
Sbjct: 59 Q 59
>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 = 35.5 bits (82), Expect = 0.001
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 74 YVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMER 133
YVGN+ +TT+AD+ +P F + + + +GF V L + E ++ + +
Sbjct: 4 YVGNIPPYTTQADL--------IPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQ 55
Query: 134 LPTLELHGR 142
L +HGR
Sbjct: 56 LQGFPVHGR 64
>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 = 34.6 bits (80), Expect = 0.003
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
NL+V L+ T AD+ G + K NA + ++ F VT+ S E + +
Sbjct: 1 NLWVSGLSSTTKAADLKQLFSKYG--KVVGAKIVTNARSPGARCFGFVTMASVEEAAKCI 58
Query: 132 ERLPTLELHGR 142
+ L ELHGR
Sbjct: 59 QHLHRTELHGR 69
>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 = 34.5 bits (79), Expect = 0.003
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG L+W TT+ D+ + G + +D + G+S+GF V S+ V++
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFG--EVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD 58
>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 = 34.8 bits (81), Expect = 0.003
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS-EESMSLVM 131
L + L TTE D+ A+ +I DV+ + G S+GF V S E++ +
Sbjct: 5 LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64
Query: 132 E--RLPTLELHGRKPMVAY 148
L + GR V+Y
Sbjct: 65 ALNNLDPFVIDGRVVRVSY 83
>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 = 34.2 bits (78), Expect = 0.004
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
+++G L+W T++ D+++ + G + +D + G+S+GF V S+ V+E
Sbjct: 2 MFIGGLSWDTSKKDLTEYLSRFG--EVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLE 59
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 34.6 bits (79), Expect = 0.004
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 2/86 (2%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
++A +C L V L+ +TTE D+ + G DV + + +S+GF V
Sbjct: 2 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYG--PIADVSIVYDQQSRRSRGFAFVYFE 59
Query: 123 SEESMSLVMERLPTLELHGRKPMVAY 148
+ + ER +EL GR+ V +
Sbjct: 60 NVDDAKEAKERANGMELDGRRIRVDF 85
>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 = 32.9 bits (75), Expect = 0.013
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
+++G L W TT+ + + G + D +++ G+S+GF +T +S++ VM+
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFG--EVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMK 58
Query: 133 R 133
+
Sbjct: 59 K 59
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 33.1 bits (76), Expect = 0.013
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 1/72 (1%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L++G+L + E + A S+G + VK N G G+C V E + +
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGET-VLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60
Query: 133 RLPTLELHGRKP 144
+L + G P
Sbjct: 61 KLNGKPIPGSNP 72
>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 = 32.2 bits (74), Expect = 0.022
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 5/78 (6%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
++VG L + TT+ + G + + + G+S+G+ VT +ES
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFG--EIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58
Query: 131 MERL-PTLELHGRKPMVA 147
+ P ++ GRK V
Sbjct: 59 CKDPNPIID--GRKANVN 74
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 32.3 bits (74), Expect = 0.023
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
L+VGNL TE + + G P VK ++ NG+ K F VT E S+
Sbjct: 2 RTLFVGNLDARVTEEILYELFLQAG-P-LEGVKIPKD-PNGKPKSFAFVTFKHEVSVPYA 58
Query: 131 MERLPTLELHGRK 143
++ L + L GR+
Sbjct: 59 IQLLNGIRLFGRE 71
>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 = 34.1 bits (78), Expect = 0.023
Identities = 26/87 (29%), Positives = 36/87 (41%), Gaps = 2/87 (2%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
H + LYVGNL + TE ++ G D DV+ + G+SKGF +
Sbjct: 178 HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFG--DIEDVQLHRDPETGRSKGFGFIQF 235
