RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2204
(231 letters)
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 224 bits (572), Expect = 6e-71
Identities = 98/271 (36%), Positives = 117/271 (43%), Gaps = 62/271 (22%)
Query: 8 LNTGAAGQIPANVIIPETTVA--------AAAAAAVPVVGSTITRQARRLYVGNIPFGVT 59
+P P T V TRQARRLYVG IP
Sbjct: 129 AKASQVFSVPGTAPRPAMTDPEKLLAEGSIITPLPVLPYQQQATRQARRLYVGGIPPEFV 188
Query: 60 EDEMMEFFNQQMHLSGLAQA-AGNPVLACQINLDKNFAFLEFRSIDETTQAMAFDGINFK 118
E+ +++FFN M +G +A G V + IN +KNFAFLEFR+++E T AMA D I +
Sbjct: 189 EEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYS 248
Query: 119 GQSLKIRRPHDYQPTPGVT--------DNAAVAVPAGVISTVVPDSPHKIFIGGLPNYLN 170
LKIRRPHDY P P +T D+ A V V ST V DS +I+IG LP YL
Sbjct: 249 NVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLG 308
Query: 171 EDQ-----------------------------------------AIAGLNGMQLGDKKLI 189
EDQ AIA LNG GD KL
Sbjct: 309 EDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLH 368
Query: 190 VQRASVGAKNA----SGQQAPVQIQVPGLTQ 216
VQRA VGA A S APV + L+Q
Sbjct: 369 VQRACVGANQATIDTSNGMAPVTLLAKALSQ 399
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 160 bits (407), Expect = 3e-51
Identities = 55/82 (67%), Positives = 69/82 (84%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
ARRLYVGN+P G+TE+E+++FFNQ M +GL QA GNPVL+ QIN +KNFAF+EFR+++E
Sbjct: 1 ARRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEE 60
Query: 106 TTQAMAFDGINFKGQSLKIRRP 127
T A+A DGI FKGQ LKIRRP
Sbjct: 61 ATAALALDGIIFKGQPLKIRRP 82
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 77
Score = 63.8 bits (156), Expect = 9e-14
Identities = 33/77 (42%), Positives = 35/77 (45%), Gaps = 41/77 (53%)
Query: 158 HKIFIGGLPNYLNEDQ-----------------------------------------AIA 176
+KIFIGGLPNYL+EDQ AIA
Sbjct: 1 NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60
Query: 177 GLNGMQLGDKKLIVQRA 193
GLNGMQLGDKKL VQRA
Sbjct: 61 GLNGMQLGDKKLTVQRA 77
Score = 33.0 bits (76), Expect = 0.016
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 16/85 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAG-----NPVLACQINLDKNFAFLEFRS 102
++++G +P ++ED++ E L ++ G N V L K +AF E+
Sbjct: 2 KIFIGGLPNYLSEDQVKE----------LLESFGKLKAFNLVKDSATGLSKGYAFCEYLD 51
Query: 103 IDETTQAMA-FDGINFKGQSLKIRR 126
T QA+A +G+ + L ++R
Sbjct: 52 PSVTDQAIAGLNGMQLGDKKLTVQR 76
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 58.0 bits (141), Expect = 1e-11
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 18/84 (21%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
L+VGN+P TE+E+ E F++ V + ++ D K FAF+EF
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKF-----------GKVESVRLVRDKETGKSKGFAFVEFE 49
Query: 102 SIDETTQAM-AFDGINFKGQSLKI 124
S ++ +A+ A +G G+ LK+
Sbjct: 50 SEEDAEKALEALNGKELDGRPLKV 73
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. This
subfamily also includes some p54nrb/PSF/PSP1 homologs
from invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 57.7 bits (140), Expect = 2e-11
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 18/82 (21%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
RL+VGN+P +TE+E E F G V +N +K F F+ +D T
Sbjct: 3 RLFVGNLPNDITEEEFKELF----------SKYGE-VSEVFLNKEKGFGFIR---LDTRT 48
Query: 108 QAM----AFDGINFKGQSLKIR 125
A DGI KG+ L++R
Sbjct: 49 NAEKAKAELDGIMRKGRQLRVR 70
>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 = 55.4 bits (134), Expect = 1e-10
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 17/83 (20%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-----KNFAFLEFRSI 103
L+VGN+P TE+++ E F++ + + +I D K FAF+EF S
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFG-----------EIESVRIVRDKDGKSKGFAFVEFESP 49
Query: 104 DETTQAM-AFDGINFKGQSLKIR 125
++ +A+ A +G G+ LK+
Sbjct: 50 EDAEKALEALNGKELDGRKLKVS 72
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 57.3 bits (137), Expect = 1e-09
Identities = 30/137 (21%), Positives = 61/137 (44%), Gaps = 21/137 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEF 100
L+VGN+P+ VTE+++ E F + PV ++ D + FAF+EF
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKF-----------GPVKRVRLVRDRETGKSRGFAFVEF 164
Query: 101 RSIDETTQAM-AFDGINFKGQSLKIRR-PHDYQPTPGVTDNAAVAVPAGVISTVVPDSPH 158
S + +A+ +G +G+ L++++ QP +++N + +
Sbjct: 165 ESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEK 224
Query: 159 --KIFIGGLPNYLNEDQ 173
+++G LP E++
Sbjct: 225 SDNLYVGNLPLKTAEEE 241
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 52.2 bits (126), Expect = 2e-09
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 16/80 (20%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDK----NFAFLEFRSID 104
LYV N+P VTE+++ EFF+ V ++ +K FAF+EF S +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSP-----------YGKVEGVRLVRNKDRPRGFAFVEFASPE 49
Query: 105 ETTQAMA-FDGINFKGQSLK 123
+ A+ +G+ G++L+
Sbjct: 50 DAEAALKKLNGLVLDGRTLR 69
>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 = 51.4 bits (124), Expect = 3e-09
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 17/81 (20%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-----KNFAFLEFRSI 103
L+VGN+P TE+++ + F++ P+ + +I D K FAF+EF
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKF-----------GPIESIRIVRDETGRSKGFAFVEFEDE 49
Query: 104 DETTQAM-AFDGINFKGQSLK 123
++ +A+ A +G G+ L+
Sbjct: 50 EDAEKALEALNGKELGGRELR 70
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 48.4 bits (116), Expect = 4e-08
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 12/76 (15%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQ 108
+YVGN+P G+TE+E+ F+ + ++ DK +AF+ F + +
Sbjct: 3 VYVGNLPHGLTEEELQRTFSP-----------FGAIEEVRVFKDKGYAFVRFDTHEAAAT 51
Query: 109 AM-AFDGINFKGQSLK 123
A+ A +G + GQ++K
Sbjct: 52 AIVAVNGTSINGQTVK 67
>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 = 48.4 bits (116), Expect = 6e-08
Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 18/82 (21%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFRSI 103
+VGNIP+ TE++++E F++ G PV++ ++ D K + F EF I
Sbjct: 2 FVGNIPYDATEEQLIEIFSE----------VG-PVVSFRLVTDRDTGKPKGYGFCEFEDI 50
Query: 104 DETTQAM-AFDGINFKGQSLKI 124
+ A+ +G F G++L++
Sbjct: 51 ETAASAIRNLNGYEFNGRALRV 72
>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 = 46.5 bits (111), Expect = 3e-07
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 18/85 (21%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
LYVGN+P+ VTE+++ + F Q G V + ++ D+ F F+E
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQ----------FG-EVTSARVITDRETGRSRGFGFVEME 49
Query: 102 SIDETTQAM-AFDGINFKGQSLKIR 125
+ +E A+ +G +F G++L +
Sbjct: 50 TAEEANAAIEKLNGTDFGGRTLTVN 74
>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 = 45.7 bits (109), Expect = 5e-07
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 17/81 (20%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRSI 103
+VGN+ +G T +E+ E F ++ G + I DK FA++EF
Sbjct: 3 FVGNVDYGTTPEELQEHF----------KSCGT-INRITILCDKFTGQPKGFAYIEFLDK 51
Query: 104 DETTQAMAFDGINFKGQSLKI 124
A+ + F+G+ +K+
Sbjct: 52 SSVENALLLNESEFRGRQIKV 72
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 44.9 bits (106), Expect = 9e-07
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 14/80 (17%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAF--LEFRSIDE 105
RL+VGN+P +TE+EM + F + + I+ DK F F LE R++ E
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIF-----------IHKDKGFGFIRLETRTLAE 51
Query: 106 TTQAMAFDGINFKGQSLKIR 125
+A D + +G+ L++R
Sbjct: 52 IAKA-ELDNMPLRGKQLRVR 70
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 44.9 bits (107), Expect = 1e-06
Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 21/86 (24%)
Query: 48 RLYVGNIPFGVTEDEMMEFF-------NQQMHLSGLAQAAGNPVLACQINLDKNFAFLEF 100
RL+VG + VTE ++ E F + ++ A D+ FA+++
Sbjct: 1 RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDA------------GPDRGFAYIDL 48
Query: 101 RSIDET-TQAM-AFDGINFKGQSLKI 124
R+ + + +G +KG LKI
Sbjct: 49 RTSEAQLKKCKSTLNGTKWKGSVLKI 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 = 44.6 bits (106), Expect = 1e-06
Identities = 26/83 (31%), Positives = 39/83 (46%), Gaps = 13/83 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLA---QAAGNPVLACQINLDKNFAFLEFRSI 103
R L+VGN+ VTE+ + E F Q L G+ G P K+FAF+ F+
Sbjct: 2 RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKP---------KSFAFVTFKHE 52
Query: 104 DETTQAMA-FDGINFKGQSLKIR 125
A+ +GI G+ L+I+
Sbjct: 53 VSVPYAIQLLNGIRLFGRELRIK 75
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 44.1 bits (104), Expect = 2e-06
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 10/82 (12%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
R AR L+V N+P+ +T DE+ E F + + + G+ K A++EF++
Sbjct: 1 RDARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGKDGS---------SKGIAYIEFKTE 51
Query: 104 DETTQAMA-FDGINFKGQSLKI 124
E +A+ G G+S+ +
Sbjct: 52 AEAEKALEEKQGAEVDGRSIVV 73
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 43.9 bits (104), Expect = 2e-06
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 17/83 (20%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFN-----QQMHLSGLAQAAGNPVLACQINLDKNFAFLEFR 101
R ++VG I ++ED++ EFF+ ++ L G Q FAF+EF
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH------------SARFAFVEFA 48
Query: 102 SIDETTQAMAFDGINFKGQSLKI 124
+ A+ G G L++
Sbjct: 49 DAESALSALNLSGTLLGGHPLRV 71
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM2 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 73
Score = 43.3 bits (103), Expect = 4e-06
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 19/82 (23%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQI------NLDKNFAFLEFRSI 103
+VGN+PF + E+E+ + F V A +I + K F ++ F++
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCG-----------DVEAVRIVRDRKTGIGKGFGYVLFKTK 51
Query: 104 DETTQAMAFDGINFKGQSLKIR 125
D A+ +GI KG+ KIR
Sbjct: 52 DSVALALKLNGIKLKGR--KIR 71
>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 = 42.5 bits (101), Expect = 6e-06
Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 18/83 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRS 102
LYVGN+ F TE+++ E F++ + + LD+ F F+E+ +
Sbjct: 1 LYVGNLSFYTTEEQIYELFSR-----------CGDIKRIIMGLDRFTKTPCGFCFVEYYT 49
Query: 103 IDETTQAMAF-DGINFKGQSLKI 124
++ A+ + +G + +++
Sbjct: 50 REDAENAVKYLNGTKLDDRIIRV 72
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 41.9 bits (99), Expect = 1e-05
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 16/83 (19%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQ-----QMHLSGLAQAAGNPVLACQINLDKNFAFLEFRS 102
RL+V N+PF TE+E+ E F ++HL L + K FAF+ F
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLP-LDKETKRS---------KGFAFVSFMF 50
Query: 103 IDETTQAM-AFDGINFKGQSLKI 124
+ +A DG F+G+ L +
Sbjct: 51 PEHAVKAYSELDGSIFQGRLLHV 73
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 44.9 bits (106), Expect = 1e-05
Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 22/117 (18%)
Query: 24 ETTVAAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNP 83
E AA AA P +LYVGN+ F +TE E+ + F
