RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10320
(262 letters)
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 134 bits (338), Expect = 2e-40
Identities = 55/72 (76%), Positives = 64/72 (88%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
+RLIVENLSSRVSWQDLKDFMR+ GEV YADAHK+ NEGVVEF + SDMK+A++KLD
Sbjct: 1 YRLIVENLSSRVSWQDLKDFMRKAGEVTYADAHKQRPNEGVVEFATYSDMKRAIEKLDGT 60
Query: 174 ELNGRRIRLIED 185
ELNGR+I+LIED
Sbjct: 61 ELNGRKIKLIED 72
Score = 26.9 bits (60), Expect = 3.0
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 40 GFVEFEDYRDADDAVYELNGKSLLGERVTV 69
G VEF Y D A+ +L+G L G ++ +
Sbjct: 40 GVVEFATYSDMKRAIEKLDGTELNGRKIKL 69
>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 = 121 bits (306), Expect = 1e-35
Identities = 54/70 (77%), Positives = 60/70 (85%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
+VYIG LPY RERD+E+F KGYGRIR++ LKNGFGFVEFED RDADDAVYELNGK L G
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINLKNGFGFVEFEDPRDADDAVYELNGKELCG 60
Query: 65 ERVTVEIAKG 74
ERV VE A+G
Sbjct: 61 ERVIVEHARG 70
Score = 29.2 bits (66), Expect = 0.41
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
R+ + L R +D++ F + G + + + + G VEFE D A+ +L+ E
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRI--REINLK-NGFGFVEFEDPRDADDAVYELNGKE 57
Query: 175 LNGRRI 180
L G R+
Sbjct: 58 LCGERV 63
>gnl|CDD|241210 cd12766, RRM2_SRSF6, RNA recognition motif 2 found in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subgroup corresponds to the RRM2 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, an essential splicing
regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 107 bits (268), Expect = 5e-30
Identities = 56/73 (76%), Positives = 63/73 (86%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
+RLIVENLSSR SWQDLKDFMRQ GEV YADAHK NEGV+EF S SDMK+AL+KLD
Sbjct: 1 YRLIVENLSSRCSWQDLKDFMRQAGEVTYADAHKERANEGVIEFRSYSDMKRALEKLDGT 60
Query: 174 ELNGRRIRLIEDK 186
E+NGR+IRL+EDK
Sbjct: 61 EINGRKIRLVEDK 73
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of 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). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising 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. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It 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 with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 103 bits (259), Expect = 1e-28
Identities = 38/71 (53%), Positives = 46/71 (64%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
R++V L SWQDLKDF RQ G+V YAD + EGVVEF S DM++AL KLD
Sbjct: 1 FRVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGT 60
Query: 174 ELNGRRIRLIE 184
E GRR+R+ E
Sbjct: 61 EFRGRRVRVEE 71
Score = 43.0 bits (102), Expect = 5e-06
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN------GFGFVEFEDYRDADDAVYELN 58
+V + GLP G +DL+ F + G DV + G G VEF D + A+ +L+
Sbjct: 2 RVVVSGLPEGASWQDLKDFGRQAG---DVTYADVDRDQEGEGVVEFTSQEDMERALRKLD 58
Query: 59 GKSLLGERVTVE 70
G G RV VE
Sbjct: 59 GTEFRGRRVRVE 70
>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM2 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4), a splicing
regulatory serine/arginine (SR) protein that plays an
important role in both constitutive splicing and
alternative splicing of many pre-mRNAs. For instance, it
interacts with heterogeneous nuclear ribonucleoproteins,
hnRNP G and hnRNP E2, and further regulates the 5'
splice site of tau exon 10, whose misregulation causes
frontotemporal dementia. SFRS4 also induces production
of HIV-1 vpr mRNA through the inhibition of the
5'-splice site of exon 3. In addition, SRSF4 activates
splicing of the cardiac troponin T (cTNT) alternative
exon by direct interactions with the cTNT exon 5
enhancer RNA. SRSF4 can shuttle between the nucleus and
cytoplasm. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine-rich region, an
internal region homologous to the RRM, and a very long,
highly phosphorylated C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 102 bits (255), Expect = 3e-28
Identities = 54/72 (75%), Positives = 63/72 (87%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
+RLIVENLSSR SWQDLKD+MRQ GEV YADAHK +NEGV+EF S SDMK+AL+KLD
Sbjct: 1 YRLIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRKNEGVIEFRSYSDMKRALEKLDGT 60
Query: 174 ELNGRRIRLIED 185
E+NGR+IRL+ED
Sbjct: 61 EVNGRKIRLVED 72
>gnl|CDD|241209 cd12765, RRM2_SRSF5, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM2 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5), is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 75
Score = 102 bits (255), Expect = 4e-28
Identities = 52/74 (70%), Positives = 63/74 (85%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
R+++RLIVENLSSRVSWQDLKDFMRQ GEV +ADAH+ NEGVVEF S SD+K A++KL
Sbjct: 1 RTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAHRPKLNEGVVEFASYSDLKNAIEKL 60
Query: 171 DNAELNGRRIRLIE 184
E+NGR+I+LIE
Sbjct: 61 SGKEINGRKIKLIE 74
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 97.3 bits (242), Expect = 3e-26
Identities = 47/70 (67%), Positives = 58/70 (82%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
+VYIG L Y VRE+D+++F GYG++ ++ LKNG+GFVEFED RDADDAVYELNGK L G
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLKNGYGFVEFEDSRDADDAVYELNGKDLCG 60
Query: 65 ERVTVEIAKG 74
ERV VE A+G
Sbjct: 61 ERVIVEHARG 70
Score = 28.7 bits (64), Expect = 0.64
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
R+ + LS V +D++ F G++ D + G VEFE S D A+ +L+ +
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLKNGY---GFVEFEDSRDADDAVYELNGKD 57
Query: 175 LNGRRI 180
L G R+
Sbjct: 58 LCGERV 63
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or
splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4
is a splicing regulatory serine/arginine (SR) protein
that plays an important role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
For instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4
also induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In
addition, it activates splicing of the cardiac troponin
T (cTNT) alternative exon by direct interactions with
the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between
the nucleus and cytoplasm. It contains an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 87.4 bits (216), Expect = 2e-22
Identities = 51/73 (69%), Positives = 59/73 (80%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
+VYIG L Y RERD+E+F KGYG+I +V LKNG+GFVEF+D RDADDAVYELNGK L G
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCG 60
Query: 65 ERVTVEIAKGIDR 77
ERV VE A+G R
Sbjct: 61 ERVIVEHARGPRR 73
Score = 26.5 bits (58), Expect = 4.4
Identities = 17/66 (25%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
R+ + LS + +D++ F + G++ D + G VEF+ D A+ +L+ +
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDLKNGY---GFVEFDDLRDADDAVYELNGKD 57
Query: 175 LNGRRI 180
L G R+
Sbjct: 58 LCGERV 63
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 85.8 bits (212), Expect = 8e-22
Identities = 46/69 (66%), Positives = 56/69 (81%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
+V+IG L RE+D+E+F KGYGRIRD+ LK GFGFVEF+D RDADDAVYEL+GK L
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFDDPRDADDAVYELDGKELCN 60
Query: 65 ERVTVEIAK 73
ERVT+E A+
Sbjct: 61 ERVTIEHAR 69
>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 = 84.2 bits (209), Expect = 3e-21
Identities = 35/73 (47%), Positives = 49/73 (67%), Gaps = 3/73 (4%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN--GFGFVEFEDYRDADDAVYELNGKS 61
KVY+G L +R+LE + YG +R V + +N GF FVEFED RDA+DAV L+G+
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60
Query: 62 LLGERVTVEIAKG 74
+ G RV VE+++G
Sbjct: 61 ICGNRVRVELSRG 73
Score = 29.5 bits (67), Expect = 0.36
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
++ V NL R + ++L+D + G + + VEFE D + A+ LD
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60
Query: 175 LNGRRIR 181
+ G R+R
Sbjct: 61 ICGNRVR 67
>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 = 74.6 bits (184), Expect = 2e-17
Identities = 32/79 (40%), Positives = 46/79 (58%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
G K+++ GL E++LE +GR+ +V ++K+ GFGFV FE DAD A+
Sbjct: 1 GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60
Query: 55 YELNGKSLLGERVTVEIAK 73
+LNGK L G + VE AK
Sbjct: 61 RDLNGKELEGRVIKVEKAK 79
Score = 38.7 bits (91), Expect = 2e-04
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV--CY--ADAH-KRHRNEGVVEFESSSDMKKALDKL 170
L V LS+R + ++L+ + G V D R G V FES D A+ L
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 171 DNAELNGRRIR 181
+ EL GR I+
Sbjct: 64 NGKELEGRVIK 74
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 73.4 bits (181), Expect = 4e-17
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
+++G LP E +L + +G++ V L GF FVEFE DA+ A+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 57 LNGKSLLGERVTV 69
LNGK L G + V
Sbjct: 61 LNGKELDGRPLKV 73
Score = 66.5 bits (163), Expect = 2e-14
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYAD-----AHKRHRNEGVVEFESSSDMKKALDK 169
L V NL + ++L++ + G+V + + VEFES D +KAL+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 170 LDNAELNGRRIRL 182
L+ EL+GR +++
Sbjct: 61 LNGKELDGRPLKV 73
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands
and two helices arranged in an alpha/beta sandwich,
with a third helix present during RNA binding in some
cases The C-terminal beta strand (4th strand) and final
helix are hard to align and have been omitted in the
SEED alignment The LA proteins have an N terminal rrm
which is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 71.9 bits (177), Expect = 1e-16
Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 7/70 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYELN 58
+++G LP E DL+ +G I + + GF FVEFED DA+ A+ LN
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 59 GKSLLGERVT 68
GK L G +
Sbjct: 61 GKELGGRELR 70
Score = 71.5 bits (176), Expect = 2e-16
Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLD 171
L V NL + +DLKD + G + D R + VEFE D +KAL+ L+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 172 NAELNGRRIR 181
EL GR +R
Sbjct: 61 GKELGGRELR 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 = 70.0 bits (172), Expect = 6e-16
Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYELN 58
+++G LP E DL + +G I V + GF FVEFE DA+ A+ LN
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 59 GKSLLGERVTVE 70
GK L G ++ V
Sbjct: 61 GKELDGRKLKVS 72
Score = 63.9 bits (156), Expect = 1e-13
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLD 171
L V NL + +DL++ + GE+ D + + VEFES D +KAL+ L+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 172 NAELNGRRIRL 182
EL+GR++++
Sbjct: 61 GKELDGRKLKV 71
>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 = 69.7 bits (171), Expect = 1e-15
Identities = 33/71 (46%), Positives = 43/71 (60%), Gaps = 5/71 (7%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNG-----FGFVEFEDYRDADDAVYELNG 59
++Y+G LP +RERD+E YG I+ + LKN F FVEFED RDA+DAV +G
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60
Query: 60 KSLLGERVTVE 70
G R+ VE
Sbjct: 61 YDFDGYRLRVE 71
Score = 33.1 bits (76), Expect = 0.015
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEG--VVEFESSSDMKKALDKLDN 172
R+ V NL + +D++D + G + D R R VEFE D + A+ D
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60
Query: 173 AELNGRRIRL 182
+ +G R+R+
Sbjct: 61 YDFDGYRLRV 70
>gnl|CDD|241045 cd12601, RRM2_SRSF1_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF9 and
similar proteins. This subfamily corresponds to the
RRM2 of serine/arginine-rich splicing factor SRSF1,
SRSF9 and similar proteins. SRSF1, also termed ASF-1, 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, also termed SRp30C, 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. 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. .