Query: 122 GSEESMSLVMERLPTLELHGRKPMVAY 148
E +E + EL GR V Y
Sbjct: 236 HDAEEAKEALEVMNGFELAGRPIKVGY 262
>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 = 32.5 bits (74), Expect = 0.024
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+VG L+W TT+ + G + +D ++ + +S+GF V + V+
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYG--EVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLA 59
Query: 133 RLPTLELHGR 142
P L GR
Sbjct: 60 GGPHT-LDGR 68
>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 = 32.0 bits (73), Expect = 0.027
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 14/66 (21%)
Query: 73 LYVGNLTWWTTEADMSD------AIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
++VG L+ TTE + + I I +P + +N + +GFC +T SEE
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELP-------MDKKTN-KRRGFCFITFDSEEP 53
Query: 127 MSLVME 132
+ ++E
Sbjct: 54 VKKILE 59
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 31.9 bits (73), Expect = 0.030
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+VGNL + TT D+ ++ G P V+ + G+SKG V + E+M+ ++
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAP--PSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK 60
Query: 133 RLPTLELHGRK 143
T L GRK
Sbjct: 61 LHHT-LLKGRK 70
>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 = 31.9 bits (72), Expect = 0.032
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 75 VGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERL 134
V L+ +TTE D+ + G ++V + + G+S+GF V + ME
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVY--DQRTGRSRGFAFVYFERIDDSKEAMEHA 61
Query: 135 PTLELHGRKPMVAY 148
+EL GR+ V Y
Sbjct: 62 NGMELDGRRIRVDY 75
>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 = 31.8 bits (73), Expect = 0.032
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L V L+ +TTE D+ + G V+ + G+S+GF V S E E
Sbjct: 2 LGVFGLSLYTTERDLREVFSRYG--PIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKE 59
Query: 133 RLPTLELHGRKPMVAY 148
RL +E+ GR+ V Y
Sbjct: 60 RLNGMEIDGRRIRVDY 75
>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 = 31.8 bits (73), Expect = 0.033
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 8/73 (10%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L++G+L W EA + A G VK N G+S G+ V + E E
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEV--TSVKIIRNKQTGKSAGYGFVEFATHE----AAE 55
Query: 133 RLPTLELHGRKPM 145
+ L+ KP+
Sbjct: 56 Q--ALQSLNGKPI 66
>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 = 31.9 bits (72), Expect = 0.035
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG L+W T++ D+ D G + D + + G+S+GF + S+ V+E
Sbjct: 2 MFVGGLSWDTSKKDLKDYFTKFG--EVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLE 59
Query: 133 R 133
+
Sbjct: 60 Q 60
>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 = 31.6 bits (72), Expect = 0.040
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG L TE + + G +D + ++ G+S+GF VT SE ++ V
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFG--KVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFS 59
Query: 133 RLPTLELHGRK 143
LEL G++
Sbjct: 60 A-GMLELGGKQ 69
>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 = 31.8 bits (73), Expect = 0.040
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 61 HHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVT 120
H Q S++ +Y+G L + TE D+ G +D+ + G+SKGF +
Sbjct: 2 WHDQYKDSAY--IYIGGLPYELTEGDILCVFSQYGEI--VDINLVRDKKTGKSKGFAFLA 57
Query: 121 LGSEESMSLVMERLPTLELHGR 142
+ S L ++ L ++L GR
Sbjct: 58 YEDQRSTILAVDNLNGIKLLGR 79
>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 = 31.1 bits (71), Expect = 0.048
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 11/57 (19%)
Query: 98 DFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVL 154
++ D+K + G+SKGF VT + S E+ L+G + YP N L
Sbjct: 27 EYCDLK--RDPYTGKSKGFAYVTYSNPASAIYAKEK-----LNGFE----YPPGNRL 72
>gnl|CDD|179304 PRK01574, lspA, signal peptidase II; Provisional.