Sbjct: 168 EKNRAAKAATHQPGDI----PNFLKLYVGNLHFNITEQELRQIFE-----------PFGD 212
Query: 84 VLACQINLD------KNFAFLEFRSIDETTQAM-AFDGINFKGQSLKIRRPHDYQPT 133
+ Q++ D K F F++F +E +A+ +G G+ +K+ D
Sbjct: 213 IEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYL 269
Score = 38.3 bits (89), Expect = 0.002
Identities = 29/136 (21%), Positives = 55/136 (40%), Gaps = 26/136 (19%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAF 97
R R ++V + E ++ EFF++ G V Q D+N A+
Sbjct: 87 RDDRTVFVLQLALKARERDLYEFFSK----------VG-KVRDVQCIKDRNSRRSKGVAY 135
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSP 157
+EF ++ +A+A G G+ + + Q + + AA A A +P +
Sbjct: 136 VEFYDVESVIKALALTGQMLLGRPIIV------QSSQAEKNRAAKA--ATHQPGDIP-NF 186
Query: 158 HKIFIGGLPNYLNEDQ 173
K+++G L + E +
Sbjct: 187 LKLYVGNLHFNITEQE 202
>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 = 41.2 bits (97), Expect = 2e-05
Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 18/83 (21%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
+Y+GN+ + +TED++ EFF G + + ++ DK F ++F
Sbjct: 1 TVYIGNLAWDITEDDVREFF------------KGCEITSVRLATDKETGEFKGFGHVDFA 48
Query: 102 SIDETTQAMAFDGINFKGQSLKI 124
+ A+ DG G+ ++I
Sbjct: 49 DEESLDAALKLDGTVLCGRPIRI 71
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 41.1 bits (97), Expect = 3e-05
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
R +YVGN+ T D+++EFF+Q + + AG+ +AF+EF
Sbjct: 5 RTIYVGNLDPTTTADQLLEFFSQAGEVK-YVRMAGDE------TQPTRYAFVEFAEQTSV 57
Query: 107 TQAMAFDGINFKGQSLKI 124
A+ +G F G+ LK+
Sbjct: 58 INALKLNGAMFGGRPLKV 75
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 40.3 bits (94), Expect = 4e-05
Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 14/80 (17%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAF--LEFRSIDE 105
RL+VGN+P +TE++ + F + G P IN D+ F F LE R++ E
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKY----------GEPS-EVFINRDRGFGFIRLESRTLAE 51
Query: 106 TTQAMAFDGINFKGQSLKIR 125
+A DG K + L+IR
Sbjct: 52 IAKA-ELDGTILKNRPLRIR 70
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 39.2 bits (92), Expect = 9e-05
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 15/80 (18%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---FAFLEFRSIDE 105
LYVGN+ VTED + E F+Q P+ +C++ + +AF+E+
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQ-----------IGPIKSCKLIREHGNDPYAFVEYYDHRS 49
Query: 106 TTQA-MAFDGINFKGQSLKI 124
A +G GQ +K+
Sbjct: 50 AAAALQTMNGRLILGQEIKV 69
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 39.4 bits (92), Expect = 9e-05
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 13/80 (16%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLA----QAAGNPVLACQINLDKNFAFLEFRSID 104
+YVGN+ +G T +E+ F+ ++ + + +G+P K FA++EF +
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP---------KGFAYIEFSDKE 52
Query: 105 ETTQAMAFDGINFKGQSLKI 124
A+A D F+G+ +K+
Sbjct: 53 SVRTALALDESLFRGRQIKV 72
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 84
Score = 39.7 bits (93), Expect = 9e-05
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNF--AFLEFRSIDE 105
R+Y+ N+ + +E+++ EF +S L + V + + A+ EF S ++
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPS--QTVRGFRSRRVRPLGIAYAEFSSPEQ 58
Query: 106 TTQAM-AFDGINFKGQSLKIR 125
+ + +G FK + L ++
Sbjct: 59 AEKVVKDLNGKVFKNRKLFVK 79
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 18/83 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFRS 102
LYVGN+ F +TED++ F + Q+ D K + F++F
Sbjct: 1 LYVGNLHFNITEDDLRGIFE-----------PFGEIEFVQLQRDPETGRSKGYGFIQFAD 49
Query: 103 IDETTQAMA-FDGINFKGQSLKI 124
++ +A+ +G G+ +K+
Sbjct: 50 AEDAKKALEQLNGFELAGRPIKV 72
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 38.4 bits (89), Expect = 2e-04
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 14/80 (17%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAF--LEFRSIDE 105
RL+VGN+P +TEDE + F + G P IN K F F LE R++ E
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKY----------GEPG-EVFINKGKGFGFIKLESRALAE 51
Query: 106 TTQAMAFDGINFKGQSLKIR 125
+A D +G+ L++R
Sbjct: 52 IAKA-ELDDTPMRGRQLRVR 70
>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 = 38.1 bits (89), Expect = 3e-04
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 16/82 (19%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-----KNFAFLEFRS 102
L+VGN+ + +D++ EFF + G V+ +I D K F +EF +
Sbjct: 1 TLFVGNLSWSAEQDDLEEFF----------KECG-EVVDVRIAQDDDGRSKGFGHVEFAT 49
Query: 103 IDETTQAMAFDGINFKGQSLKI 124
+ +A+ G G+ +++
Sbjct: 50 EEGAQKALEKSGEELLGREIRV 71
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a transcription
coactivator of LEF-1 and AML-1 for the TCRalpha enhancer
function. In addition, THOC4 specifically binds to
rhesus (RH) promoter in erythroid, and might be a novel
transcription cofactor for erythroid-specific genes.
SKAR shows high sequence homology with THOC4 and
possesses one RRM as well. SKAR is widely expressed and
localizes to the nucleus. It may be a critical player in
the function of S6K1 in cell and organism growth control
by binding the activated, hyperphosphorylated form of
S6K1 but not S6K2. Furthermore, SKAR functions as a
protein partner of the p50 subunit of DNA polymerase
delta. In addition, SKAR may have particular importance
in pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 37.6 bits (88), Expect = 4e-04
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 17/83 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRS 102
RL V N+ + VTE+++ E F V +IN D++ A + F
Sbjct: 2 RLRVSNLHYDVTEEDLEELF-----------GRVGEVKKVKINYDRSGRSEGTADVVFEK 50
Query: 103 IDETTQAMA-FDGINFKGQSLKI 124
++ +A+ F+G+ GQ +++
Sbjct: 51 REDAERAIKQFNGVLLDGQPMQV 73
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 37.3 bits (87), Expect = 6e-04
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 16/84 (19%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-----KNFAFLEFRS 102
R++VG IP TE+E+ +FF++ V +I D K + F+ F +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGS-----------VKDVKIITDRAGVSKGYGFVTFET 52
Query: 103 IDETTQAMAFDGINFKGQSLKIRR 126
++ + +A +NF+G+ L I
Sbjct: 53 QEDAEKILAMGNLNFRGKKLNIGP 76
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 37.0 bits (86), Expect = 8e-04
Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 13/81 (16%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQA---AGNPVLACQINLDKNFAFLEFRSID 104
+L+V +PF VT++E+ + F + + + +G P K A++E+ +
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKP---------KGLAYVEYENES 54
Query: 105 ETTQA-MAFDGINFKGQSLKI 124
+QA + DG K +++ +
Sbjct: 55 SASQAVLKMDGTEIKEKTISV 75
>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 = 36.8 bits (85), Expect = 9e-04
Identities = 29/85 (34%), Positives = 41/85 (48%), Gaps = 17/85 (20%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFR 101
R L+VGN+ VTE+ + E F Q AG PV+ +I DK+ FAF+ F+
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQ----------AG-PVIKVKIPKDKDGKPKQFAFVNFK 50
Query: 102 SIDETTQAMA-FDGINFKGQSLKIR 125
AM +GI G+ L I+
Sbjct: 51 HEVSVPYAMNLLNGIKLYGRPLNIQ 75
>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 = 36.3 bits (84), Expect = 0.001
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 18/83 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFRS 102
++VGNIP+ TE+++ + F++ G PV++ ++ D K + F E++
Sbjct: 1 VFVGNIPYEATEEQLKDIFSE----------VG-PVVSFRLVYDRETGKPKGYGFCEYKD 49
Query: 103 IDETTQAMA-FDGINFKGQSLKI 124
+ AM +G G+ L++
Sbjct: 50 QETALSAMRNLNGYELNGRQLRV 72
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 36.4 bits (85), Expect = 0.001
Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 23/92 (25%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
R +++ N+PF TE+E+ E F+Q G V +I DK AF++F
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQ----------FG-EVKYARIVKDKLTGHSKGTAFVKF 49
Query: 101 RSID------ETTQAMAFDGINFKGQSLKIRR 126
++ + E G++ G+ L +
Sbjct: 50 KTKESAQKCLEAADNAEDSGLSLDGRRLIVTL 81
>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 = 36.2 bits (84), Expect = 0.001
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSG--LAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
Y+GN+P+ VTE+++ EFF + +++S L + G+P + F + EF D
Sbjct: 5 YLGNLPYDVTEEDIKEFF-RGLNVSSVRLPREPGDPGRL------RGFGYAEFEDRDSLL 57
Query: 108 QAMAFDGINFKGQSLKI 124
QA++ + + K + +++
Sbjct: 58 QALSLNDESLKNRRIRV 74
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 36.1 bits (84), Expect = 0.001
Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 16/70 (22%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRS 102
RL V N+P G+ ED++ + F A + Q+ K+ F F+ +++
Sbjct: 2 RLIVKNLPKGIKEDKLRKLF-----------EAFGTITDVQLKYTKDGKFRKFGFVGYKT 50
Query: 103 IDETTQAMAF 112
+E +A+
Sbjct: 51 EEEAQKALKH 60
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 36.4 bits (84), Expect = 0.001
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 13/80 (16%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLA----QAAGNPVLACQINLDKNFAFLEFRSID 104
+YVGN+ +G T +E+ F+ ++ + + +G+P K +A++EF + D
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHP---------KGYAYIEFATRD 52
Query: 105 ETTQAMAFDGINFKGQSLKI 124
A+A D +F+G+ +K+
Sbjct: 53 SVEAAVALDESSFRGRVIKV 72
>gnl|CDD|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM1 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa,which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 74
Score = 35.9 bits (83), Expect = 0.001
Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 21/84 (25%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
R +Y+GN+P T E+ L+ P+ +I +KN AF+ F +D +
Sbjct: 2 RTVYLGNLPPNTTVKEL------------LSHVRSGPIENVRILPEKNCAFISF--LDPS 47
Query: 107 TQAMAF------DGINFKGQSLKI 124
A AF ++ KG LKI
Sbjct: 48 A-ATAFHSDAILKRLSIKGVELKI 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 = 35.8 bits (83), Expect = 0.002
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 17/83 (20%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINL---DKNF---AFLEFRS 102
+YVG IP+ TEDE+ +F G + + F AF+ F++
Sbjct: 1 VYVGGIPYYSTEDEIRSYF----------SYCG-EIEELDLMTFPDTGRFRGIAFITFKT 49
Query: 103 IDETTQAMAFDGINFKGQSLKIR 125
+ +A+A DG + G+ LK+
Sbjct: 50 EEAAKRALALDGEDMGGRFLKVE 72
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 35.3 bits (82), Expect = 0.003
Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 18/83 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRS 102
L+V N+P+ T++++ EFF++ G P+ C + DK F ++ F
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSE----------VG-PIKRCFVVKDKGSKKCRGFGYVTFAL 50
Query: 103 IDETTQAMA-FDGINFKGQSLKI 124
++ +A+ F G+ + +
Sbjct: 51 EEDAKRALEEKKKTKFGGRKIHV 73
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM3 in
hnRNP R, hnRNP Q, and APOBEC-1 complementation factor
(ACF). hnRNP R is a ubiquitously expressed nuclear
RNA-binding protein that specifically bind mRNAs with a
preference for poly(U) stretches and has been implicated
in mRNA processing and mRNA transport, and also acts as
a regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as a
component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA transport.