Length = 74
Score = 63.7 bits (155), Expect = 2e-13
Identities = 31/61 (50%), Positives = 41/61 (67%), Gaps = 2/61 (3%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
+R+IV L SWQDLKD MR+ G+VCYAD ++ GVVEF DMK A+ KLD++
Sbjct: 1 YRVIVSGLPPTGSWQDLKDHMREAGDVCYADVYR--DGTGVVEFLRYEDMKYAVKKLDDS 58
Query: 174 E 174
+
Sbjct: 59 K 59
>gnl|CDD|241046 cd12602, RRM2_SF2_plant_like, RNA recognition motif 2 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subfamily corresponds to the RRM2 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 = 76
Score = 62.9 bits (153), Expect = 4e-13
Identities = 28/61 (45%), Positives = 40/61 (65%), Gaps = 1/61 (1%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRN-EGVVEFESSSDMKKALDKLDNA 173
R++V L S SWQDLKD MR+ G+VC++ + R G+V+F + DMK A+ KLD+
Sbjct: 2 RVLVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDGRGTTGIVDFTNYDDMKYAIRKLDDT 61
Query: 174 E 174
E
Sbjct: 62 E 62
>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 = 62.5 bits (152), Expect = 5e-13
Identities = 36/71 (50%), Positives = 44/71 (61%), Gaps = 5/71 (7%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNG-----FGFVEFEDYRDADDAVYELNG 59
++Y+G LP VRE+DLE YGRIRD+ LKN F FV FED RDA+DAV+ NG
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNG 60
Query: 60 KSLLGERVTVE 70
R+ VE
Sbjct: 61 YDFGQCRLRVE 71
>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 = 62.3 bits (152), Expect = 5e-13
Identities = 26/69 (37%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAH----KRHRNEGVVEFESSSDMKKALDKLD 171
+ V NL V+WQDLKD R+ G V AD R + G V FES D ++A++ +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60
Query: 172 NAELNGRRI 180
+L GR +
Sbjct: 61 GYDLEGREL 69
Score = 31.9 bits (73), Expect = 0.050
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--RDVILKN-----GFGFVEFEDYRDADDAVYELN 58
+++ LP+ V +DL+ + G + DV N GFG V FE DA A+ N
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60
Query: 59 GKSLLGERVTV 69
G L G + V
Sbjct: 61 GYDLEGRELEV 71
>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 = 60.9 bits (148), Expect = 1e-12
Identities = 31/71 (43%), Positives = 44/71 (61%), Gaps = 5/71 (7%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK-----NGFGFVEFEDYRDADDAVYELNGK 60
VY+G LP +RER++E YG I D+ LK G+ F+EFED RDA+DA+ +G
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDGY 61
Query: 61 SLLGERVTVEI 71
G+R+ VE+
Sbjct: 62 DFDGQRLRVEL 72
>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 = 59.4 bits (144), Expect = 6e-12
Identities = 24/62 (38%), Positives = 34/62 (54%)
Query: 12 PYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEI 71
P RE D+EK + +G + ++ F FVEFED DA A+ L+G + G +TVE
Sbjct: 9 PGTTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEF 68
Query: 72 AK 73
K
Sbjct: 69 VK 70
Score = 29.3 bits (66), Expect = 0.41
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 150 RNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
+ VEFE S D KAL+ L + ++G + +
Sbjct: 34 KTFAFVEFEDSEDATKALEALHGSRIDGSVLTV 66
>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 = 59.5 bits (145), Expect = 6e-12
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
+Y+G LPY V E DL+ +G + + GFGFVE E +A+ A+ +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 57 LNGKSLLGERVTVEIAK 73
LNG G +TV A+
Sbjct: 61 LNGTDFGGRTLTVNEAR 77
Score = 48.8 bits (117), Expect = 4e-08
Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADA-----HKRHRNEGVVEFESSSDMKKALDK 169
L V NL V+ +DLKD Q GEV A R R G VE E++ + A++K
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 170 LDNAELNGRRIRLIEDKP 187
L+ + GR + + E +P
Sbjct: 61 LNGTDFGGRTLTVNEARP 78
>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 = 59.4 bits (144), Expect = 7e-12
Identities = 34/70 (48%), Positives = 44/70 (62%), Gaps = 4/70 (5%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN----GFGFVEFEDYRDADDAVYELNGK 60
++Y+G LP +R +D+E YG IRD+ LKN F FVEFED RDA+DAVY +G
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60
Query: 61 SLLGERVTVE 70
G R+ VE
Sbjct: 61 DYDGYRLRVE 70
Score = 26.7 bits (59), Expect = 3.2
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYAD-AHKRHRNEGVVEFESSSDMKKALDKLDNA 173
R+ V NL + +D++D + G + D ++R VEFE D + A+ D
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60
Query: 174 ELNGRRIRL 182
+ +G R+R+
Sbjct: 61 DYDGYRLRV 69
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its
median region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated
in protein shuttling and protein-protein interactions.
.