Length = 163
Score = 32.7 bits (75), Expect = 0.048
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 92 RSIGVPDFIDVKFF 105
R GV DF+DVKFF
Sbjct: 114 RPEGVVDFLDVKFF 127
>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 = 31.5 bits (72), Expect = 0.051
Identities = 23/79 (29%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFI--DVKFFENASNGQSKGFCTVTLGSEESMSL 129
NL++GNL E + D + GV I K + G SKGF ++ S E+
Sbjct: 3 NLFIGNLDPEVDEKLLYDTFSAFGV---ILQTPKIMRDPDTGNSKGFAFISYDSFEASDA 59
Query: 130 VMERLPTLELHGRKPMVAY 148
+E + L R V+Y
Sbjct: 60 AIEAMNGQYLCNRPITVSY 78
>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 = 31.4 bits (71), Expect = 0.052
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+VGNL TE + + G I VK ++ +G+ K F V E S+ M
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAG--PVIKVKIPKD-KDGKPKQFAFVNFKHEVSVPYAMN 60
Query: 133 RLPTLELHGR 142
L ++L+GR
Sbjct: 61 LLNGIKLYGR 70
>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 = 30.7 bits (70), Expect = 0.064
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 9/75 (12%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESM--SLV 130
++V NL + E ++ G + DV+ +N G+SKG+ V +EES+ +L
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCG--EITDVRLVKN-YKGKSKGYAYVEFENEESVQEALK 58
Query: 131 MERLPTLELHGRKPM 145
++R + GR PM
Sbjct: 59 LDREL---IKGR-PM 69
>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 = 30.7 bits (70), Expect = 0.082
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
+YVGNL TE ++ G +V+ F++ KG+ V + E+
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGA--IEEVRVFKD------KGYAFVRFDTHEA 48
>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 = 30.7 bits (70), Expect = 0.093
Identities = 23/80 (28%), Positives = 33/80 (41%), Gaps = 2/80 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
L+V L+ TTE ++ G +V ++ G+S+GF VT S E +
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFG--RVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60
Query: 132 ERLPTLELHGRKPMVAYPTR 151
L EL GR V R
Sbjct: 61 RDLNGKELEGRVIKVEKAKR 80
>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 = 30.2 bits (69), Expect = 0.10
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L++G L+W TTE + + G + +D ++ G+S+GF VT S+ V+
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYG--EVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58
>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 = 30.4 bits (68), Expect = 0.11
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG L+ T E + + + G + I++ +N +N + +GFC +T EE + +ME
Sbjct: 2 IFVGGLSPDTPEEKIREYFGAFGEVESIELPM-DNKTN-KRRGFCFITFKEEEPVKKIME 59
Query: 133 R 133
+
Sbjct: 60 K 60
>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 = 30.3 bits (69), Expect = 0.12
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 74 YVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMER 133
+VGN+ + TE + + +G + + + G+ KG+ E+ + +
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVG--PVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN 59
Query: 134 LPTLELHGRKPMVAYP 149
L E +GR V +
Sbjct: 60 LNGYEFNGRALRVDFA 75
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 30.1 bits (68), Expect = 0.13
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+VGNL++ TTE ++ +G + + FE++ G+ KGF V E + ++
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDS--GKCKGFAFVDFEEIEFATNALK 58
>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 = 29.9 bits (68), Expect = 0.14
Identities = 20/74 (27%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDV-KFFENASNGQSKGFCTVTLGSEESM--SL 129
+YV NL + E D+ G + I + K + + GF VT S +L
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62
Query: 130 VMERLPTLELHGRK 143
+ EL GRK
Sbjct: 63 QLNG---TELGGRK 73
>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 = 30.1 bits (68), Expect = 0.16
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVK-------FFENASNGQSKGFCTVTLGSEE 125
++V NL TTE D+++ SIG+ ID K +++ G+ KG TVT
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIK-IDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPH 59
Query: 126 SMSLVMERLPTLELHGRK 143
+ S +E + G
Sbjct: 60 AASAAIEWFNNKDFMGNT 77
>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 = 29.7 bits (66), Expect = 0.17
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
NL+V L+ T AD+ + G + K NA + +K + VT+ S ++ +
Sbjct: 1 NLWVSGLSSNTKAADLKNLFGKYG--KVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCI 58
Query: 132 ERLPTLELHGRK 143
L ELHG++
Sbjct: 59 SHLHRTELHGQQ 70
>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 = 29.6 bits (67), Expect = 0.18
Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
+YVG + +++TE ++ G + +D+ F + G+ +G +T +EE
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPD--TGRFRGIAFITFKTEE 51
>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 = 29.7 bits (67), Expect = 0.18
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+VGNL TE ++ + + G + ++V+ G+ F V E++ ++
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFG--NVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILA 63
Query: 133 RLPTLELHGRK 143
P +
Sbjct: 64 NKPIYFRGDHR 74
>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 = 29.7 bits (66), Expect = 0.20
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