ACF is an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members contain three conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains).
Length = 72
Score = 35.3 bits (82), Expect = 0.003
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 14/77 (18%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQ 108
LYV N+P TE+++ E F++ + ++ K++AF+ F D+ +
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVE-------------RVKKIKDYAFVHFEERDDAVK 50
Query: 109 AM-AFDGINFKGQSLKI 124
AM +G +G +++
Sbjct: 51 AMEEMNGKELEGSPIEV 67
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 35.4 bits (82), Expect = 0.003
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 18/81 (22%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFRSI 103
+VGN+PF + ++ F LS V + ++ D K F ++EF +
Sbjct: 5 FVGNLPFNTVQGDLDAIFK---DLS---------VKSVRLVRDKETDKFKGFCYVEFEDV 52
Query: 104 DETTQAMAFDGINFKGQSLKI 124
+ +A+ +DG F +SL++
Sbjct: 53 ESLKEALEYDGALFDDRSLRV 73
>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 = 35.4 bits (82), Expect = 0.003
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 17/85 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
+++VG +P VTE+E E+F+Q V+ Q+ D + F F+ F
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQF-----------GKVVDAQLMQDHDTGRSRGFGFVTFD 49
Query: 102 SIDETTQAMAFDGINFKGQSLKIRR 126
S + + + G+ ++++R
Sbjct: 50 SESAVERVFSAGMLELGGKQVEVKR 74
>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 = 35.1 bits (81), Expect = 0.003
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQ 108
L+VGN+ F TEDE+ F + + + C K FAF++F I+ T
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKC-----KGFAFVDFEEIEFATN 55
Query: 109 AMAFDGINFK 118
A+ +N +
Sbjct: 56 ALKGKHLNGR 65
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 35.3 bits (82), Expect = 0.003
Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 23/70 (32%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQ-------MHLSGLAQAAGNPVLACQINLDKNFAFLEFR 101
L+V N+ TE+E+ + F++Q MH G G PV F+EF
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKG-----GGPV-----------CFVEFE 48
Query: 102 SIDETTQAMA 111
+ TQA+
Sbjct: 49 DVSFATQALN 58
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 34.7 bits (80), Expect = 0.005
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 16/85 (18%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---FAFLEFR 101
R ++V G +E+++M++F A G + + +DK+ +A +EF
Sbjct: 1 AERSVFVSGFKRGTSEEQLMDYF----------SAFGPVM---NVIMDKDKGVYAIVEFD 47
Query: 102 SIDETTQAMAFDGINFKGQSLKIRR 126
S + + ++ G L++R
Sbjct: 48 SKEGVDKVLSEPQHTLNGHRLRVRP 72
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM2 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two RRMs.
.
Length = 82
Score = 34.9 bits (81), Expect = 0.005
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN--FAFLEFRS 102
RL+VG IP T++E++E F++ G+ + +KN FAF+E+ S
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSK--VTEGVVDVIVYRSPD---DKNKNRGFAFVEYES 54
>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 = 34.6 bits (80), Expect = 0.005
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 17/84 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDK------NFAFLEFR 101
+L+VGN+P+ V E+ E+F+Q V +C + DK + F+ F
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGK-----------VKSCNVPFDKETGLSKGYGFVSFS 49
Query: 102 SIDETTQAMAFDGINFKGQSLKIR 125
S D A+ +G L+++
Sbjct: 50 SRDGLENALQKQKHILEGNKLQVQ 73
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 34.4 bits (79), Expect = 0.005
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 15/83 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---FAFLEFRSID 104
+YVGN+P + E E+ + F + P++ + L +AF+EF
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKY-----------GPIVDIDLKLPPRPPGYAFIEFEDAR 49
Query: 105 ETTQAM-AFDGINFKGQSLKIRR 126
+ A+ DG +F GQ L++
Sbjct: 50 DAEDAIRGRDGYDFDGQRLRVEL 72
>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 = 34.5 bits (80), Expect = 0.006
Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
R +YV N+ F + ED++ F++ + + Q L+ FAF+ F+
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQ--DEKQGRLNNGFAFVTFKDASSA 58
Query: 107 TQAMAFDGINFKGQSLKI 124
A+ +G G+ + +
Sbjct: 59 ENALQLNGTELGGRKISV 76
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 34.1 bits (79), Expect = 0.006
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 15/59 (25%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQ-----QMHLSGLAQAAGNPVLACQINLDKNFAFLEFRS 102
+Y+G++P G E E+ ++F+Q ++ LS ++ G K +AF+EF S
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLS-RSKKTGKS---------KGYAFVEFES 50
>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 = 34.4 bits (79), Expect = 0.007
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 24/92 (26%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQIN---------------LDK 93
+++GN+ F T++ + +FF + +G+ + QI +K
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSK---------SGDRITDEQITRVHMPDSKAKRKGVKQNK 51
Query: 94 NFAFLEFRSIDETTQAMAFDGINFKGQSLKIR 125
FA+++F S + T A+A G+ L I+
Sbjct: 52 GFAYVDFTSQEATKAAIALSEKILNGRKLLIK 83
>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 = 34.3 bits (79), Expect = 0.007
Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 17/60 (28%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQIN------LDKNFAFLEFRS 102
L+VGN+P +TEDE+ EFF + GN VL +IN NF F+ F
Sbjct: 6 LFVGNLPHDITEDELKEFF----------KEFGN-VLEVRINSKGGGGRLPNFGFVVFDD 54
Score = 26.6 bits (59), Expect = 3.3
Identities = 10/20 (50%), Positives = 16/20 (80%), Gaps = 1/20 (5%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ 173
PDS H++F+G LP+ + ED+
Sbjct: 1 PDS-HQLFVGNLPHDITEDE 19
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 34.2 bits (79), Expect = 0.008
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 21/86 (24%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQI---------NLDKNFAFLE 99
LYVGN+ VTE+ + + F + G P+ + +I ++N F+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGR----FG-------PLASVKIMWPRTEEERRRNRNCGFVA 52
Query: 100 FRSIDETTQAM-AFDGINFKGQSLKI 124
F + + +A+ DG + G LK+
Sbjct: 53 FMNRADAERALDELDGKDVMGYELKL 78
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to the
RRM1 of hnRNP A0 which is a low abundance hnRNP protein
that has been implicated in mRNA stability in mammalian
cells. It has been identified as the substrate for
MAPKAP-K2 and may be involved in the lipopolysaccharide
(LPS)-induced post-transcriptional regulation of tumor
necrosis factor-alpha (TNF-alpha), cyclooxygenase 2
(COX-2) and macrophage inflammatory protein 2 (MIP-2).
hnRNP A0 contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 79
Score = 34.0 bits (78), Expect = 0.009
Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 17/88 (19%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
Q +L+VG + ++ + F + C + +D N F F+
Sbjct: 1 QLCKLFVGGLNLKTSDSGLRRHF-----------TRYGKLTECVVMVDPNTKRSRGFGFI 49
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRR 126
F S DE +AM + G ++++R
Sbjct: 50 TFSSADEADEAMEAQPHSIDGNQIELKR 77
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to the
RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a TRBP-interacting
domain. RBM4 is a ubiquitously expressed splicing factor
with two isoforms, RBM4A (also known as Lark homolog)
and RBM4B (also known as RBM30), which are very similar
in structure and sequence. RBM4 may also function as a
translational regulator of stress-associated mRNAs as
well as play a role in micro-RNA-mediated gene
regulation. RBM4 contains two N-terminal RRMs, a
CCHC-type zinc finger, and three alanine-rich regions
within their C-terminal regions. This family also
includes Drosophila RNA-binding protein lark (Dlark), a
homolog of human RBM4. It plays an important role in
embryonic development and in the circadian regulation of
adult eclosion. Dlark shares high sequence similarity
with RBM4 at the N-terminal region. However, Dlark has
three proline-rich segments instead of three
alanine-rich segments within the C-terminal region. .