Length = 77
Score = 58.9 bits (142), Expect = 1e-11
Identities = 38/76 (50%), Positives = 50/76 (65%), Gaps = 3/76 (3%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN--GFGFVEFEDYRDADDAVYELNGKS 61
KVY+G L G + +LE+ YG +R V I +N GF FVEFED RDA+DAV L+GK
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 60
Query: 62 LLGERVTVEIAKGIDR 77
+ G RV VE++ G+ R
Sbjct: 61 ICGSRVRVELSTGMPR 76
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. Moreover, hnRNP M is able to
interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. hnRNP M
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 58.6 bits (142), Expect = 1e-11
Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 5/76 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMR-QVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
R+ + N+ + WQDLKD R +VGEV Y D + R GVVEF+ ++KAL+
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60
Query: 170 LDNAELNGRRIRLIED 185
++ EL GR++ + ED
Sbjct: 61 MNRYELKGRKLVVKED 76
Score = 28.2 bits (63), Expect = 0.99
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 25/77 (32%)
Query: 5 KVYIGGLPYGVRERDL--------------EKFVKGYGRIRDVILKNGFGFVEFEDYRDA 50
+V+I +PY ++ +DL E F G+ R G G VEF+D
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSR------GCGVVEFKDKESV 54
Query: 51 DDAV-----YELNGKSL 62
A+ YEL G+ L
Sbjct: 55 QKALETMNRYELKGRKL 71
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that 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.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains 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 = 81
Score = 58.9 bits (142), Expect = 1e-11
Identities = 37/76 (48%), Positives = 49/76 (64%), Gaps = 3/76 (3%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN--GFGFVEFEDYRDADDAVYELNGKS 61
KVY+G L + +LE+ YG +R V + +N GF FVEFED RDA DAV EL+G++
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 65
Query: 62 LLGERVTVEIAKGIDR 77
L G RV VE++ G R
Sbjct: 66 LCGCRVRVELSNGEKR 81
>gnl|CDD|241212 cd12768, RRM2_SRSF9, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM2 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C, 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 = 76
Score = 58.5 bits (141), Expect = 2e-11
Identities = 32/61 (52%), Positives = 38/61 (62%), Gaps = 2/61 (3%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
R+IV L SWQDLKD MR+ G+VCYAD K GVVEF DM+ AL KLD+ +
Sbjct: 2 RVIVSGLPPSGSWQDLKDHMREAGDVCYADVQK--DGMGVVEFLRKEDMEYALRKLDDTK 59
Query: 175 L 175
Sbjct: 60 F 60
>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 = 57.6 bits (140), Expect = 2e-11
Identities = 24/67 (35%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
K+++G LP +L + YG + + ++KN +GFV E+ DA+DA+ LNG +
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN-YGFVHMEEEEDAEDAIKALNGYEFM 59
Query: 64 GERVTVE 70
G+R+ VE
Sbjct: 60 GKRINVE 66
Score = 38.7 bits (91), Expect = 1e-04
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
+L V NL + ++L+ + G V D K N G V E D + A+ L+ E
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVK---NYGFVHMEEEEDAEDAIKALNGYE 57
Query: 175 LNGRRIR 181
G+RI
Sbjct: 58 FMGKRIN 64
>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 = 57.0 bits (138), Expect = 6e-11
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 8/79 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
T +Y+ + R DL + YG I DV + GF +V+FED RDA+DA+Y
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60
Query: 56 ELNGKSLLGERVTVEIAKG 74
L+ LG + ++ A+G
Sbjct: 61 YLDRTRFLGREIEIQFAQG 79
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 55.6 bits (135), Expect = 1e-10
Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVG---EVCYADAHKRHRNEGVVEFESSSDMKKALDKLDN 172
L V NL V+ +DL++F G V R R VEF S D + AL KL+
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 173 AELNGRRIR 181
L+GR +R
Sbjct: 61 LVLDGRTLR 69
Score = 53.7 bits (130), Expect = 6e-10
Identities = 26/68 (38%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK------NGFGFVEFEDYRDADDAVYELNG 59
+Y+ LP V E DL +F YG++ V L GF FVEF DA+ A+ +LNG
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 60 KSLLGERV 67
L G +
Sbjct: 61 LVLDGRTL 68
>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 = 54.5 bits (132), Expect = 3e-10
Identities = 23/66 (34%), Positives = 39/66 (59%), Gaps = 2/66 (3%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAVYELNGKS 61
T VY+G LP+G+ E +L++ +G I +V + G+ FV F+ + A A+ +NG S
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60
Query: 62 LLGERV 67
+ G+ V
Sbjct: 61 INGQTV 66
>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM1 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 54.3 bits (130), Expect = 5e-10
Identities = 31/76 (40%), Positives = 44/76 (57%), Gaps = 5/76 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQ-VGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
R + N+ V WQ LKD +++ VGEV Y DA + R VVEF+ MKKA++
Sbjct: 1 RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEV 60
Query: 170 LDNAELNGRRIRLIED 185
L+ LNGR +++ ED
Sbjct: 61 LNKHVLNGRPLKVKED 76
>gnl|CDD|241211 cd12767, RRM2_SRSF1, RNA recognition motif 2 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM2
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit, 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 SR domains rich in serine-arginine
dipeptides. .
Length = 76
Score = 53.9 bits (129), Expect = 7e-10
Identities = 30/62 (48%), Positives = 38/62 (61%), Gaps = 2/62 (3%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
+R++V L SWQDLKD MR+ G+VCYAD + GVVEF DM A+ KLDN
Sbjct: 1 YRVVVSGLPPSGSWQDLKDHMREAGDVCYADVFR--DGTGVVEFVRKEDMTYAVRKLDNT 58
Query: 174 EL 175
+
Sbjct: 59 KF 60
>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 = 52.2 bits (126), Expect = 3e-09
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KN-GFGFVEFEDYRDADDAVYEL 57
+Y+GGL V E+ L +G I+D+ + K+ GF FVEFE+ DA A+ +
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 58 NGKSLLGERVTV 69
N L G + V
Sbjct: 61 NESELFGRTIRV 72
Score = 46.1 bits (110), Expect = 4e-07
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
++HR VEFE D A+D ++ +EL GR IR
Sbjct: 37 QKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTIR 71
>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 51.9 bits (124), Expect = 3e-09
Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 5/76 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQ-VGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
R+ + N+ + WQ +KD MR+ VGEV Y DA + R GVVEF+ +KKAL+
Sbjct: 1 RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEV 60
Query: 170 LDNAELNGRRIRLIED 185
++ +LNGR + + ED
Sbjct: 61 MNKYDLNGRPLNIKED 76
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and
an RS domain at their C-terminus.
Length = 72
Score = 51.4 bits (123), Expect = 6e-09
Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL--L 63
V+ G Y R+ ++E+ YGR+ V +K+GF FV ED RDA+DA+ L+
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRVDMKSGFAFVYMEDERDAEDAIRGLDNFEFGRQ 62
Query: 64 GERVTVEIAK 73
R+ VE AK
Sbjct: 63 RRRLRVEWAK 72
>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 = 51.4 bits (123), Expect = 7e-09
Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 8/76 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K++IGGL + E+ LE+ YG+I +V++ GFGFV FE+ DA DA+
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 57 LNGKSLLGERVTVEIA 72
+NGKS+ G ++ V+ A
Sbjct: 62 MNGKSVDGRQIRVDQA 77
Score = 29.8 bits (67), Expect = 0.27
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDK 169
+L + LS + Q L+ + G++ K R R G V FE+ D K A+
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 170 LDNAELNGRRIRL 182
++ ++GR+IR+
Sbjct: 62 MNGKSVDGRQIRV 74
>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 = 51.3 bits (123), Expect = 8e-09
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 7/75 (9%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYEL 57
K+++ GLP+ V + +LEK K +G ++ V L G +VE+E+ A AV ++
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63
Query: 58 NGKSLLGERVTVEIA 72
+G + + ++V I+
Sbjct: 64 DGTEIKEKTISVAIS 78
Score = 29.3 bits (66), Expect = 0.46
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYAD--AHKRHRNEGV--VEFESSSDMKKALDK 169
H+L V L V+ ++L+ ++ G V ++ + +G+ VE+E+ S +A+ K
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLK 62
Query: 170 LDNAELNGRRI 180
+D E+ + I
Sbjct: 63 MDGTEIKEKTI 73
>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 = 50.3 bits (121), Expect = 1e-08
Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 5 KVYIGGLPYG-VRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
+V++G L V + DLE+ YG+I + L G+GFV+F++ DA AV NG+ +
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDARAAVAGENGREIA 61
Query: 64 GERVTV 69
G+++ +
Sbjct: 62 GQKLDI 67
>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 = 49.7 bits (119), Expect = 2e-08
Identities = 18/65 (27%), Positives = 31/65 (47%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
++Y+ P E + + YG +++V + + F FVEFE A A ++GK L
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISNFAFVEFESLESAIRAKDSVHGKVLNN 60
Query: 65 ERVTV 69
+ V
Sbjct: 61 NPLYV 65
>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 = 54.0 bits (130), Expect = 2e-08
Identities = 45/190 (23%), Positives = 75/190 (39%), Gaps = 29/190 (15%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVI-------LKNGFGFVEFEDYRDADDAVYE 56
T +Y+ L V E L + +G I GF FV FE + DA AV E
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEE 238
Query: 57 LNGKSL----LGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRS 112
+NGK + G+++ V A+ + RR + + + G +