NL+V L+ T D+ + G + K NA + ++ + VT+ + E + +
Sbjct: 3 NLWVSGLSSTTRATDLKNLFSKYG--KVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60
Query: 132 ERLPTLELHGR 142
L ELHGR
Sbjct: 61 NHLHRTELHGR 71
>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 = 29.6 bits (66), Expect = 0.21
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESM-SLVM 131
++VG + T E + D G + I+V E+ +G+ +GF VT +++ +V+
Sbjct: 3 IFVGGIKEDTEEYHLRDYFEKYGKIETIEV--MEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 132 ERLPTLELH 140
++ T+ H
Sbjct: 61 QKYHTINGH 69
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. Moreover, hnRNP M is able to
interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. hnRNP M
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 29.3 bits (66), Expect = 0.22
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 74 YVGNLTW---WTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
++ N+ + W D+ D R V + V+ F++ G+S+G V +ES+
Sbjct: 3 FISNIPYDLKWQ---DLKDLFREK-VGEVTYVELFKDE-EGKSRGCGVVEFKDKESVQKA 57
Query: 131 MERLPTLELHGRKPMV 146
+E + EL GRK +V
Sbjct: 58 LETMNRYELKGRKLVV 73
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein 3
(RBM3) and similar proteins. This subfamily corresponds
to the RRM domain of two structurally related
heterogenous nuclear ribonucleoproteins, CIRBP (also
termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL),
both of which belong to a highly conserved cold shock
proteins family. The cold shock proteins can be induced
after exposure to a moderate cold-shock and other
cellular stresses such as UV radiation and hypoxia.
CIRBP and RBM3 may function in posttranscriptional
regulation of gene expression by binding to different
transcripts, thus allowing the cell to response rapidly
to environmental signals. However, the kinetics and
degree of cold induction are different between CIRBP and
RBM3. Tissue distribution of their expression is
different. CIRBP and RBM3 may be differentially
regulated under physiological and stress conditions and
may play distinct roles in cold responses of cells.
CIRBP, also termed glycine-rich RNA-binding protein
CIRP, is localized in the nucleus and mediates the
cold-induced suppression of cell cycle progression.
CIRBP also binds DNA and possibly serves as a chaperone
that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore, RBM3
may be essential for cell proliferation and mitosis.
Both, CIRBP and RBM3, contain an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), that is
involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 29.4 bits (66), Expect = 0.24
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L++G L++ T E + G + V ++ +S+GF VT + + M
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVV--VKDRETQRSRGFGFVTFENPDDAKDAMM 60
Query: 133 RLPTLELHGR 142
+ + GR
Sbjct: 61 AMNGKSVDGR 70
>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 = 29.4 bits (66), Expect = 0.26
Identities = 21/81 (25%), Positives = 31/81 (38%), Gaps = 23/81 (28%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFF-------ENASNGQSKGFCTVTLGSE 124
+L+VGNL ++ AI +FF ++ G SK F V S
Sbjct: 2 SLFVGNLNPNKDFDELKTAIS----------EFFSKKNLAVQDVRIGSSKKFGYVDFESA 51
Query: 125 ESMSLVMERLPTLELHGRKPM 145
E + LEL G+K +
Sbjct: 52 EDLE------KALELTGKKLL 66
>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 = 28.8 bits (65), Expect = 0.34
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 9/73 (12%)
Query: 74 YVGNLTWWTTEADMSDAIRSIGVPDFIDV---KFFENASNGQSKGFCTVTLGSEESMSLV 130
+VGN+ + TT ++ + +S G + I + KF GQ KGF + + S+
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKF-----TGQPKGFAYIEFLDKSSVENA 57
Query: 131 MERLPTLELHGRK 143
+ L E GR+
Sbjct: 58 LL-LNESEFRGRQ 69
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 81
Score = 28.9 bits (65), Expect = 0.36
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 82 TTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMER 133
TE D+ +A+ S GV + DV+ + G S+GF V S E + ME
Sbjct: 14 VTEEDIRNALVSHGV-EPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMEL 64
>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 = 28.4 bits (64), Expect = 0.48
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
L+VGNL W ++ + G +V F + G SKG+ V+ S +
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPF--DKETGLSKGYGFVSFSSRD 52
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 28.5 bits (64), Expect = 0.54
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
C +YVG++++ E + A G ID+ + + + KGF V E+ L
Sbjct: 1 CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSW--DPVTMKHKGFAFVEYEVPEAAQLA 58
Query: 131 MERLPTLELHGR 142
+E++ + L GR
Sbjct: 59 LEQMNGVMLGGR 70
>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM1 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), 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 carboxyl terminus which
also harbors a methionine-rich region. The subgroup also
includes NAM8, 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 = 81
Score = 28.5 bits (64), Expect = 0.60
Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
L++G+L W E + S+G+ + ++VK + ++G + G+C V S
Sbjct: 2 LWMGDLEPWMDENFIKQVWASLGL-EPVNVKVIRSRNSGLNAGYCFVEFPSPH 53
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in yeast.