Length = 66
Score = 33.7 bits (78), Expect = 0.009
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 14/78 (17%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
+L+VGN+P T +E+ F + G V C + KN+ F+ ++
Sbjct: 1 KLFVGNLPDATTSEELRALF----------EKYG-TVTECDVV--KNYGFVHMEEEEDAE 47
Query: 108 QAM-AFDGINFKGQSLKI 124
A+ A +G F G+ + +
Sbjct: 48 DAIKALNGYEFMGKRINV 65
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM2
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the 35
S pre-rRNA. MRD1 contains 5 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which may play an
important structural role in organizing specific rRNA
processing events. .
Length = 79
Score = 33.9 bits (78), Expect = 0.009
Identities = 20/86 (23%), Positives = 43/86 (50%), Gaps = 16/86 (18%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFN-----QQMHLSGLAQAAGNPVLACQINLDKNFAFLE 99
+ RL+V N+P+ ED++ + F+ ++H++ + + +G K FA++
Sbjct: 1 ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVA-IDKKSGKS---------KGFAYVL 50
Query: 100 FRSIDETTQA-MAFDGINFKGQSLKI 124
F ++ +A DG F+G+ + I
Sbjct: 51 FLDPEDAVKAYKELDGKVFQGRLIHI 76
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 33.7 bits (78), Expect = 0.010
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 18/85 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDK------NFAFLEFRS 102
+YVGN+ VTE+ + E F Q AG PV+ I D+ + F+EF S
Sbjct: 1 VYVGNLDEKVTEELLWELFIQ----------AG-PVVNVHIPKDRVTQAHQGYGFVEFLS 49
Query: 103 IDETTQAMA-FDGINFKGQSLKIRR 126
++ A+ + I G+ +++ +
Sbjct: 50 EEDADYAIKIMNMIKLYGKPIRVNK 74
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 33.7 bits (78), Expect = 0.011
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 6/79 (7%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
++VGNIP GV++D + + + + + K F F EF +
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDP-----STGKLKAFGFCEFEDPEGA 55
Query: 107 TQAM-AFDGINFKGQSLKI 124
+A+ +G+ G+ L +
Sbjct: 56 LRALRLLNGLELGGKKLLV 74
>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 = 33.7 bits (78), Expect = 0.011
Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 22/73 (30%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQI-----------NLDKNFAF 97
L+V N+ F TE+ + + F + V + I L + F
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKC-----------GGVRSVTIAKKKDPKGPGKLLSMGYGF 51
Query: 98 LEFRSIDETTQAM 110
+EF+S + +A+
Sbjct: 52 VEFKSKEAAQKAL 64
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 33.5 bits (77), Expect = 0.012
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 13/53 (24%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEF 100
R+Y+G +P+ E ++ FF G + +INL F F+EF
Sbjct: 1 RVYIGRLPYRARERDVERFF------KGYGRIR-------EINLKNGFGFVEF 40
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 84
Score = 33.7 bits (77), Expect = 0.013
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQA----AGNPVLACQINLDKNFAFLEFRSID 104
L+V N+ F T + + F HL G A +P Q L F F+ F++ +
Sbjct: 3 LFVKNLNFSTTNQHLTDAFK---HLDGFVFARVKTKPDPKRPGQT-LSMGFGFVGFKTKE 58
Query: 105 ETTQAM-AFDGINFKGQSLKIRRPH 128
+ A+ A DG G +L ++ H
Sbjct: 59 QAQAALKAMDGFVLDGHTLVVKFSH 83
>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 = 33.4 bits (76), Expect = 0.013
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 59 TEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQAMAF-DGINF 117
TE ++ E F++ L+G+ N V + + FAF+ F ID++ +AM +G+
Sbjct: 12 TERDLREVFSRYGPLAGV-----NVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66
Query: 118 KGQSLKIRRPHDYQPT 133
G+ +++ DY T
Sbjct: 67 DGRRIRV----DYSIT 78
>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 = 33.2 bits (76), Expect = 0.014
Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 22/88 (25%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
R+YVG+I F + ED + + F + P+ + ++ D K FAF+E+
Sbjct: 2 RVYVGSISFELGEDTIRQAF-----------SPFGPIKSIDMSWDPVTMKHKGFAFVEY- 49
Query: 102 SIDETTQAMAFD---GINFKGQSLKIRR 126
+ E Q +A + G+ G+++K+ R
Sbjct: 50 EVPEAAQ-LALEQMNGVMLGGRNIKVGR 76
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is an integral part of the U2
small nuclear ribonucleoprotein (snRNP) and the U11/U12
di-snRNP. SF3B is essential for the accurate excision of
introns from pre-messenger RNA and has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 33.4 bits (77), Expect = 0.015
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 19/82 (23%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQ-----QMHLSGLAQAAGNPVLACQINLDKNFAFLEFR 101
R LYV N+PF ++ +E+ + F + Q+ + + G AF+ +
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGT-------------AFVVYE 49
Query: 102 SIDETTQAM-AFDGINFKGQSL 122
I + A G N + L
Sbjct: 50 DIYDAKNACDHLSGFNVANRYL 71
>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 = 33.0 bits (76), Expect = 0.015
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 20/72 (27%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-------FAFLEFR 101
++V N+ + V EDE+ + F G + L KN +A++EF
Sbjct: 2 VFVSNLDYSVPEDELRKLF----------SKCGEIT---DVRLVKNYKGKSKGYAYVEFE 48
Query: 102 SIDETTQAMAFD 113
+ + +A+ D
Sbjct: 49 NEESVQEALKLD 60
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 33.1 bits (76), Expect = 0.016
Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 18/84 (21%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
RL++ N+ + TE+++ + F++ P+ + +D K FAF+ +
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKY-----------GPLSEVHLPIDKLTKKPKGFAFVTYM 52
Query: 102 SIDETTQAMA-FDGINFKGQSLKI 124
+ +A A DG F+G+ L +
Sbjct: 53 IPEHAVKAFAELDGTVFQGRLLHL 76
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 33.0 bits (75), Expect = 0.016
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 13/83 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAA---GNPVLACQINLDKNFAFLEFRSI 103
R L+VGN+ V E+ + E F Q L+ + G P K+F F+ F+
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKP---------KSFGFVCFKHS 52
Query: 104 DETTQAMA-FDGINFKGQSLKIR 125
+ A+A +GI G+ +K+
Sbjct: 53 ESVPYAIALLNGIRLYGRPIKVH 75
>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 = 33.0 bits (76), Expect = 0.018
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 17/83 (20%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-----KNFAFLEFRSI 103
++V N+PF VT ++ + F + GN VL + D K F + F S
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRE----------CGN-VLRADVKTDNDGRSKGFGTVLFESP 49
Query: 104 DETTQAM-AFDGINFKGQSLKIR 125
++ +A+ F+G + +G+ L++R
Sbjct: 50 EDAQRAIEMFNGYDLEGRELEVR 72
>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 = 33.0 bits (76), Expect = 0.020
Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 21/91 (23%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQ---------QMHLSGLAQAAGNPVLACQINLDKNFAFL 98
RL++GN+ +TE +++ F++ H SG G P + F+
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSG--PLKGQPR---------GYCFV 49
Query: 99 EFRSIDETTQAMA-FDGINFKGQSLKIRRPH 128
F + +E +A+ +G G+ L +R H
Sbjct: 50 TFETKEEAEKALKSLNGKTALGKKLVVRWAH 80
Score = 30.3 bits (69), Expect = 0.17
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRAS 194
++A+ LNG KKL+V+ A
Sbjct: 58 EKALKSLNGKTALGKKLVVRWAH 80
>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 = 33.0 bits (76), Expect = 0.020
Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 17/83 (20%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
+++VG +P+ T+D + ++F+Q + + D+ + F+ F
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQF-----------GEIEEAVVITDRQTGKSRGYGFVTF 49
Query: 101 RSIDETTQAMAFDGINFKGQSLK 123
+ + +A G+
Sbjct: 50 KDKESAERACKDPNPIIDGRKAN 72
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 33.0 bits (76), Expect = 0.020
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
R+ V N+P VTED + E F + ++ + V+ + + F F+ F+S ++
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVK------VMRTRDGKSRRFGFVGFKSEEDAQ 55
Query: 108 QAMAFDGINFKGQSLKI 124
QA+ + F S KI
Sbjct: 56 QAVKYFNKTFIDTS-KI 71
>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 = 32.7 bits (75), Expect = 0.023
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 23/84 (27%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINL--------DKNFAFLEF 100
L+VGN+P+ T ++++ F + AG P + L K AF+EF
Sbjct: 3 LFVGNLPYDTTAEDLLAHF----------KNAGAP---PSVRLLTDKKTGKSKGCAFVEF 49
Query: 101 RSIDETTQAMAFDGINFKGQSLKI 124
+ + T+A+ KG+ KI
Sbjct: 50 DTAEAMTKALKLHHTLLKGR--KI 71
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 32.6 bits (75), Expect = 0.023
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 20/83 (24%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQI----NLDKNF---AFLEFR 101
+YV P T D++ EFF + G I +LDK F F+EF+
Sbjct: 2 VYVKGFPKDATLDDIQEFFEK----------FGKVN---NIRMRRDLDKKFKGSVFVEFK 48
Query: 102 SIDETTQAMAFDGINFKGQSLKI 124
+ ++ + + + + +K + L +
Sbjct: 49 TEEDAKKFLEKEKLKYKEKELTV 71
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM4 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 32.6 bits (75), Expect = 0.025
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 19/68 (27%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINL-----DKNFAFLEFRSI 103
L++ NIP VTE+++ E F Q G D+ A ++ S+
Sbjct: 2 LHLSNIPPSVTEEDLKELF---------TQTGGTVK-----AFKFFPKDRKMALIQMGSV 47
Query: 104 DETTQAMA 111
+E +A+
Sbjct: 48 EEAIEALI 55
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 32.4 bits (74), Expect = 0.028
Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 14/76 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
RLYV P +E + E F + V + + NFAF+EF S++
Sbjct: 1 RLYVRPFPPDTSESAIREIF-----------SPYGAVKEVK--MISNFAFVEFESLESAI 47
Query: 108 QAM-AFDGINFKGQSL 122
+A + G L
Sbjct: 48 RAKDSVHGKVLNNNPL 63
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 32.1 bits (74), Expect = 0.029
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNF---AFLEFRSIDE 105
+ + +PF TE+++ +FF SGL + + D A++EF S ++
Sbjct: 2 VRLRGLPFSATEEDIRDFF------SGLDIPPDGIHIVY--DDDGRPTGEAYVEFASPED 53
Query: 106 TTQAMAFDGINFKG 119
+A+ G
Sbjct: 54 ARRALRKHNNKMGG 67
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein
19 (RBM19) and similar proteins. This subfamily
corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 72
Score = 32.3 bits (74), Expect = 0.029
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 21/78 (26%)
Query: 54 IPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-------FAFLEFRSIDET 106
PF V E + EFF +P+ I + KN FAF++ +S ++
Sbjct: 8 APFNVKEKHIREFF--------------SPLKPVAIRIVKNDHGRKTGFAFVDLKSEEDL 53
Query: 107 TQAMAFDGINFKGQSLKI 124
+A+ + G+ +++
Sbjct: 54 KKALKRNKDYMGGRYIEL 71
>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 = 32.6 bits (75), Expect = 0.029
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 22/85 (25%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINL--DKN------FAFLEF 100
+Y+G +P+ +TE +++ F+Q G V INL DK FAFL +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQY----------GEIV---DINLVRDKKTGKSKGFAFLAY 58
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI 124
T A+ +GI G+++++
Sbjct: 59 EDQRSTILAVDNLNGIKLLGRTIRV 83
>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 = 32.5 bits (75), Expect = 0.031
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 22/85 (25%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRS 102
LYVG++ VTE + E F+ AG PVL+ ++ D +A++ F++
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSP----------AG-PVLSIRVCRDLITRRSLGYAYVNFQN 50
Query: 103 IDETTQAMAFDGINF---KGQSLKI 124
+ +A+ D +NF KG+ ++I
Sbjct: 51 PADAERAL--DTLNFDVIKGKPIRI 73
>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 = 32.3 bits (74), Expect = 0.032
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 13/66 (19%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLA----QAAGNPVLACQINLDKNFAFLEFRSID 104
L+VGN+ F ED + E F + +S + +G P K F ++EF S +
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRP---------KGFGYVEFSSQE 51
Query: 105 ETTQAM 110
A+
Sbjct: 52 AAQAAL 57
>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 = 32.5 bits (74), Expect = 0.034
Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 18/83 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFRS 102
L+V N+ F VT++++ +FF+ P+ + D + + F+ F
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVA-----------PIKHAVVVTDPETGESRGYGFVTFAM 50
Query: 103 IDETTQAMA-FDGINFKGQSLKI 124
+++ +A+A G+ L++
Sbjct: 51 LEDAQEALAKLKNKKLHGRILRL 73
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 32.2 bits (73), Expect = 0.034
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
++ L V N+ + +ED + E F + + + Q G P K +AF+EF S ++
Sbjct: 1 SKVLVVNNLSYSASEDSLQEVFEKATSIR-IPQNNGRP---------KGYAFVEFESAED 50
Query: 106 TTQAM 110
+A+
Sbjct: 51 AKEAL 55
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 32.2 bits (74), Expect = 0.036
Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 18/87 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
R+YV ++ ++ED++ F +A G + +C + D K + F+E+
Sbjct: 2 RIYVASVHPDLSEDDIKSVF----------EAFG-KIKSCSLAPDPETGKHKGYGFIEYE 50
Query: 102 SIDETTQAMA-FDGINFKGQSLKIRRP 127
+ A+A + + GQ L++ +
Sbjct: 51 NPQSAQDAIASMNLFDLGGQQLRVGKA 77
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 32.4 bits (73), Expect = 0.037
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
Q R+L++G + F T+D + E F + L+ +P Q + F F+ + ++
Sbjct: 1 QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCV-VMRDP----QTKRSRGFGFVTYSCVE 55
Query: 105 ETTQAM 110
E AM
Sbjct: 56 EVDAAM 61
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 32.0 bits (73), Expect = 0.038
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 11/57 (19%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
R +Y+GN+P +E+E+ E + P+ +I +KN AF+ F SI
Sbjct: 4 RNVYIGNLPESYSEEELREDLEKF-----------GPIDQIKIVKEKNIAFVHFLSI 49
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 31.9 bits (73), Expect = 0.038
Identities = 22/84 (26%), Positives = 36/84 (42%), Gaps = 19/84 (22%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVL--ACQINLDKNF-----AFLEFR 101
+ + NIPF VT+ E++ FF AG + I DK A++EF
Sbjct: 2 IKIKNIPFDVTKGEVLAFF------------AGIAIAEQGIHILYDKTGKTLGEAYVEFV 49
Query: 102 SIDETTQAMAFDGINFKGQSLKIR 125
S ++ +A KG+ + +R
Sbjct: 50 SEEDAMRAERLHRKKLKGREILLR 73
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 32.1 bits (73), Expect = 0.041
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 14/83 (16%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQ--QMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
R+YVGN+P + ++ + F + + L G P FAF+EF +
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPP-----------FAFVEFEDPRD 49
Query: 106 TTQAM-AFDGINFKGQSLKIRRP 127
A+ DG ++ G L++ P
Sbjct: 50 AEDAVYGRDGYDYDGYRLRVEFP 72
>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 = 32.0 bits (73), Expect = 0.049
Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 20/87 (22%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFRS 102
L V +P+ TE ++ ++F+ +L Q+ D K F F+ F
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTF-----------GELLMVQVKKDPKTGQSKGFGFVRFA- 49
Query: 103 IDETTQAMAFDGINF-KGQSLKIRRPH 128
D Q + G+ ++ P+
Sbjct: 50 -DYEDQVKVLSQRHMIDGRWCDVKIPN 75
>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 = 31.8 bits (73), Expect = 0.053
Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 18/85 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDK------NFAFLEFRS 102
L+V + TE E+ F++ V + D F F+ F S
Sbjct: 4 LFVSGLSTRTTEKELEALFSKF-----------GRVEEVLLMKDPETGESRGFGFVTFES 52
Query: 103 IDETTQAM-AFDGINFKGQSLKIRR 126
+++ A+ +G +G+ +K+ +
Sbjct: 53 VEDADAAIRDLNGKELEGRVIKVEK 77
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 31.6 bits (72), Expect = 0.054
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 15/81 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQIN---LDKNFAFLEFRSID 104
R+YVGN+P + E ++ + F + P+ A + FAF+EF
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKY-----------GPIKAIDLKNRRRGPPFAFVEFEDPR 49
Query: 105 ETTQAM-AFDGINFKGQSLKI 124
+ A+ DG +F G L++
Sbjct: 50 DAEDAVRGRDGYDFDGYRLRV 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 = 31.7 bits (72), Expect = 0.058
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 14/83 (16%)
Query: 49 LYVGNIPFGVTEDEMM----EFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
L+VGN+ DE+ EFF+++ LA V +I K F +++F S +
Sbjct: 3 LFVGNLNPNKDFDELKTAISEFFSKK----NLA------VQDVRIGSSKKFGYVDFESAE 52
Query: 105 ETTQAMAFDGINFKGQSLKIRRP 127
+ +A+ G G +K+ +
Sbjct: 53 DLEKALELTGKKLLGNEIKLEKA 75
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM1
of hnRNP A2/B1 which is an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Moreover, the
overexpression of hnRNP A2/B1 has been described in many
cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 81
Score = 31.6 bits (71), Expect = 0.064
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 17/88 (19%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFL 98
Q R+L++G + F TE+ + ++ Q L+ C + D + F F+
Sbjct: 1 QFRKLFIGGLSFETTEESLRNYYEQWGKLTD-----------CVVMRDPASKRSRGFGFV 49
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRR 126
F ++E AMA G+ ++ +R
Sbjct: 50 TFSCMNEVDAAMAARPHTIDGRVVEPKR 77
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 31.5 bits (72), Expect = 0.065
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 93 KNFAFLEFRSIDETTQAM-AFDGINFKGQSLKIR 125
++FAF+ FRS +E +A+ DG +KG+ L R
Sbjct: 42 QDFAFVTFRSEEERQKALEILDGFKWKGRVLSAR 75
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 31.1 bits (71), Expect = 0.072
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 17/84 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRS 102
+L V N+ FGV++D++ E F + + ++ D++ A + F
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEF-----------GALKKAAVHYDRSGRSLGTADVVFER 50
Query: 103 IDETTQAMA-FDGINFKGQSLKIR 125
+ +AM ++G+ G+ +KI+
Sbjct: 51 RADALKAMKQYNGVPLDGRPMKIQ 74
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 30.6 bits (70), Expect = 0.078
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 83 PVLACQINLDK-NFAFLEFRSIDETTQAM-AFDGINFKGQSLKIR 125
V ++ K FAF+EF + + +A+ +G+ F G+ L++
Sbjct: 10 NVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 31.0 bits (71), Expect = 0.078
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 15/80 (18%)
Query: 47 RRLYVGNIP-FGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
R++VGN+ V+++++ E F++ + G I+L K + F++F + ++
Sbjct: 1 SRVFVGNLNTDKVSKEDLEEIFSKYGKILG-------------ISLHKGYGFVQFDNEED 47
Query: 106 TTQAMA-FDGINFKGQSLKI 124
A+A +G GQ L I
Sbjct: 48 ARAAVAGENGREIAGQKLDI 67
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 31.0 bits (70), Expect = 0.086
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 14/78 (17%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD---KNFAFLEFRS 102
+ +L+VGN+P V + E+ EFF Q GN V+ +IN NF F+ F
Sbjct: 3 SHQLFVGNLPHDVDKSELKEFF----------QQYGN-VVELRINSGGKLPNFGFVVFDD 51
Query: 103 IDETTQAMAFDGINFKGQ 120
+ + ++ I F+G
Sbjct: 52 SEPVQKILSNRPIMFRGD 69
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 31.3 bits (71), Expect = 0.089
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAA----GNPV-LACQINLDKNFAFLEFRSI 103
LY+ N+P T+ E+ +F Q G+ A P A + D F F+S
Sbjct: 3 LYISNLPPDTTQLELESWFTQY----GVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSH 58
Query: 104 DETTQAMAFDG 114
+E +A+A +G
Sbjct: 59 EEAMEALALNG 69
>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 = 31.0 bits (71), Expect = 0.094
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 15/72 (20%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
L + + TE+++++ + A P+ ++ DK FAF+EF
Sbjct: 3 NTLILRGLDLLTTEEDILQAL---------SAIASVPIKDVRLIRDKLTGTSRGFAFVEF 53
Query: 101 RSIDETTQAMAF 112
S+++ TQ M
Sbjct: 54 PSLEDATQWMDA 65
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 30.9 bits (70), Expect = 0.098
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 15/77 (19%)
Query: 48 RLYVGNIPFG-VTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
RL++GN+P V+++++ F+ L+ QI L + F++F S +
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELA-------------QIVLKNAYGFVQFDSPESC 47
Query: 107 TQAM-AFDGINFKGQSL 122
A+ G +G+ L
Sbjct: 48 ANAINCEQGKMIRGRKL 64
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 31.1 bits (70), Expect = 0.11
Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 17/81 (20%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLE 99
+ +L+VGN+P + E E+ EFF + GN V+ +IN NF F+
Sbjct: 5 SHQLFVGNLPHDIDESELKEFF----------MSFGN-VVELRINTKGVGGKLPNFGFVV 53
Query: 100 FRSIDETTQAMAFDGINFKGQ 120
F + + + I F+G+
Sbjct: 54 FDDSEPVQRILGAKPIMFRGE 74
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 30.8 bits (69), Expect = 0.11
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 17/72 (23%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
Q R+L++G + F T++ + F Q L+ C + D N F F+
Sbjct: 1 QLRKLFIGGLSFETTDESLRSHFEQWGTLTD-----------CVVMRDPNTKRSRGFGFV 49
Query: 99 EFRSIDETTQAM 110
+ S++E AM
Sbjct: 50 TYSSVEEVDAAM 61
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 30.7 bits (70), Expect = 0.13
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 174 AIAGLNGMQLGDKKLIVQ 191
AI +NG Q+G K+L VQ
Sbjct: 56 AIKAMNGFQVGGKRLKVQ 73
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 30.3 bits (69), Expect = 0.13
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 17/59 (28%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
+L+VG + VTE+++ E+F+Q V + +I DK FAF+ F
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQY-----------GNVESVEIVTDKETGKKRGFAFVTF 48
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 30.3 bits (69), Expect = 0.14
Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 13/79 (16%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEF--RSIDET 106
LYVG + VTE ++ + F Q + + + AF+ F R E
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVVP-----------RQQCAFVTFTTREAAEK 52
Query: 107 TQAMAFDGINFKGQSLKIR 125
F+ + G+ LK++
Sbjct: 53 AAERLFNKLIINGRRLKLK 71
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM1
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 74
Score = 30.2 bits (68), Expect = 0.17
Identities = 23/86 (26%), Positives = 34/86 (39%), Gaps = 25/86 (29%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNF-----AFLEFRSI 103
LYVGN+ VTED + + F G PV +I DKN F+E+
Sbjct: 1 LYVGNLDPRVTEDILKQIFQ-----------VGGPVQNVKIIPDKNNKGVNYGFVEYHQS 49
Query: 104 DETTQAMAFDGINFKGQSLKIRRPHD 129
+ A+ Q+L R+ +
Sbjct: 50 HDAEIAL---------QTLNGRQIEN 66
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 29.9 bits (68), Expect = 0.19
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 13/83 (15%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGL---AQAAGNPVLACQINLDKNFAFLEFRSID 104
+L V N+PF T+ E+ E F+ + + + G+ + FAF+EF +
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGS---------HRGFAFVEFVTKQ 52
Query: 105 ETTQAM-AFDGINFKGQSLKIRR 126
E AM A + G+ L +
Sbjct: 53 EAQNAMEALKSTHLYGRHLVLEY 75
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 30.4 bits (69), Expect = 0.20
Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 18/93 (19%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFRS 102
LYV N+ D++ F + P++ I LD + FA+++F
Sbjct: 3 LYVRNVADATRPDDLRRLFGKY-----------GPIVDVYIPLDFYTRRPRGFAYVQFED 51
Query: 103 IDETTQAMAF-DGINFKGQSLKIRRPHDYQPTP 134
+ + A+ + D F G+ ++I+ + TP
Sbjct: 52 VRDAEDALYYLDRTRFLGREIEIQFAQGDRKTP 84
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 29.8 bits (68), Expect = 0.21
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 172 DQAIAGLNGMQLGDKKLIV 190
+AI +NGM L DKK+ V
Sbjct: 57 VRAIEKVNGMLLNDKKVFV 75
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 29.9 bits (68), Expect = 0.21
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 15/80 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEF---RSID 104
++YVGN+ T+ E+ + F + L + A NP FAF+EF R +
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSV-WVARNP---------PGFAFVEFEDPRDAE 50
Query: 105 ETTQAMAFDGINFKGQSLKI 124
+ +A+ DG G +++
Sbjct: 51 DAVRAL--DGRRICGNRVRV 68
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 30.1 bits (68), Expect = 0.22
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 93 KNFAFLEFRSIDETTQAMAFDGINFKGQSLKI 124
K FA++EF+S+D +A+ DG + G +L +
Sbjct: 45 KGFAYIEFKSVDGVEKALELDGSDLGGGNLVV 76
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 30.3 bits (69), Expect = 0.24
Identities = 15/67 (22%), Positives = 26/67 (38%), Gaps = 14/67 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------------F 95
RL + N+P V E ++ E F + +S A + +I D +
Sbjct: 2 RLSIRNLPKSVDEKKLKELFLK--AVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGY 59
Query: 96 AFLEFRS 102
F+EF +
Sbjct: 60 GFVEFTN 66
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 29.6 bits (66), Expect = 0.26
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQ 108
LYV N+ +ED + + F Q NP ++ +++AF+ F S ++
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQ-----------FNPGCVERVKKIRDYAFVHFTSREDAVH 52
Query: 109 AM-AFDGINFKGQSLKI 124
AM +G +G +++
Sbjct: 53 AMNNLNGTELEGSCIEV 69
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of RBM23
remains unclear, it shows high sequence homology to
RBM39 and contains two RRMs. It may possibly function as
a pre-mRNA splicing factor. .
Length = 73
Score = 29.5 bits (67), Expect = 0.27
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 17/82 (20%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRSI 103
+V + V E ++ EFF AG V +I D+N A++EF
Sbjct: 3 FVMQLSLKVRERDLYEFF----------SKAG-KVRDVRIIRDRNSRRSKGVAYVEFYDE 51
Query: 104 DETTQAMAFDGINFKGQSLKIR 125
+ A+ G GQ + ++
Sbjct: 52 ESVPLALGLTGQRLLGQPIMVQ 73
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 29.4 bits (67), Expect = 0.37
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 17/64 (26%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNF------AFLEFR 101
+L+VG +P TE+++ F + GN + I DK+ AF++F
Sbjct: 1 KLFVGQLPKTATEEDVRALFEE----------YGN-IEEVTIIRDKDTGQSKGCAFVKFS 49
Query: 102 SIDE 105
S +E
Sbjct: 50 SREE 53
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 29.3 bits (66), Expect = 0.37
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 15/72 (20%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN----FAFLEFRS 102
R +YV +I VTE+++ F S Q V+ C++ D N FAF+EF
Sbjct: 3 RTVYVSDIDQQVTEEQLAALF------SNCGQ-----VVDCRVCGDPNSVLRFAFIEFTD 51
Query: 103 IDETTQAMAFDG 114
+ A++ G
Sbjct: 52 EEGARAALSLSG 63
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 80
Score = 29.2 bits (66), Expect = 0.39
Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 20/87 (22%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQI----NLDKNFAFLEFRS 102
++VG + VT++E+ E F++ +L + N FAF++F
Sbjct: 4 YSIFVGQLSPDVTKEELNERFSRH-----------GKILEVNLIKRANHTNAFAFIKFE- 51
Query: 103 IDETTQAMAFDGIN---FKGQSLKIRR 126
E A A + N K +++ ++
Sbjct: 52 -REQAAARAVESENHSMLKNKTMHVQY 77
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 28.8 bits (65), Expect = 0.48
Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 11/78 (14%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
R+++VG + +TE+++ ++F+Q ++ + P A FAF+ F E
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIP--KPFRA--------FAFVTFAD-PEV 49
Query: 107 TQAMAFDGINFKGQSLKI 124
Q++ + KG S+ +
Sbjct: 50 AQSLCGEDHIIKGVSVHV 67
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 28.8 bits (65), Expect = 0.50
Identities = 15/69 (21%), Positives = 24/69 (34%), Gaps = 22/69 (31%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQI------NLDKNFAFLEFRS 102
L VGN+P T++ L G V C + K + F+E+
Sbjct: 2 LCVGNLPLEFTDE----------QFRELVSPFG-AVERCFLVYSESTGESKGYGFVEY-- 48
Query: 103 IDETTQAMA 111
++A A
Sbjct: 49 ---ASKASA 54
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 29.0 bits (65), Expect = 0.50
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
++ V N+PF T+ ++ F+ L + V + FAF+EF + E
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVR------VPKKFDQSARGFAFVEFSTAKEAL 55
Query: 108 QAM-AFDGINFKGQSLKIR 125
AM A + G+ L ++
Sbjct: 56 NAMNALKDTHLLGRRLVLQ 74
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 29.1 bits (66), Expect = 0.53
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 12/83 (14%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-----KNFAFLEFRS 102
RLYV N+ VTE++++ F + + S + I L K AF+ F S
Sbjct: 3 RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKN------MFDIRLMTEGRMKGQAFVTFPS 56
Query: 103 IDETTQAMA-FDGINFKGQSLKI 124
+ T+A+ +G KG+ + I
Sbjct: 57 EEIATKALNLVNGYVLKGKPMVI 79
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 80
Score = 28.9 bits (65), Expect = 0.61
Identities = 8/25 (32%), Positives = 19/25 (76%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQ 69
+ ++++VG +P VTE ++ ++F+Q
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQ 25
Score = 26.2 bits (58), Expect = 5.3
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 159 KIFIGGLPNYLNEDQ 173
KIF+GGLP + E
Sbjct: 4 KIFVGGLPPNVTETD 18
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 28.6 bits (64), Expect = 0.61
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 14/76 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
+++VGN+ +++E L L +A G VL+C + + FAF+ R
Sbjct: 2 KIFVGNVDEDTSQEE----------LRALFEAYGA-VLSCAVM--RQFAFVHLRGEAAAD 48
Query: 108 QAMA-FDGINFKGQSL 122
+A+ +G G+ L
Sbjct: 49 RAIEELNGRELHGRKL 64
>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 = 28.5 bits (64), Expect = 0.71
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 16/85 (18%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD----KNFAFLEFRS 102
+RL+V NIPF + ++ + F Q P+L +I + K F F+ F +
Sbjct: 1 KRLHVSNIPFRFRDPDLRQMFGQF-----------GPILDVEIIFNERGSKGFGFVTFAN 49
Query: 103 IDETTQAM-AFDGINFKGQSLKIRR 126
+ +A G +G+ +++
Sbjct: 50 SADADRAREKLHGTVVEGRKIEVNN 74
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 28.4 bits (63), Expect = 0.78
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 10/62 (16%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQ 108
L++ NIP VTE+++ F G V A + D A L+ +++E Q
Sbjct: 6 LHLSNIPQSVTEEDLRTLFAN----------TGGTVKAFKFFQDHKMALLQMSTVEEAIQ 55
Query: 109 AM 110
A+
Sbjct: 56 AL 57
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 28.5 bits (64), Expect = 0.79
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 19/84 (22%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINL--DKNFAFLEFRSI 103