Sbjct: 239 MNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVN----------- 287
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALD 168
L V+NL V+ + L++ + GE+ A D R G V F + + +A+
Sbjct: 288 ---LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT 344
Query: 169 KLDNAELNGR 178
++ L G+
Sbjct: 345 EMHGRMLGGK 354
Score = 44.8 bits (106), Expect = 2e-05
Identities = 48/231 (20%), Positives = 84/231 (36%), Gaps = 46/231 (19%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVILKN-GFGFVEFEDYRDADDAVYE 56
+++ L V + L +G I D K+ G+GFV FE A A+ +
Sbjct: 89 GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRL 116
+NG L + V V G + + +R P + L
Sbjct: 149 VNGMLLNDKEVYV-----------------GRFIK----------KHEREAAPLKKFTNL 181
Query: 117 IVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLDN 172
V+NL V+ L++ + GE+ A D R R V FE D KA+++++
Sbjct: 182 YVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNG 241
Query: 173 AELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSK 223
++ + E K GR + R+ R R + + +++
Sbjct: 242 KKIGLAK----EGKKLYVGRAQKRA----EREAELRRKFEELQQERKMKAQ 284
Score = 37.9 bits (88), Expect = 0.005
Identities = 22/100 (22%), Positives = 44/100 (44%), Gaps = 7/100 (7%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVY 55
G +Y+ L V + L + G I + GFGFV F + +A+ AV
Sbjct: 285 GVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVT 344
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPR 95
E++G+ L G+ + V +A+ ++ + + + + +
Sbjct: 345 EMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQ 384
Score = 30.9 bits (70), Expect = 0.67
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVG-----EVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V +L V+ L D + G VC +R G V F++ +D ++AL+ +
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 171 DNAELNGRRIRL 182
+ L G+ IR+
Sbjct: 63 NFKRLGGKPIRI 74
Score = 29.8 bits (67), Expect = 1.9
Identities = 48/188 (25%), Positives = 76/188 (40%), Gaps = 44/188 (23%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI------RDVILKN--GFGFVEFEDYRDADDAVYEL 57
+Y+G L V E L K +G + RD + + G+G+V F++ DA+ A+ +
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 58 NGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRR-GWGHDRDDRYGPPTRSDHRL 116
N K L G+ + R S R P RR G G+ +
Sbjct: 63 NFKRLGGKPI----------------RIMWSQRDPSLRRSGVGN---------------I 91
Query: 117 IVENLSSRVSWQDLKDFMRQVGEV--C--YADAHKRHRNEGVVEFESSSDMKKALDKLDN 172
V+NL V + L D + G + C D + + R G V FE K A+ K++
Sbjct: 92 FVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNG 151
Query: 173 AELNGRRI 180
LN + +
Sbjct: 152 MLLNDKEV 159
>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 = 48.9 bits (117), Expect = 4e-08
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-----GFGFVEFEDYRDADDAVYELN 58
++++ +P+ R+ DL + +G I DV I+ N GFGFV F + DAD A +L+
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLH 61
Query: 59 GKSLLGERVTVEIA 72
G + G ++ V A
Sbjct: 62 GTVVEGRKIEVNNA 75
Score = 30.1 bits (68), Expect = 0.22
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 3/69 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNE---GVVEFESSSDMKKALDKLD 171
RL V N+ R DL+ Q G + + R G V F +S+D +A +KL
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLH 61
Query: 172 NAELNGRRI 180
+ GR+I
Sbjct: 62 GTVVEGRKI 70
>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 = 48.8 bits (117), Expect = 5e-08
Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 11/80 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRD---VILKNG--------FGFVEFEDYRDADDA 53
+++IG L + E L K YG+I+ + K+G + FV FE +A+ A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 54 VYELNGKSLLGERVTVEIAK 73
+ LNGK+ LG+++ V A
Sbjct: 61 LKSLNGKTALGKKLVVRWAH 80
Score = 32.6 bits (75), Expect = 0.031
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADA--HK------RHRNEGVVEFESSSDMKKA 166
RL + NL SR++ L + G++ D HK + R V FE+ + +KA
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 167 LDKLDNAELNGRRI 180
L L+ G+++
Sbjct: 61 LKSLNGKTALGKKL 74
>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 = 48.8 bits (117), Expect = 5e-08
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 12/78 (15%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-----------KNGFGFVEFEDYRDADDA 53
++Y+ L + + E DL +G + + + NGF FV F+D A++A
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 54 VYELNGKSLLGERVTVEI 71
+ +LNG L G +++V +
Sbjct: 62 L-QLNGTELGGRKISVSL 78
Score = 41.1 bits (97), Expect = 3e-05
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEV------CYADAHKRHRNEGV--VEFESSSDMKK 165
+ V NL ++ DL+ + GEV D + N G V F+ +S +
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60
Query: 166 ALDKLDNAELNGRRI 180
AL +L+ EL GR+I
Sbjct: 61 AL-QLNGTELGGRKI 74
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 48.8 bits (117), Expect = 7e-08
Identities = 29/73 (39%), Positives = 37/73 (50%), Gaps = 8/73 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+YIGGLPY + E D+ YG I D+ L GF F+ +ED R AV L
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71
Query: 58 NGKSLLGERVTVE 70
NG LLG + V+
Sbjct: 72 NGIKLLGRTIRVD 84
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM2 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 48.4 bits (116), Expect = 7e-08
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYEL 57
++ + LP+ E DL+K +G + +V + K GF FV+F DA+ A+ +
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60
Query: 58 NGKSLLGERVTVEIA 72
NGK + G V V+ A
Sbjct: 61 NGKKIKGRPVAVDWA 75
Score = 43.4 bits (103), Expect = 4e-06
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKL 170
RLIV NL + + DLK G V + + V+F S +D +KA+ +
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60
Query: 171 DNAELNGRRI 180
+ ++ GR +
Sbjct: 61 NGKKIKGRPV 70
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 8/73 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-KN-------GFGFVEFEDYRDADDAVYE 56
K++IGGLP + E +++ ++ +G+++ L K+ G+ F E+ D D A+
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 57 LNGKSLLGERVTV 69
LNG L +++TV
Sbjct: 62 LNGMQLGDKKLTV 74
>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 = 47.8 bits (114), Expect = 1e-07
Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 5 KVYIGGLP-YGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
+++IG LP V + DL + YG + ++LKN +GFV+F+ +A+ GK +
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNAYGFVQFDSPESCANAINCEQGKMIR 60
Query: 64 GERVTVEIAK 73
G ++ +E++K
Sbjct: 61 GRKLHLEVSK 70
>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 = 47.6 bits (113), Expect = 1e-07
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
K+++G LP E+++ + YG++ + I+KN +GFV +D AD+A+ L+ L
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN-YGFVHMDDKTAADEAIRNLHHYKLH 60
Query: 64 GERVTVE 70
G + VE
Sbjct: 61 GVAINVE 67
Score = 32.5 bits (74), Expect = 0.028
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
+L V NL + Q+++ Q G+V D K N G V + + +A+ L + +
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIK---NYGFVHMDDKTAADEAIRNLHHYK 58
Query: 175 LNGRRI 180
L+G I
Sbjct: 59 LHGVAI 64
>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 = 47.3 bits (113), Expect = 2e-07
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVYELN 58
+++G L + + DLE+F K G + DV + GFG VEF A A+ E +
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EKS 60
Query: 59 GKSLLGERVTVEIAK 73
G+ LLG + V++A
Sbjct: 61 GEELLGREIRVDLAT 75
Score = 41.1 bits (97), Expect = 3e-05
Identities = 27/72 (37%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKL 170
L V NLS DL++F ++ GEV D R + G VEF + +KAL+K
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK- 59
Query: 171 DNAELNGRRIRL 182
EL GR IR+
Sbjct: 60 SGEELLGREIRV 71
>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 = 47.0 bits (112), Expect = 2e-07
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 9/78 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
K+++GGLP V E DL K+ +G + +V++ GFGF+ FE D+ D V
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFES-EDSVDQV 60
Query: 55 YELNGKSLLGERVTVEIA 72
+ + G++V V+ A
Sbjct: 61 VNEHFHDINGKKVEVKRA 78
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes.
Since the Hu proteins share high homology with the
Drosophila embryonic lethal abnormal vision (ELAV)
protein, the Hu family is sometimes referred to as the
ELAV family. Drosophila ELAV is exclusively expressed
in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress.
Moreover, HuR has an anti-apoptotic function during
early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Hu proteins
perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 79
Score = 46.9 bits (112), Expect = 3e-07
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 10/77 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI-RDVILKN-------GFGFVEFEDYRDADDAVYEL 57
+Y+ GLP + +++LE YGRI IL + G GF+ F+ +A+ A+ L
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 58 NGKSLLG--ERVTVEIA 72
NG G E +TV+ A
Sbjct: 63 NGTIPPGATEPITVKFA 79
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins from plants. This
subgroup corresponds to the RRM2 in a family that
represents a novel group of arginine/serine (RS) or
serine/arginine (SR) splicing factors existing in
plants, such as A. thaliana RSp31, RSp35, RSp41 and
similar proteins. Like vertebrate RS splicing factors,
these proteins function as plant splicing factors and
play crucial roles in constitutive and alternative
splicing in plants. They all contain two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
at their N-terminus, and an RS domain at their
C-terminus.