Yra2p belongs to the evolutionarily conserved REF (RNA
and export factor binding proteins) family of hnRNP-like
proteins. It is a major component of endogenous Yra1p
complexes. It interacts with Yra1p and functions as a
negative regulator of Yra1p. Yra2p 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). .
Length = 74
Score = 28.1 bits (63), Expect = 0.61
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 89 DAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRK 143
D I+ G P + KF+++ + + V+E+ EL+G K
Sbjct: 19 DLIKEFGEPVYS--KFYDHKDSRT----AVFEFEDPSILEKVVEKYNGKELNGAK 67
>gnl|CDD|235717 PRK06153, PRK06153, hypothetical protein; Provisional.
Length = 393
Score = 29.9 bits (68), Expect = 0.64
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 89 DAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLE 138
D + ++G+P FIDV SNG G VTL + + V RLP +
Sbjct: 285 DYLEALGIP-FIDVGMGLELSNGSLGGILRVTLSTPDKRDHVDGRLPFSD 333
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 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 = 85
Score = 28.3 bits (63), Expect = 0.68
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 18/84 (21%)
Query: 73 LYVGNLTWWTTEADMSD-------------AIRSIGVPDFIDVKFFENASNGQSKGFCTV 119
+++GNL++ TT+ + I + +PD K + Q+KGF V
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPD---SKA-KRKGVKQNKGFAYV 56
Query: 120 TLGSEESMSLVMERLPTLELHGRK 143
S+E+ + L L+GRK
Sbjct: 57 DFTSQEATKAAIA-LSEKILNGRK 79
>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 = 28.1 bits (62), Expect = 0.73
Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 70 HCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSL 129
H +++VG+L+ T D+ A G D + ++ + G+SKG+ V+ ++
Sbjct: 1 HFHVFVGDLSPEITTDDIKAAFAPFG--RISDARVVKDMATGKSKGYGFVSFFNKWDAEN 58
Query: 130 VMERLPTLELHGRKPMVAYPTR 151
++++ L GR+ + TR
Sbjct: 59 AIQQMGGQWLGGRQIRTNWATR 80
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation
initiation factor 4B (eIF-4B) and similar proteins.
This subfamily corresponds to the RRM of eIF-4B, a
multi-domain RNA-binding protein that has been primarily
implicated in promoting the binding of 40S ribosomal
subunits to mRNA during translation initiation. It
contains two RNA-binding domains; the N-terminal
well-conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), binds the 18S rRNA of the 40S ribosomal subunit
and the C-terminal basic domain (BD), including two
arginine-rich motifs (ARMs), binds mRNA during
initiation, and is primarily responsible for the
stimulation of the helicase activity of eIF-4A. eIF-4B
also contains a DRYG domain (a region rich in Asp, Arg,
Tyr, and Gly amino acids) in the middle, which is
responsible for both, self-association of eIF-4B and
binding to the p170 subunit of eIF3. Additional research
indicates that eIF-4B can interact with the poly(A)
binding protein (PABP) in mammalian cells, which can
stimulate both, the eIF-4B-mediated activation of the
helicase activity of eIF-4A and binding of poly(A) by
PABP. eIF-4B has also been shown to interact
specifically with the internal ribosome entry sites
(IRES) of several picornaviruses which facilitate
cap-independent translation initiation. .