+R +Y+GNI +TE+++ F+Q + +N +KN AF+ F +I
Sbjct: 3 SRNVYIGNIDDSLTEEKLRNDFSQYGEIE-------------SVNYLREKNCAFVNFTNI 49
Query: 104 DETTQAMAFDGINFKG--QSLKIR 125
+A+ DG+ + KI
Sbjct: 50 SNAIKAI--DGVKSHPLFKKFKIS 71
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 28.2 bits (63), Expect = 0.91
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 48 RLYVGNIPFGVTEDEMMEFF 67
R+YVGN+P V E ++ + F
Sbjct: 1 RIYVGNLPSDVREKDLEDLF 20
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by
YNL110C from Saccharomyces cerevisiae, and localizes to
the nucleoplasm and nucleolus. Nop15p has been
identified as a component of a pre-60S particle. It
interacts with RNA components of the early pre-60S
particles. Furthermore, Nop15p binds directly to a
pre-rRNA transcript in vitro and is required for
pre-rRNA processing. It functions as a ribosome
synthesis factor required for the 5' to 3' exonuclease
digestion that generates the 5' end of the major, short
form of the 5.8S rRNA as well as for processing of 27SB
to 7S pre-rRNA. Nop15p also play a specific role in
cell cycle progression. Nop15p contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 28.2 bits (63), Expect = 0.94
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQ 69
+Y+G++P G E E+ ++F+Q
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQ 22
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs) connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 27.9 bits (63), Expect = 1.1
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 13/78 (16%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQ 108
L++ N+P T++ + FNQ G + P + AF+EF + ++ T
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQF---PGFKEVRLVPR--------RGIAFVEFETEEQATV 53
Query: 109 AM-AFDG-INFKGQSLKI 124
A+ A G G ++KI
Sbjct: 54 ALQALQGFKITPGHAMKI 71
>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 = 28.0 bits (63), Expect = 1.1
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 19/69 (27%)
Query: 49 LYVGNIPFGVTEDEMMEFF-------NQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFR 101
LYVG + V E + F + Q+ L Q + FAF+EF
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQ------------KHRGFAFVEFE 48
Query: 102 SIDETTQAM 110
++ A+
Sbjct: 49 EPEDAAAAI 57
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 27.8 bits (62), Expect = 1.2
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
R++VG I F E+++ +FF+Q + + ++ + + K + F+ F + ++
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVK------IVNDRAGVSKGYGFVTFETQEDAQ 57
Query: 108 QAMA-FDGINFKGQSLKI 124
+ + + + F+ + L I
Sbjct: 58 KILQEANRLCFRDKKLNI 75
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 27.5 bits (61), Expect = 1.3
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 13/63 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
+L+VGN+P TE E+ F Q VL C I KN+ F+
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQY-----------GKVLECDII--KNYGFVHMDDKTAAD 48
Query: 108 QAM 110
+A+
Sbjct: 49 EAI 51
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 28.0 bits (62), Expect = 1.3
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 11/65 (16%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPV-LACQINLDKNFAFLEFRSIDETT 107
L++ N+P+ TE+E++E L + G V C + ++N AF+EF +++
Sbjct: 5 LHLRNLPWECTEEELIE----------LCKPFGKIVNTKCNVGANRNQAFVEFADLNQAI 54
Query: 108 QAMAF 112
+++
Sbjct: 55 AMVSY 59
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 27.7 bits (61), Expect = 1.5
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 165 LPNYLNEDQAIAGLNGMQLGDKKLIV 190
+ NY AIA LNG +LGDK L V
Sbjct: 50 MTNYEEAAMAIASLNGYRLGDKILQV 75
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 27.7 bits (61), Expect = 1.5
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN----FAFLEFRSID 104
LYVGN+ VTE +++ F+Q P +C++ +D + F+EF
Sbjct: 2 LYVGNLSRDVTEALILQLFSQI-----------GPCKSCKMIMDTAGNDPYCFVEFFEHR 50
Query: 105 ETTQAM-AFDGINFKGQSLKI 124
++ A +G G+ +K+
Sbjct: 51 HAAASLAAMNGRKIMGKEVKV 71
>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 = 27.6 bits (62), Expect = 1.6
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 92 DKNFAFLEFRSIDETTQA 109
+N+A++E+ SI+ A
Sbjct: 33 GRNYAYIEYESIEAAQAA 50
>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 = 27.5 bits (61), Expect = 1.6
Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
+L++G + F E + + F++ +S + V + + F F+ F + D+
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVV-----VKDRETQRSRGFGFVTFENPDDAK 56
Query: 108 QAM-AFDGINFKGQSLKI 124
AM A +G + G+ +++
Sbjct: 57 DAMMAMNGKSVDGRQIRV 74
>gnl|CDD|104071 PRK09629, PRK09629, bifunctional thiosulfate
sulfurtransferase/phosphatidylserine decarboxylase;
Provisional.
Length = 610
Score = 29.7 bits (66), Expect = 1.6
Identities = 37/159 (23%), Positives = 59/159 (37%), Gaps = 3/159 (1%)
Query: 6 EVLNTGAAGQIPANVIIPETTVAAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMME 65
EV AA V P A A V V +T + + Y G+ G + + +
Sbjct: 270 EVPTVAAAPIEAVEVAQPAAPAQPAPAETVEPVRATEPSKGSQKYSGHSSSGPSMKDRLF 329
Query: 66 FFNQQMHLSGLAQAAGNPVLACQINLDKN--FAFLEFRSIDETTQAMAFDGINFKGQSLK 123
+Q + L V C++ KN A+ R + +QA+ D +++ +
Sbjct: 330 IISQYLLPHHLLSRLAGCVAECRVRWFKNAFTAWFARRYQVDMSQALVEDLTSYEHFNAF 389
Query: 124 IRRPHDYQPTPGVTDNAAVAVPA-GVISTVVPDSPHKIF 161
R P T A+ PA G IS + P +IF
Sbjct: 390 FTRALKADARPLDTTPGAILSPADGAISQLGPIDHGRIF 428
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 27.4 bits (61), Expect = 1.7
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 83 PVLACQINLDKNFAFLEFRSIDETTQA 109
P++ C I K FAF+EF ++ T+A
Sbjct: 26 PLVRCDIR--KTFAFVEFEDSEDATKA 50
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 29.0 bits (65), Expect = 2.1
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 16/92 (17%)
Query: 38 VGSTITRQARR---------LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQ 88
VG I + R LYV N+ V ED++ E F + ++ A V+
Sbjct: 161 VGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA------VMKDG 214
Query: 89 INLDKNFAFLEFRSIDETTQAM-AFDGINFKG 119
+ FAF+ F ++ +A+ +G
Sbjct: 215 SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
>gnl|CDD|219933 pfam08612, Med20, TATA-binding related factor (TRF) of subunit 20
of Mediator complex. This family of proteins is related
to TATA-binding protein (TBP). TBP is a highly conserved
RNA polymerase II general transcription factor that
binds to the core promoter and initiates assembly of the
preinitiation complex. Human TRF has been shown to
associate with an RNA polymerase II-SRB complex. This
Med20 subunit of Mediator is found in the non-essential
part of the head.
Length = 197
Score = 28.4 bits (64), Expect = 2.1
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 145 PAGVISTVVPDSPHKIFIGGLPNYLNEDQAIAGLNGM--QLGD 185
I+T+V DS ++ + L ++ + Q + G G +LGD
Sbjct: 78 NNTAITTLVADSFFQLLMEKLQSFWTQRQTVKGEGGGTYELGD 120
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. This family also includes the sex-lethal
protein (SXL) from Drosophila melanogaster. SXL governs
sexual differentiation and X chromosome dosage
compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own pre-mRNA
and promotes female-specific alternative splicing. It
contains an N-terminal Gly/Asn-rich domain that may be
responsible for the protein-protein interaction, and
tandem RRMs that show high preference to bind
single-stranded, uridine-rich target RNA transcripts. .
Length = 77
Score = 27.3 bits (61), Expect = 2.1
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 164 GLPNYLNE---DQAIAGLNGMQLGDKKLIVQRA 193
G +Y++E +AI LNG ++ +K+L V A
Sbjct: 45 GFVDYVDENDAQKAINTLNGFEIRNKRLKVSYA 77
>gnl|CDD|165574 PHA03330, PHA03330, putative primase; Provisional.
Length = 771
Score = 28.9 bits (64), Expect = 2.3
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 6/63 (9%)
Query: 161 FIGGLPNYLNEDQA-IAGLNGMQLGDKKLIVQRASVGA-----KNASGQQAPVQIQVPGL 214
F L + N Q+ A L + D ++ + R S G K G Q Q+P L
Sbjct: 610 FPDELEFFSNPGQSPSACLAAVPADDLRIFLPRLSSGMLEQLEKEEEGAQEDAAHQMPAL 669
Query: 215 TQV 217
+
Sbjct: 670 DEA 672
>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM1 of the CPEB family of proteins
that bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate
their translation. CPEB proteins are well conserved in
both, vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins have been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bind to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The
second subfamily includes CPEB-2, CPEB-3, CPEB-4, and
related protiens. Due to high sequence similarity,
members in this subfamily may share similar expression
patterns and functions. CPEB-2 is an RNA-binding
protein that is abundantly expressed in testis and
localized in cytoplasm in transfected HeLa cells. It
preferentially binds to poly(U) RNA oligomers and may
regulate the translation of stored mRNAs during
spermiogenesis. CPEB-2 impedes target RNA translation
at elongation; it directly interacts with the
elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a Zn-finger motif. CPEB-2, -3, and -4 have
conserved nuclear export signals that are not present
in CPEB-1. .
Length = 112
Score = 27.6 bits (61), Expect = 2.6
Identities = 7/21 (33%), Positives = 16/21 (76%)
Query: 47 RRLYVGNIPFGVTEDEMMEFF 67
R+++VG +P+ +TE +++ F
Sbjct: 1 RKVFVGGLPWDITEADILNSF 21
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog of
DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 27.1 bits (60), Expect = 2.8
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 7/76 (9%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQ 108
++VG I + E E+ FF + + + ++ + + K + F+ F D Q
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVK------IITDRTGVSKGYGFVSF-YDDVDVQ 60
Query: 109 AMAFDGINFKGQSLKI 124
+ INF G+ LK+
Sbjct: 61 KIVESQINFHGKKLKL 76
>gnl|CDD|221988 pfam13223, DUF4031, Protein of unknown function (DUF4031). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria and
viruses. Proteins in this family are typically between
91 and 130 amino acids in length. There is a conserved
HYD sequence motif.