Length = 70
Score = 46.0 bits (109), Expect = 4e-07
Identities = 21/61 (34%), Positives = 34/61 (55%)
Query: 12 PYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEI 71
P R RDLE+ + YG++ +V ++ F FV++E DA A+ N +L ++VE
Sbjct: 9 PINTRTRDLERHFEPYGKLVNVRIRRNFAFVQYETQEDATKALESTNMSKVLDRVISVEY 68
Query: 72 A 72
A
Sbjct: 69 A 69
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 46.2 bits (110), Expect = 4e-07
Identities = 26/75 (34%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYEL 57
VY+ LP+ + DL K YG++ V I+K+ G F+ F D DA V L
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63
Query: 58 NGKSLLGERVTVEIA 72
N K L G + IA
Sbjct: 64 NNKELFGRTLKCSIA 78
>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 = 46.0 bits (110), Expect = 4e-07
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYE 56
T VY+ L + + L++ YG+I + GFGFV FE++ A AV E
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61
Query: 57 LNGKSLLGERVTV 69
LNGK + G+++ V
Sbjct: 62 LNGKEVNGKKLYV 74
Score = 35.6 bits (83), Expect = 0.003
Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 4/67 (5%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
V+NL + + LK+ + G++ A D + + G V FE+ +KA+++L+
Sbjct: 6 VKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGK 65
Query: 174 ELNGRRI 180
E+NG+++
Sbjct: 66 EVNGKKL 72
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 45.8 bits (109), Expect = 5e-07
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNG--FGFVEFEDYRDADDAVYELNGKS 61
T V++GGL V E +L +G I V + G GFV+F A+ A+ +L G
Sbjct: 2 TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTI 61
Query: 62 LLGERV 67
+ G R+
Sbjct: 62 IGGSRI 67
Score = 30.0 bits (68), Expect = 0.23
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 1/67 (1%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
+ V L V+ +L+ GE+ Y + G V+F + + A+ +L +
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKI-PPGKGCGFVQFVHRAAAEAAIQQLQGTII 62
Query: 176 NGRRIRL 182
G RIRL
Sbjct: 63 GGSRIRL 69
>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 = 46.1 bits (110), Expect = 5e-07
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRD-VILKN-------GFGFVEFEDYRDADDAVYEL 57
+++ LPY + LE+F G I+ ++K+ GFG+V F DA A+ E
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 58 NGKSLLGERVTVEIAK 73
G ++ VE AK
Sbjct: 62 KKTKFGGRKIHVEFAK 77
Score = 37.6 bits (88), Expect = 5e-04
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYAD-----AHKRHRNEGVVEFESSSDMKKALDKL 170
L V NL + + L++F +VG + K+ R G V F D K+AL++
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 171 DNAELNGRRIRLIEDKPR 188
+ GR+I + K +
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
>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 = 45.7 bits (109), Expect = 5e-07
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
V++G +PY E L + G + RD G+GF EFED A A+ L
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 58 NGKSLLGERVTVEIA 72
NG G + V+ A
Sbjct: 61 NGYEFNGRALRVDFA 75
Score = 34.1 bits (79), Expect = 0.009
Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 5/70 (7%)
Query: 117 IVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKKALDKLD 171
V N+ + + L + +VG V + + G EFE A+ L+
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 172 NAELNGRRIR 181
E NGR +R
Sbjct: 62 GYEFNGRALR 71
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 45.3 bits (108), Expect = 7e-07
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI---RDVILKN-----GFGFVEFEDYRDADDAVY 55
T VYI GLP + DLEK + +G+I + ++ K G+GFV+F+ A A+
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
Query: 56 ELNGK 60
LNG+
Sbjct: 61 GLNGR 65
>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 = 45.6 bits (108), Expect = 7e-07
Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKALDKL 170
L V NL+ V+ +DL DF V + +A R G V F D ++AL KL
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 171 DNAELNGRRIRLIEDKPR 188
N +L+GR +RL + R
Sbjct: 62 KNKKLHGRILRLDIAERR 79
Score = 39.0 bits (91), Expect = 2e-04
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRD-VILKN-------GFGFVEFEDYRDADDAVYEL 57
+++ L + V + DL F I+ V++ + G+GFV F DA +A+ +L
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 58 NGKSLLGERVTVEIAK 73
K L G + ++IA+
Sbjct: 62 KNKKLHGRILRLDIAE 77
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 44.8 bits (107), Expect = 7e-07
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 27 YGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIA 72
+G + + L K GF FVEF A+ AV LNG G + V+ +
Sbjct: 8 FGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
Score = 38.3 bits (90), Expect = 1e-04
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 147 KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
K+ VEF + +KA+ L+ GR +R+
Sbjct: 18 KKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53
>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 = 45.6 bits (108), Expect = 8e-07
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 8/76 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+YIG LP+G E++L+K+ +G +++V + +GF++F + A A +
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 58 NGKSLLGERVTVEIAK 73
N L+G+ + V +
Sbjct: 62 NNYLLMGKVLQVHVLP 77
>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 = 45.1 bits (107), Expect = 1e-06
Identities = 29/80 (36%), Positives = 40/80 (50%), Gaps = 21/80 (26%)
Query: 7 YIGGLPYGVRERDLEKFVKG--------------YGRIRDVILKNGFGFVEFEDYRDADD 52
Y+G LPY V E D+++F +G GR+R GFG+ EFED
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLR------GFGYAEFEDRDSLLQ 58
Query: 53 AVYELNGKSLLGERVTVEIA 72
A+ LN +SL R+ V+IA
Sbjct: 59 AL-SLNDESLKNRRIRVDIA 77
Score = 27.0 bits (60), Expect = 2.9
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 148 RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRL 182
R R G EFE + +AL L++ L RRIR+
Sbjct: 41 RLRGFGYAEFEDRDSLLQAL-SLNDESLKNRRIRV 74
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 48.0 bits (113), Expect = 2e-06
Identities = 37/171 (21%), Positives = 66/171 (38%), Gaps = 7/171 (4%)
Query: 76 DRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMR 135
Q G RGY R + + ++ L V NL V+ +DL++ +
Sbjct: 80 MEEQNDGERGYTKEFEEELFRSSESPKSRQ--KSKEENNTLFVGNLPYDVTEEDLRELFK 137
Query: 136 QVGEVCYADAH-----KRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGG 190
+ G V + R VEFES +KA+++L+ EL GR +R+ + +P
Sbjct: 138 KFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ 197
Query: 191 GRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSP 241
R ++ S +K SR ++ + P K+ + +
Sbjct: 198 PRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKS 248
Score = 46.5 bits (109), Expect = 4e-06
Identities = 33/103 (32%), Positives = 48/103 (46%), Gaps = 8/103 (7%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVY 55
+++G LPY V E DL + K +G ++ V L GF FVEFE A+ A+
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175
Query: 56 ELNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGW 98
ELNGK L G + V+ A+ + + + A RG
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGK 218
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has
been identified as a regulator of the hematopoietic
stem cell (HSC) compartment and of leukemic stem cells
after transplantation of cells with loss and gain of
function of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 44.3 bits (105), Expect = 2e-06
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV-- 54
K+++GGL E D++K+ +G++ D +L GFGFV FE D
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 55 --YELNGKS 61
+E+N K
Sbjct: 61 HFHEINNKM 69
Score = 33.2 bits (76), Expect = 0.018
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKKALDK 169
++ V LS+ + D+K + Q G+V + RHR G V FES + K +
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE- 59
Query: 170 LDNAELNGRRI 180
+ E+N + +
Sbjct: 60 IHFHEINNKMV 70
>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 = 44.2 bits (105), Expect = 2e-06
Identities = 24/68 (35%), Positives = 34/68 (50%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGE 65
+Y+ LP E L + YG + V + FV FE+ DA A+ E+NGK L G
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDYAFVHFEERDDAVKAMEEMNGKELEGS 63
Query: 66 RVTVEIAK 73
+ V +AK
Sbjct: 64 PIEVSLAK 71
Score = 29.5 bits (67), Expect = 0.36
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L V NL + + L++ + GEV + K+ ++ V FE D KA+++++ EL
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEV---ERVKKIKDYAFVHFEERDDAVKAMEEMNGKEL 60
Query: 176 NGRRIRLIEDKP 187
G I + KP
Sbjct: 61 EGSPIEVSLAKP 72
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM1 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 44.3 bits (105), Expect = 2e-06
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL----KNGFGFVEFEDYRDADDAVYELNGKS 61
VY G P D+++ + G +R V + F+ FE+ A A+ LNG S
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGAS 61
Query: 62 LLGERVTVE 70
+ G + V+
Sbjct: 62 VDGNCIKVQ 70
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor 12 (SRSF12) and
similar proteins. This subgroup corresponds to the RRM
of SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19). SRSF12 is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates
distal alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. SRSF12 contains a single N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
followed by a C-terminal RS domain rich in
serine-arginine dipeptides. .
Length = 84
Score = 44.6 bits (105), Expect = 2e-06
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 8/79 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVY 55
T +++ + R DL + YG I DV + GF +++FED RDA+DA+Y
Sbjct: 1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60
Query: 56 ELNGKSLLGERVTVEIAKG 74
LN K + G ++ ++ A+G
Sbjct: 61 NLNRKWVCGRQIEIQFAQG 79
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 43.9 bits (104), Expect = 3e-06
Identities = 26/66 (39%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 7 YIGGLPYGVRERDLEK-FVKGYGRIRDVIL-KNGFGFVEFEDYRDADDAVYELNGKSLLG 64
YIG L V E DL + F + + V++ K G+ FV+ D AD A+ +LNGK L G
Sbjct: 2 YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKILQG 61
Query: 65 ERVTVE 70
+ + VE
Sbjct: 62 KVIEVE 67
>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 = 43.7 bits (103), Expect = 3e-06
Identities = 19/66 (28%), Positives = 32/66 (48%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
K+++G + + +L + YG + + F FV AD A+ ELNG+ L G
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQFAFVHLRGEAAADRAIEELNGRELHG 61
Query: 65 ERVTVE 70
++ VE
Sbjct: 62 RKLVVE 67
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM1 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 76
Score = 43.5 bits (103), Expect = 3e-06
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
+++G L + V + L+ + +G + + GFG+V+FE DA A+
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 57 LNGKSLLGERVTVEIA 72
++GK L G + V+ +
Sbjct: 61 MDGKELDGRPINVDFS 76
Score = 40.8 bits (96), Expect = 4e-05
Identities = 27/73 (36%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGE-----VCYADAHKRHRNEGVVEFESSSDMKKALDK 169
L V NLS V + LK + G V R R G V+FES D KKA++
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 170 LDNAELNGRRIRL 182
+D EL+GR I +
Sbjct: 61 MDGKELDGRPINV 73
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 44.1 bits (105), Expect = 3e-06
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 12/50 (24%)
Query: 23 FVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIA 72
FVKGY +E+E ++A A+ LNGK LLG+ ++V+ A
Sbjct: 46 FVKGYA------------LIEYETKKEAQAAIEGLNGKELLGQTISVDWA 83
Score = 26.8 bits (60), Expect = 4.5
Identities = 8/26 (30%), Positives = 17/26 (65%)
Query: 155 VEFESSSDMKKALDKLDNAELNGRRI 180
+E+E+ + + A++ L+ EL G+ I
Sbjct: 53 IEYETKKEAQAAIEGLNGKELLGQTI 78
>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 = 43.4 bits (103), Expect = 4e-06
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRD--VILKNG---FGFVEFEDYRDADDAVYELNGK 60
+Y+G L V E L + G I+ +I ++G + FVE+ D+R A A+ +NG+
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60
Query: 61 SLLGERVTV 69
+LG+ + V
Sbjct: 61 LILGQEIKV 69
>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 = 43.4 bits (103), Expect = 4e-06
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRD-VILKN-------GFGFVEFEDYRDADDAVY 55
TK+++GGLPY + L K+ +G I + V++ + G+GFV F+D A+ A
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 56 ELNGKSLLGERVTVEIA 72
+ N + G + V +A
Sbjct: 61 DPN-PIIDGRKANVNLA 76
>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 = 43.7 bits (103), Expect = 4e-06
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYE 56
TK+ + LP+ ++D+ YG+++ V + GF FVEF ++A +A+
Sbjct: 1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60
Query: 57 LNGKSLLGERVTVEIA 72
L LLG R+ ++ A
Sbjct: 61 LKDTHLLGRRLVLQYA 76
Score = 26.7 bits (59), Expect = 3.8
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRH----RNEGVVEFESSSDMKKALDKL 170
+++V+NL + +D++ G++ K+ R VEF ++ + A++ L
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNAL 61
Query: 171 DNAELNGRRIRL 182
+ L GRR+ L
Sbjct: 62 KDTHLLGRRLVL 73
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for
growth. Srp1p is closely related to the SR protein
family found in metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. Some family members also contain another RRM
domain.