Length = 77
Score = 28.1 bits (63), Expect = 0.79
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 74 YVGNLTWWTTEADMSDAIRSIGVPDFIDVKF-FENASNGQSKGFCTVTLGSEESMSLVME 132
Y+GNL + TE D+ + R + V V+ E G+ +GF +S+ +
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGLNV---SSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61
Query: 133 RLPTLELHGRK 143
L L R+
Sbjct: 62 -LNDESLKNRR 71
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 27.7 bits (62), Expect = 0.81
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L V NL+ + D+ D +R G + D ++ Q V + M +E
Sbjct: 3 LIVENLSSRVSWQDLKDFMRKAGEVTYAD-------AHKQRPNEGVVEFATYSDMKRAIE 55
Query: 133 RLPTLELHGRK 143
+L EL+GRK
Sbjct: 56 KLDGTELNGRK 66
>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 = 27.8 bits (62), Expect = 0.82
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 2/70 (2%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VGN+ + TE + D +G + + + G+ KG+ +E+ M
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGP--VVSFRLVYDRETGKPKGYGFCEYKDQETALSAMR 58
Query: 133 RLPTLELHGR 142
L EL+GR
Sbjct: 59 NLNGYELNGR 68
>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 = 28.0 bits (62), Expect = 0.82
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
C +++G L+W TT+ + + G + + + +S+GF VT + + V
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFG--EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58
Query: 131 M 131
+
Sbjct: 59 L 59
>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 = 27.6 bits (62), Expect = 1.2
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 1/78 (1%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFEN-ASNGQSKGFCTVTLGSEESMSLV 130
L++GNL TE + G D F ++ GQ +G+C VT ++E
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 131 MERLPTLELHGRKPMVAY 148
++ L G+K +V +
Sbjct: 61 LKSLNGKTALGKKLVVRW 78
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the RRM
of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or
splicing component, 35 kDa (splicing factor SC35 or
SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of pre-mRNA.
It is also involved in transcription elongation by
directly or indirectly mediating the recruitment of
elongation factors to the C-terminal domain of
polymerase II. SRSF2 is exclusively localized in the
nucleus and is restricted to nuclear processes. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory elements
on the pre-mRNA. The RS domain modulates SRSF2 activity
through phosphorylation, directly contacts RNA, and
promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 27.3 bits (61), Expect = 1.2
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 2/75 (2%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L V NLT+ TT D+ G + DV + +S+GF V + M+
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYG--EVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMD 58
Query: 133 RLPTLELHGRKPMVA 147
+ EL GR+ V
Sbjct: 59 AMDGKELDGRELRVQ 73
>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 = 27.4 bits (61), Expect = 1.4
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 4/78 (5%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+V N+ + + D+ G +DV+ N SKGF VT + E
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGP--ILDVEIIFNERG--SKGFGFVTFANSADADRARE 58
Query: 133 RLPTLELHGRKPMVAYPT 150
+L + GRK V T
Sbjct: 59 KLHGTVVEGRKIEVNNAT 76
>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 = 27.2 bits (61), Expect = 1.4
Identities = 18/70 (25%), Positives = 28/70 (40%), Gaps = 2/70 (2%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
LYVG L E + A G D D++ + + +GF V E + ++
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFG--DIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAID 58
Query: 133 RLPTLELHGR 142
+ EL GR
Sbjct: 59 NMNESELFGR 68
>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 = 27.1 bits (60), Expect = 1.9
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIG-VPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
L+V NL + T+ D++D + + + V + G+S+G+ VT E +
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVT---DPETGESRGYGFVTFAMLEDAQEAL 58
Query: 132 ERLPTLELHGR 142
+L +LHGR
Sbjct: 59 AKLKNKKLHGR 69
>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 = 26.5 bits (59), Expect = 3.1
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPD--FIDVKFFENASNGQSKGF 116
L VGNL T+ + + G + F+ + S G+SKG+