Length = 83
Score = 26.8 bits (60), Expect = 3.1
Identities = 14/29 (48%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 22 IPETTVAAA-AAAAVPVVGSTITRQARRL 49
+PE A A AA AVPV I RRL
Sbjct: 51 VPEERRAEAVAAGAVPVDRREIVALVRRL 79
>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 = 27.0 bits (60), Expect = 3.1
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 93 KNFAFLEFRSIDETTQAM 110
+ FAF+EF S++E T+ M
Sbjct: 45 RGFAFVEFMSLEEATRWM 62
>gnl|CDD|205122 pfam12875, DUF3826, Protein of unknown function (DUF3826). This is
a putative sugar-binding family.
Length = 187
Score = 28.2 bits (63), Expect = 3.1
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 158 HKIFIGGLPNYLNEDQAIAGLNGMQLG 184
H F L YL E+Q A +GM G
Sbjct: 82 HFAFPADLSLYLTEEQIEAVKDGMTYG 108
>gnl|CDD|236242 PRK08326, PRK08326, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 311
Score = 28.4 bits (64), Expect = 3.3
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 42 ITRQARRLYVGNIPFGVTEDEMMEFFNQQ-MH-LSGLAQAAGNPVLACQINLDKNFAFLE 99
+ + LY IPF ++ DE +++ + L + +A G PV +I++D + LE
Sbjct: 248 LIDEIFALYGDQIPFELSNDEFVDYAADRGQRRLGAIERARGRPVE--EIDVDYSPEQLE 305
Query: 100 FRSIDE 105
+E
Sbjct: 306 DTFAEE 311
>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 = 26.3 bits (58), Expect = 3.9
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 12/75 (16%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQA 109
YVGNIP T+ +++ F + +L + D+ FAF++ + ++ A
Sbjct: 4 YVGNIPPYTTQADLIPLFQNFGY-----------ILEFRHQPDRGFAFVKLDTHEQAAMA 52
Query: 110 M-AFDGINFKGQSLK 123
+ G G+ L+
Sbjct: 53 IVQLQGFPVHGRPLR 67
>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM2 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 93
Score = 26.8 bits (60), Expect = 4.0
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 48 RLYVGNIPFGVTEDEMMEFF 67
+Y G +P VT++++ EFF
Sbjct: 4 TVYCGKLPKKVTDEDLREFF 23
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 26.6 bits (58), Expect = 4.1
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 16/81 (19%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN----FAFLEFRSID 104
LYVGN+ VTE +++ F+Q P +C++ + + F+EF
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQI-----------GPCKSCKMITEHTSNDPYCFVEFYEHR 50
Query: 105 ETTQAM-AFDGINFKGQSLKI 124
+ A+ A +G G+ +K+
Sbjct: 51 DAAAALAAMNGRKILGKEVKV 71
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 26.3 bits (58), Expect = 4.5
Identities = 14/65 (21%), Positives = 32/65 (49%), Gaps = 13/65 (20%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHL--SGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
++V N+P VTE++++ + + + ++ G K A +EF + ++
Sbjct: 10 IHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNG-----------KKQALVEFATEEQA 58
Query: 107 TQAMA 111
T+A+A
Sbjct: 59 TEALA 63
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 86
Score = 26.6 bits (58), Expect = 4.5
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 165 LPNYLNEDQAIAGLNGMQLGDKKLIV 190
+ NY AIA LNG +LGD+ L V
Sbjct: 52 MTNYDEAAMAIASLNGYRLGDRVLQV 77
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 26.6 bits (58), Expect = 4.7
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 165 LPNYLNEDQAIAGLNGMQLGDKKLIV 190
+ NY AIA LNG +LGD+ L V
Sbjct: 52 MTNYDEAAMAIASLNGYRLGDRVLQV 77
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 26.1 bits (57), Expect = 4.7
Identities = 13/54 (24%), Positives = 30/54 (55%), Gaps = 13/54 (24%)
Query: 48 RLYVGNIPFGVTEDEMMEFF-NQQMHLSGLAQAAGNPVLACQINLDKNFAFLEF 100
+LY+GN+ VT +++ + F ++++ L+G Q+ L +AF+++
Sbjct: 3 KLYIGNLSPAVTAEDLRQLFGDRKLPLTG------------QVLLKSGYAFVDY 44
>gnl|CDD|241195 cd12751, RRM5_RBM12, RNA recognition motif 5 in RNA-binding
protein 12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM5 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RBMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative
transmembrane domains. The biological role of RBM12
remains unclear. .
Length = 76
Score = 26.1 bits (57), Expect = 6.1
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 51 VGNIPFGVTEDEMMEFF 67
V N+PF VT DE+++FF
Sbjct: 6 VQNMPFTVTVDEILDFF 22
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 26.0 bits (58), Expect = 6.4
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 164 GLPNYLNEDQA---IAGLNGMQLGDKKLIVQRA 193
G N+ N + A + LNG ++ KKL V RA
Sbjct: 45 GFVNFENHEAAQKAVEELNGKEVNGKKLYVGRA 77
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 25.7 bits (57), Expect = 7.2
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQ 108
++VG++ VT+ + E F + A+ +PV K + F+ F DE +
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTG----RSKGYGFVRFGDEDERDR 59
Query: 109 AM 110
A+
Sbjct: 60 AL 61
>gnl|CDD|178443 PLN02851, PLN02851, 3-hydroxyisobutyryl-CoA hydrolase-like protein.
Length = 407
Score = 27.3 bits (60), Expect = 7.4
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 136 VTDNAAVAVPAGVISTVVPDSPHKIFIGGLPNYLNEDQAIAG--LNGMQL 183
VTD A P + PD+ ++ LP YL E A+ G LNG+++
Sbjct: 165 VTDKTVFAHPEVQMG-FHPDAGASYYLSRLPGYLGEYLALTGQKLNGVEM 213
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 27.7 bits (61), Expect = 7.4
Identities = 15/101 (14%), Positives = 24/101 (23%)
Query: 127 PHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIGGLPNYLNEDQAIAGLNGMQLGDK 186
G + S V G P+ ++ + +
Sbjct: 93 GPGPGRPMGQQMGGPGTASNLLQSLNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQ 152
Query: 187 KLIVQRASVGAKNASGQQAPVQIQVPGLTQVGQAGPATECP 227
+ Q S QQ Q Q G+ Q Q + P
Sbjct: 153 QSSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQP 193
>gnl|CDD|188060 TIGR00531, BCCP, acetyl-CoA carboxylase, biotin carboxyl carrier
protein. This model is designed to identify biotin
carboxyl carrier protein as a peptide of acetyl-CoA
carboxylase. Scoring below the trusted cutoff is a
related protein encoded in a region associated with
polyketide synthesis in the prokaryote Saccharopolyspora
hirsuta, and a reported chloroplast-encoded biotin
carboxyl carrier protein that may be highly derived from
the last common ancestral sequence. Scoring below the
noise cutoff are biotin carboxyl carrier domains of
other enzymes such as pyruvate carboxylase.The gene name
is accB or fabE [Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 156
Score = 26.7 bits (59), Expect = 7.8
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 184 GDKKLIVQRASVGAKNASGQQ--APVQIQVPGLTQVGQAGPATECPVPVA 231
+ ++ + +A+ AK ++ QQ APV QVP PA P P
Sbjct: 26 EEFEVRLSKAAAAAKKSAVQQAAAPVPAQVPAAPSAQAPAPAVCAPAPAK 75
>gnl|CDD|215900 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.
Length = 254
Score = 27.2 bits (61), Expect = 7.8
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 51 VGNIPFGVTEDEMMEFFNQQ 70
VGNIP+ +T + + +
Sbjct: 98 VGNIPYNITTPIVKKLLFES 117
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 25.7 bits (56), Expect = 7.9
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 167 NYLNEDQAIAGLNGMQLGDKKLIVQ 191
N + AI +NG Q+G K+L VQ
Sbjct: 55 NPDSAQAAIQAMNGFQIGTKRLKVQ 79
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM1 of FCA, a gene
controlling flowering time in Arabidopsis, encoding a
flowering time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains),
and a WW protein interaction domain. .
Length = 80
Score = 25.7 bits (56), Expect = 8.1
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQ 69
+L+VG++P +TE E+ F +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEE 22
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM2 of the sex-lethal protein (SXL) which
governs sexual differentiation and X chromosome dosage
compensation in Drosophila melanogaster. It induces
female-specific alternative splicing of the transformer
(tra) pre-mRNA by binding to the tra uridine-rich
polypyrimidine tract at the non-sex-specific 3' splice
site during the sex-determination process. SXL binds
also to its own pre-mRNA and promotes female-specific
alternative splicing. SXL contains an N-terminal
Gly/Asn-rich domain that may be responsible for the
protein-protein interaction, and tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), that show high
preference to bind single-stranded, uridine-rich target
RNA transcripts. .
Length = 79
Score = 25.6 bits (56), Expect = 8.5
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 18/83 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDK------NFAFLEFRS 102
LYV N+P +TEDE+ + F +A GN ++ C + DK AF+ +
Sbjct: 3 LYVTNLPRQLTEDELRKIF----------EAYGN-IVQCNLLRDKSTGLPRGVAFVRYDK 51
Query: 103 IDETTQAM-AFDGINFKGQSLKI 124
+E A+ + +G G ++ +
Sbjct: 52 REEAQAAISSLNGTIPPGSTMPL 74
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in
yeast. Yra1p is associated with Pse1p and Kap123p, two
members of the beta-importin family, further mediating
transport of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission
yeast as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 25.5 bits (56), Expect = 9.4
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 51 VGNIPFGVTEDEMMEFFNQQM 71
V N+P VTE ++ E+F Q+
Sbjct: 4 VSNLPKDVTEAQIREYFVSQI 24
>gnl|CDD|187863 cd09732, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein of this family often fused to HTH domain; Some
proteins could have an additional fusion with
RecB-family nuclease domain; Core domain appears to
have a Rossmann-like fold; loosely associated with
CRISPR/Cas systems; also known as TM1812 family.
Length = 221
Score = 26.8 bits (60), Expect = 9.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 54 IPFGVTEDEMMEFFN 68
IP G +EDE+ E F+
Sbjct: 79 IPDGRSEDELWEIFD 93
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
0.316 0.133 0.381
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: 11,935,174
Number of extensions: 1152034
Number of successful extensions: 1691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1629
Number of HSP's successfully gapped: 197
Length of query: 231
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 137
Effective length of database: 6,768,326
Effective search space: 927260662
Effective search space used: 927260662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.6 bits)