Length = 78
Score = 43.3 bits (102), Expect = 5e-06
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYELN 58
+Y+ G R RDL + YGR+ + F FVE+E +RDA+DA E++
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEMH 61
Query: 59 GKSLLGERVT--VEIAK 73
G+ T V+ AK
Sbjct: 62 GRRFPDTGDTLHVQWAK 78
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 42.5 bits (100), Expect = 8e-06
Identities = 18/68 (26%), Positives = 33/68 (48%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
K+++G + +L + +GR+ + + FV E +A A+ LNGK +
Sbjct: 1 WKIFVGNVSATCTSDELRGLFEEFGRVVECDKVKDYAFVHMEREEEALAAIEALNGKEVK 60
Query: 64 GERVTVEI 71
G R+ VE+
Sbjct: 61 GRRINVEL 68
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 42.2 bits (100), Expect = 9e-06
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGF----VEFEDYRDADDAVYEL-- 57
V + LP E + +F K G IR+V + G +EFE D+A+ L
Sbjct: 1 LTVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETE---DEALAALTK 57
Query: 58 NGKSLLGERVTVEI 71
+ K L G ++V
Sbjct: 58 DHKRLGGNEISVSR 71
Score = 28.8 bits (65), Expect = 0.54
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 117 IVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHR-NEGVVEFESSSDMKKALDKLDNAEL 175
V+NL + ++ F + GE+ + V+EFE+ + AL K D+ L
Sbjct: 4 KVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLVAVIEFETEDEALAALTK-DHKRL 62
Query: 176 NGRRIR 181
G I
Sbjct: 63 GGNEIS 68
>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 = 46.0 bits (109), Expect = 9e-06
Identities = 45/190 (23%), Positives = 79/190 (41%), Gaps = 34/190 (17%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
V++ L RERDL +F G++RDV G +VEF D ++ L
Sbjct: 92 VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYD-VESVIKALAL 150
Query: 58 NGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLI 117
G+ LLG + V+ ++ E+ R + P +L
Sbjct: 151 TGQMLLGRPIIVQSSQA-----EKNRAAKAATHQPGDIPN---------------FLKLY 190
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDKLDN 172
V NL ++ Q+L+ G++ H+ R + G ++F + + K+AL+ ++
Sbjct: 191 VGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNG 250
Query: 173 AELNGRRIRL 182
EL GR I++
Sbjct: 251 FELAGRPIKV 260
Score = 36.4 bits (84), Expect = 0.012
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVYE 56
K+Y+G L + + E++L + + +G I DV L GFGF++F D +A +A+
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247
Query: 57 LNGKSLLGERVTV 69
+NG L G + V
Sbjct: 248 MNGFELAGRPIKV 260
Score = 35.6 bits (82), Expect = 0.020
Identities = 21/74 (28%), Positives = 24/74 (32%), Gaps = 2/74 (2%)
Query: 185 DKPRGGGRGRSR-SSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSP 243
D+ RG R +R S R RS+ RSRSR R R R R
Sbjct: 4 DRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRR-RDRDYYRGRRGRSRSRSPNRYYRPR 62
Query: 244 SKTRKRSRSRSDSR 257
R R R
Sbjct: 63 GDRSYRRDDRRSGR 76
Score = 34.5 bits (79), Expect = 0.056
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 198 SSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSR 257
R R + R+ +R S RSR +S S +S+ + R R RSRSRS +R
Sbjct: 2 YRDRERGRLRNDTRRSDKGRERSRRRSRSRDRSR---RRRDRDY-YRGRRGRSRSRSPNR 57
Score = 34.1 bits (78), Expect = 0.058
Identities = 19/61 (31%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 185 DKPRGGGRGRS----RSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRS 240
DK R R RS RS R R R R S+SRSP + R + + R+
Sbjct: 18 DKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRN 77
Query: 241 P 241
Sbjct: 78 T 78
Score = 32.2 bits (73), Expect = 0.26
Identities = 19/66 (28%), Positives = 24/66 (36%), Gaps = 2/66 (3%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSP-RKSKSKAKSVSRSPS 242
+ + GR RSR S R R R R R RS+S SP R + + R
Sbjct: 13 DTRRSDKGRERSRRRSRSRDRSRRRRDR-DYYRGRRGRSRSRSPNRYYRPRGDRSYRRDD 71
Query: 243 PSKTRK 248
R
Sbjct: 72 RRSGRN 77
Score = 29.5 bits (66), Expect = 2.2
Identities = 33/110 (30%), Positives = 45/110 (40%), Gaps = 18/110 (16%)
Query: 76 DRSQERGRRG----YGSYRAPPPRRGWGHDRDDR---------YGPPTRSDHRLIVENLS 122
DR RGRRG R PR + RDDR R D + V L+
Sbjct: 39 DRDYYRGRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLA 98
Query: 123 SRVSWQDLKDFMRQVGEV----CYADAH-KRHRNEGVVEFESSSDMKKAL 167
+ +DL +F +VG+V C D + +R + VEF + KAL
Sbjct: 99 LKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL 148
Score = 28.3 bits (63), Expect = 4.8
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 207 RSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRARK 260
R R R R ++ + R K + +S RS S ++R R R R R R+
Sbjct: 1 RYRDRERG------RLRNDTRRSDKGRERSRRRSRSRDRSR-RRRDRDYYRGRR 47
>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 = 42.2 bits (100), Expect = 1e-05
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEV--CYADAHKRHRNEGV--VEFESSSDMKKALDK 169
RL V NL V+ +DL++ +VGEV + + R+EG V FE D ++A+ +
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60
Query: 170 LDNAELNGRRIRL 182
+ L+G+ +++
Sbjct: 61 FNGVLLDGQPMQV 73
Score = 36.4 bits (85), Expect = 0.001
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVYE 56
T++ + L Y V E DLE+ G ++ V + G V FE DA+ A+ +
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60
Query: 57 LNGKSLLGERVTVEI 71
NG L G+ + VE+
Sbjct: 61 FNGVLLDGQPMQVEL 75
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in
mRNA surveillance. Furthermore, RNPS1 is a splicing
regulator whose activator function is controlled in
part by CK2 (casein kinase II) protein kinase
phosphorylation. It can also function as a
squamous-cell carcinoma antigen recognized by T cells-3
(SART3)-binding protein, and is involved in the
regulation of mRNA splicing. RNPS1 contains an
N-terminal serine-rich (S) domain, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and the
C-terminal arginine/serine/proline-rich (RS/P) domain.
.