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFL----VYSESTGESKGY 43
>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 = 26.4 bits (59), Expect = 3.1
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 9/70 (12%)
Query: 71 CNLYVGNLTWWTTEADMSD------AIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
L+V NL + TTE + +RS+ + D K S G+ V S+
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPK---GPGKLLSMGYGFVEFKSK 57
Query: 125 ESMSLVMERL 134
E+ ++RL
Sbjct: 58 EAAQKALKRL 67
>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 = 26.2 bits (58), Expect = 4.0
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTV 119
L+VGNL TE ++ A GV + +D+K GQ + V
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIK---RPPRGQGNAYAFV 48
>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 = 26.1 bits (57), Expect = 4.1
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG L+ TTE + + + G + I++ + + +GFC VT EE + ++E
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIELPM--DTKTNERRGFCFVTYTDEEPVQKLLE 59
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit
2 (NCBP2), or cell proliferation-inducing gene 55
protein, or NCBP-interacting protein 1 (NIP1). CBP20 is
the small subunit of the nuclear cap binding complex
(CBC), which is a conserved eukaryotic heterodimeric
protein complex binding to 5'-capped polymerase II
transcripts and plays a central role in the maturation
of pre-mRNA and uracil-rich small nuclear RNA (U
snRNA). CBP20 is most likely responsible for the
binding of capped RNA. It contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and interacts with the
second and third domains of CBP80, the large subunit of
CBC. .
Length = 78
Score = 26.0 bits (58), Expect = 4.5
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 73 LYVGNLTWWTTEA 85
LYVGNL+++TTE
Sbjct: 1 LYVGNLSFYTTEE 13
>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 = 25.8 bits (57), Expect = 4.6
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L+VGNL++ E + +A G + V+ + +G+ KGF V S+E+ ++
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYG--EISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALD 58
Query: 133 RLPTLELHGR 142
L +L GR
Sbjct: 59 ALGGTDLLGR 68
>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 = 25.8 bits (56), Expect = 4.8
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
+++G L+W T+ + D G + + + + +S+GF VT S+ V+
Sbjct: 2 MFIGGLSWQTSPDSLRDYFSKFG--EIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLA 59
Query: 133 RLPTLELHGRK--PMVAY 148
+ P EL + P VA+
Sbjct: 60 Q-PHHELDSKTIDPKVAF 76
>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 = 25.6 bits (57), Expect = 5.3
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFID 101
L+VG L WT+ A++ G ID
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRID 29
>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 = 25.6 bits (57), Expect = 6.3
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTV 119
LYVG+L TEA + + G + ++ + +S G+ V
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAG--PVLSIRVCRDLITRRSLGYAYV 46
>gnl|CDD|143426 cd07108, ALDH_MGR_2402, Magnetospirillum NAD(P)+-dependent aldehyde
dehydrogenase MSR-1-like. NAD(P)+-dependent aldehyde
dehydrogenase of Magnetospirillum gryphiswaldense MSR-1
(MGR_2402) , and other similar sequences, are present in
this CD.
Length = 457
Score = 26.6 bits (59), Expect = 7.1
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 6/34 (17%)
Query: 122 GSEESMSLVM----ERL-P-TLELHGRKPMVAYP 149
GS E ++ +RL P +LEL G+ PM+ +P
Sbjct: 203 GSTEVGKIIYRAAADRLIPVSLELGGKSPMIVFP 236
>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 = 25.3 bits (55), Expect = 7.3
Identities = 23/79 (29%), Positives = 33/79 (41%), Gaps = 9/79 (11%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L++GNL TE D+ A GV +D+K GQ T T G + +L M
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIK---RPGRGQ-----TSTYGFLKFENLDMA 61
Query: 133 RLPTLELHGRKPMVAYPTR 151
L + G K + P +
Sbjct: 62 HRAKLAMSG-KVLRRNPIK 79
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
0.317 0.132 0.404
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,592,016
Number of extensions: 735345
Number of successful extensions: 783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 758
Number of HSP's successfully gapped: 93
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
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 (21.7 bits)
S2: 55 (24.9 bits)