Length = 73
Score = 42.2 bits (100), Expect = 1e-05
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 8/73 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
+++G L V + L++ YG + R+V L G+ +VEFE DA+ A+ +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 58 NGKSLLGERVTVE 70
+G + G+ VTVE
Sbjct: 61 DGGQIDGQEVTVE 73
Score = 35.2 bits (82), Expect = 0.003
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 149 HRNEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
R VEFES D +KA+ +D +++G+ +
Sbjct: 39 PRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVT 71
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 8/58 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
K+++GGL V E DL ++ YG + V + K GF FV F+DY D V
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 41.9 bits (99), Expect = 1e-05
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIR--DVILKNGFGFVEFEDYRDADDAVYELNGKS 61
T ++IG L V E DL+ + YG I+ D+I G +V E +DA A+ +L
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRNVK 62
Query: 62 LLGERVTVEIAKG 74
L G+++ V A
Sbjct: 63 LAGKKIKVAWAPN 75
Score = 29.6 bits (67), Expect = 0.38
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
L + +LS +V+ +DLK+ + GE+ D R V E+ D +AL KL N
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-PRGCAYVCMETRQDAHRALQKLRNV 61
Query: 174 ELNGRRIRL 182
+L G++I++
Sbjct: 62 KLAGKKIKV 70
>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 = 41.8 bits (99), Expect = 2e-05
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRI------RDVILKN--GFGFVEFEDYRDADDAVYELN 58
Y+G L V E L + G + RD+I + G+ +V F++ DA+ A+ LN
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62
Score = 38.7 bits (91), Expect = 2e-04
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGE-----VCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V +L V+ L + G VC +R V F++ +D ++ALD L
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61
Query: 171 DNAELNGRRIRL 182
+ + G+ IR+
Sbjct: 62 NFDVIKGKPIRI 73
>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 = 41.5 bits (98), Expect = 2e-05
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 11 LPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVYELNGKSLL 63
LP G++E L K + +G I DV LK FGFV ++ +A A+ N +
Sbjct: 8 LPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFID 67
Query: 64 GERVTVEIA 72
++TVEI
Sbjct: 68 TSKITVEIC 76
Score = 35.4 bits (82), Expect = 0.003
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKKALDK 169
RLIV+NL + L+ G + Y + R G V +++ + +KAL
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKY-TKDGKFRKFGFVGYKTEEEAQKALKH 60
Query: 170 LDNAELNGRRIRL 182
+N+ ++ +I +
Sbjct: 61 FNNSFIDTSKITV 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 = 41.4 bits (98), Expect = 2e-05
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYE 56
K+++G LP E D+ + YG I +V I+++ G FV+F +A A+
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 57 LNGK 60
L+GK
Sbjct: 61 LHGK 64
>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 = 41.1 bits (97), Expect = 2e-05
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELN 58
Y+G L + + E DL + +G I V L G+GF++F D DA A+ +LN
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61
Query: 59 GKSLLGERVTV 69
G L G + V
Sbjct: 62 GFELAGRPIKV 72
Score = 39.5 bits (93), Expect = 9e-05
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDKL 170
L V NL ++ DL+ GE+ + + R + G ++F + D KKAL++L
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 171 DNAELNGRRIRL 182
+ EL GR I++
Sbjct: 61 NGFELAGRPIKV 72
>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 = 41.1 bits (97), Expect = 3e-05
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 9/72 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL---KN-----GFGFVEFEDYRDADDAVYEL 57
V++ L VRERDL +F G++RDV + +N G +VEF D A+ L
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60
Query: 58 NGKSLLGERVTV 69
G+ LLG+ + V
Sbjct: 61 TGQRLLGQPIMV 72
Score = 32.6 bits (75), Expect = 0.025
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 11/68 (16%)
Query: 117 IVENLSSRVSWQDLKDFMRQVGEV----CYADAH-KRHRNEGVVEFESSSDMKKALDKLD 171
V LS +V +DL +F + G+V D + +R + VEF + AL
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL---- 58
Query: 172 NAELNGRR 179
L G+R
Sbjct: 59 --GLTGQR 64
>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 = 41.5 bits (98), Expect = 3e-05
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVC--------YADAHKRHRNEGVVEFESSSDMKKAL 167
L V NL+ +V+ + L + G + + +R+RN G V F + +D ++AL
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 168 DKLDNAELNGRRIRL 182
D+LD ++ G ++L
Sbjct: 64 DELDGKDVMGYELKL 78
Score = 36.1 bits (84), Expect = 0.002
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-IL----------KNGFGFVEFEDYRDADD 52
T +Y+G L V E L + +G + V I+ GFV F + DA+
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61
Query: 53 AVYELNGKSLLGERVTVEIAKGI 75
A+ EL+GK ++G + + K +
Sbjct: 62 ALDELDGKDVMGYELKLGWGKAV 84
>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 = 41.0 bits (97), Expect = 3e-05
Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 11/74 (14%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYG-RIRDVILKN-------GFGFVEFEDYRDADDAVYEL 57
V + GLP+ E D+ F G + + G +VEF DA A+ +
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61
Query: 58 NGKSLLGERVTVEI 71
N K +G R +E+
Sbjct: 62 NNK--MGGR-YIEV 72
Score = 32.5 bits (75), Expect = 0.031
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 118 VENLSSRVSWQDLKDFMRQVG------EVCYADAHKRHRNEGVVEFESSSDMKKALDKLD 171
+ L + +D++DF + + Y D R E VEF S D ++AL K
Sbjct: 4 LRGLPFSATEEDIRDFFSGLDIPPDGIHIVY-DDDGRPTGEAYVEFASPEDARRALRK-H 61
Query: 172 NAELNGRRIRL 182
N ++ GR I +
Sbjct: 62 NNKMGGRYIEV 72
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 80
Score = 41.2 bits (97), Expect = 3e-05
Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAVY 55
V++ GLP GV E DL + + +G I V + K VEFED DA V
Sbjct: 5 VHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQALVEFEDISDAKACVN 56
>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 = 40.7 bits (95), Expect = 4e-05
Identities = 24/67 (35%), Positives = 36/67 (53%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L+V NLS S L++ + + + R + VEFES+ D K+AL+ +N E+
Sbjct: 4 LVVNNLSYSASEDSLQEVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTEI 63
Query: 176 NGRRIRL 182
GR IRL
Sbjct: 64 EGRSIRL 70
Score = 27.6 bits (61), Expect = 1.7
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERVTVE 70
G+ FVEFE DA +A+ N + G + +E
Sbjct: 39 GYAFVEFESAEDAKEALNSCNNTEIEGRSIRLE 71
>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 = 40.7 bits (96), Expect = 4e-05
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRD--VILKNGFGFVEFEDYRDADDAVYELNGKS 61
T +Y+GGL V E+DL +G IR V+ + FV F A+ A L K
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFVTFTTREAAEKAAERLFNKL 61
Query: 62 LL-GERVTV 69
++ G R+ +
Sbjct: 62 IINGRRLKL 70
Score = 33.8 bits (78), Expect = 0.011
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE- 174
L V L RV+ +DL+D Q GE+ R + V F + +KA ++L N
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR-QQCAFVTFTTREAAEKAAERLFNKLI 62
Query: 175 LNGRRIRL 182
+NGRR++L
Sbjct: 63 INGRRLKL 70
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 40.8 bits (95), Expect = 4e-05
Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 10/77 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI---RDVI-----LKNGFGFVEFEDYRDADDAVYEL 57
+Y+ GLP + ++++E+ YGRI R ++ + G GF+ F+ +A++A+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63
Query: 58 NGKSLLG--ERVTVEIA 72
NG+ LG E +TV+ A
Sbjct: 64 NGQKPLGAAEPITVKFA 80
>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 = 40.8 bits (96), Expect = 4e-05
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 8/68 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
++++ LPY +E DLEK +G + +V + GF +V F D DA A E
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63
Query: 57 LNGKSLLG 64
L+GK G
Sbjct: 64 LDGKVFQG 71
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the
RRM of SRSF2 and SRSF8. SRSF2, also termed protein
PR264, or splicing component, 35 kDa (splicing factor
SC35 or SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of
pre-mRNA. It is also involved in transcription
elongation by directly or indirectly mediating the
recruitment of elongation factors to the C-terminal
domain of polymerase II. SRSF2 is exclusively localized
in the nucleus and is restricted to nuclear processes.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory
elements on the pre-mRNA. The RS domain modulates SRSF2
activity through phosphorylation, directly contacts
RNA, and promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 40.4 bits (95), Expect = 4e-05
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 8 IGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNG 59
+ L Y DL + + YG + DV + GF FV F D RDA+DA+ ++G
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 60 KSLLGERVTV 69
K L G + V
Sbjct: 63 KELDGRELRV 72
Score = 34.2 bits (79), Expect = 0.008
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKALD 168
L V+NL+ R + DL+ + GEV D + + R V F D + A+D
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEV--GDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMD 58
Query: 169 KLDNAELNGRRIR 181
+D EL+GR +R
Sbjct: 59 AMDGKELDGRELR 71
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 40.7 bits (95), Expect = 4e-05
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GGL V E DL + +G + + K GFGFV F+++ AD A
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV- 59
Query: 57 LNGKSLLGERVTVEIA 72
+ + G RV V+ A
Sbjct: 60 VKFHPINGHRVEVKKA 75
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in
serine/arginine-rich splicing factor 10 (SRSF10) and
similar proteins. This subgroup corresponds to the RRM
of SRSF10, also termed 40 kDa SR-repressor protein
(SRrp40), or FUS-interacting serine-arginine-rich
protein 1 (FUSIP1), or splicing factor SRp38, or
splicing factor, arginine/serine-rich 13A (SFRS13A), or
TLS-associated protein with Ser-Arg repeats (TASR).
SRSF10 is a serine-arginine (SR) protein that acts as a
potent and general splicing repressor when
dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. It contains a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 40.7 bits (95), Expect = 5e-05
Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 8/79 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVY 55
+ +++ + R DL + YG I DV + GF +V+FED RDA+DA++
Sbjct: 1 SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60
Query: 56 ELNGKSLLGERVTVEIAKG 74
L+ K + G ++ ++ A+G
Sbjct: 61 NLDRKWICGRQIEIQFAQG 79
>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 = 40.3 bits (95), Expect = 5e-05
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-KN------GFGFVEFEDYRDADDAVYE 56
TK+ + +P+ +++L + +G+++ V L K GF FVEF ++A +A+
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60
Query: 57 LNGKSLLGERVTVEIA 72
L L G + +E A
Sbjct: 61 LKSTHLYGRHLVLEYA 76
Score = 35.3 bits (82), Expect = 0.003
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK----RHRNEGVVEFESSSDMKKALDKL 170
+LIV N+ + ++L++ G+V K HR VEF + + + A++ L
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61
Query: 171 DNAELNGRRIRL 182
+ L GR + L
Sbjct: 62 KSTHLYGRHLVL 73
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 83
Score = 40.4 bits (95), Expect = 5e-05
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRI-------RDVILKN--GFGFVEFEDYRDADDA 53
G ++IG L V E+ L +G I RD N GF F+ ++ + +D A
Sbjct: 1 GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAA 60
Query: 54 VYELNGKSLLGERVTVEIA 72
+ +NG+ L +TV A
Sbjct: 61 IEAMNGQYLCNRPITVSYA 79
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 41.9 bits (98), Expect = 6e-05
Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADD 52
++ TK++IGGL +G + L +G + D + GFGFV F D A
Sbjct: 32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATA 91
Query: 53 AVYELNGKSLLGERVTVEIA 72
A+ E++GK L G + V A
Sbjct: 92 AISEMDGKELNGRHIRVNPA 111
Score = 31.2 bits (70), Expect = 0.31
Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADA-----HKRHRNEGVVEFESSSDMKKALDK 169
+L + LS L+D G+V A R R G V F A+ +
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
Query: 170 LDNAELNGRRIRL 182
+D ELNGR IR+
Sbjct: 96 MDGKELNGRHIRV 108
>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 = 40.0 bits (94), Expect = 6e-05
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 9/76 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GGLP V E + +++ +G++ D L GFGFV F+ A + V+
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFS 59
Query: 57 LNGKSLLGERVTVEIA 72
L G++V V+ A
Sbjct: 60 AGMLELGGKQVEVKRA 75
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 43.4 bits (102), Expect = 6e-05
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 10/80 (12%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRI-RDVILKN-------GFGFVEFEDYRDADDAV 54
G +Y+ GLP + + +LE +G+I IL + G GF+ F+ +AD A+
Sbjct: 89 GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAI 148
Query: 55 YELNGKSLLG--ERVTVEIA 72
LNG + G E +TV+ A
Sbjct: 149 KTLNGTTPSGCTEPITVKFA 168
Score = 32.2 bits (73), Expect = 0.27
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + ++ G I RD + G+GFV + DA+ AV
Sbjct: 4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 64 SLNGLRLQNKTIKVSYAR 81
Score = 28.8 bits (64), Expect = 3.0
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERV 67
G+GFV +Y +A A+ LNG + LG RV
Sbjct: 312 GYGFVSMTNYDEAAMAILSLNGYT-LGNRV 340
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 40.3 bits (94), Expect = 6e-05
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYAD---AHKRHRNEGVVEFESSSDMKKALDKLD 171
++ V NL +W+ LKD + G V YAD + + + GVV FES ++A ++
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVRFESPEVAERACRMMN 60
Query: 172 NAELNGRRIRLIEDK 186
+LNGR I + D+
Sbjct: 61 GYKLNGREIDVRIDR 75
>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 = 39.9 bits (94), Expect = 7e-05
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 11/69 (15%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAV--- 54
++++GG+P E +L F +G ++DV + G+GFV FE DA+ +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMG 63
Query: 55 -YELNGKSL 62
GK L
Sbjct: 64 NLNFRGKKL 72
>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 = 40.0 bits (94), Expect = 7e-05
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 11 LPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKSL 62
LP + + +L + G I + G+GFV++ D DA A+ LNG +
Sbjct: 8 LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67
Query: 63 LGERVTVEIA 72
+R+ V A
Sbjct: 68 RNKRLKVSYA 77
Score = 30.0 bits (68), Expect = 0.21
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV--CYADAHKRHRNE---GVVEFESSSDMKKALDKL 170
LIV L ++ ++L+ +G + C + G V++ +D +KA++ L
Sbjct: 3 LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62
Query: 171 DNAELNGRRIR 181
+ E+ +R++
Sbjct: 63 NGFEIRNKRLK 73
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate
RNA-binding protein Raly. This subgroup corresponds to
the RRM of Raly, also termed autoantigen p542, or
heterogeneous nuclear ribonucleoprotein C-like 2, or
hnRNP core protein C-like 2, or hnRNP associated with
lethal yellow protein homolog, an RNA-binding protein
that may play a critical role in embryonic development.
It is encoded by Raly, a ubiquitously expressed gene of
unknown function. Raly shows a high degree of identity
with the 5' sequences of p542 gene encoding
autoantigen, which can cross-react with EBNA-1 of the
Epstein Barr virus. Raly contains two distinct domains,
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal auxiliary domain that
includes a unique glycine/serine-rich stretch. .
Length = 76
Score = 40.0 bits (93), Expect = 8e-05
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 4 TKVYIGGLPYG-VRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
++V+IG L V++ D+E YGR+ + G+ FV++ + R A AV NG+ L
Sbjct: 2 SRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSVHKGYAFVQYSNERHARGAVIGENGRVL 61
Query: 63 LGERVTVEIA 72
G+ + + +A
Sbjct: 62 AGQTLDINMA 71
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA
tightly, suggesting a central role in the formation of
the ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal auxiliary domain that includes the
variable region, the basic region and the KSG box rich
in repeated Lys-Ser-Gly sequences, the leucine zipper,
and the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine
zipper may be involved in dimer formation. The acidic
and hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 39.6 bits (92), Expect = 8e-05
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 4 TKVYIGGL-PYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
++V+IG L V++ D+E YG+I + GF FV++ + R+A AV +G+ +
Sbjct: 2 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMI 61
Query: 63 LGERVTVEIA 72
G+ + + +A
Sbjct: 62 AGQVLDINLA 71
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP
complex, which is one of the key factors facilitating
the splicing of pre-mRNA via interaction at the 5'
splice site, and is involved in regulation of
polyadenylation of some viral and cellular genes,
enhancing or inhibiting efficient poly(A) site usage.
U1-70K plays an essential role in targeting the U1
snRNP to the 5' splice site through protein-protein
interactions with regulatory RNA-binding splicing
factors, such as the RS protein ASF/SF2. Moreover,
U1-70K protein can specifically bind to stem-loop I of
the U1 small nuclear RNA (U1 snRNA) contained in the U1
snRNP complex. It also mediates the binding of U1C,
another U1-specific protein, to the U1 snRNP complex.
U1-70K contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region at the N-terminal half, and two
serine/arginine-rich (SR) domains at the C-terminal
half. The RRM is responsible for the binding of
stem-loop I of U1 snRNA molecule. Additionally, the
most prominent immunodominant region that can be
recognized by auto-antibodies from autoimmune patients
may be located within the RRM. The SR domains are
involved in protein-protein interaction with SR
proteins that mediate 5' splice site recognition. For
instance, the first SR domain is necessary and
sufficient for ASF/SF2 Binding. The family also
includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but
its SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 39.9 bits (94), Expect = 9e-05
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 16/85 (18%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYELN 58
++ L Y E L + + YG I+ + ++++ G+ F+EFE RD A +
Sbjct: 5 FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64
Query: 59 GKSLLGERVTVEIAKGIDRSQERGR 83
GK + G RV V++ ERGR
Sbjct: 65 GKKIDGRRVLVDV--------ERGR 81
Score = 31.1 bits (71), Expect = 0.15
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V L+ + L+ + G + + R +EFE DMK A
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63
Query: 171 DNAELNGRRI 180
D +++GRR+
Sbjct: 64 DGKKIDGRRV 73
>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 = 39.5 bits (93), Expect = 1e-04
Identities = 26/68 (38%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 6 VYIGGLPYGVRERDL-EKFVKGYGRIRDV-ILK-------NGFGFVEFEDYRDADDAVYE 56
VY+G L V E L E F++ G + +V I K G+GFVEF DAD A+
Sbjct: 1 VYVGNLDEKVTEELLWELFIQA-GPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59
Query: 57 LNGKSLLG 64
+N L G
Sbjct: 60 MNMIKLYG 67
Score = 34.9 bits (81), Expect = 0.005
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKALDKL 170
V NL +V+ + L + Q G V + H + H+ G VEF S D A+ +
Sbjct: 3 VGNLDEKVTEELLWELFIQAGPVV--NVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 171 DNAELNGRRIRL 182
+ +L G+ IR+
Sbjct: 61 NMIKLYGKPIRV 72
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 39.5 bits (93), Expect = 1e-04
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVY 55
G +V++G +P + E +L + G I ++ L G+ FV + + A AV
Sbjct: 1 GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVK 60
Query: 56 ELNGKSL-LGERVTVEI 71
+L+ + G+R+ V I
Sbjct: 61 QLHNYEIRPGKRLGVCI 77
>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 = 39.5 bits (93), Expect = 1e-04
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 11/71 (15%)
Query: 6 VYIGGLPYGVRERDL-EKFVKGYGRIRDVIL---KN-----GFGFVEFEDYRDADDAVYE 56
+Y+G L + E + E F + G I+ +I+ + GF FVE+ DA++AV
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRC-GDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKY 59
Query: 57 LNGKSLLGERV 67
LNG + L +R+
Sbjct: 60 LNG-TKLDDRI 69
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 9/70 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-KN-------GFGFVEFEDYRDADDAVYEL 57
VYIG LP+G E +L K+ +G + + L ++ G+ FVEFE A +
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 58 NGKSLLGERV 67
N LL ER+
Sbjct: 62 NN-YLLFERL 70
Score = 27.5 bits (62), Expect = 1.6
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 129 DLKDFMRQVGEV--CYADAHKR---HRNEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
+L+ + Q G V K+ + VEFES K + ++N L R ++
Sbjct: 15 ELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLK 72
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 39.2 bits (91), Expect = 1e-04
Identities = 21/68 (30%), Positives = 35/68 (51%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGE 65
+++ L V E LEK +G++ V + F+ F++ A A+ E+NGK L GE
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKELEGE 63
Query: 66 RVTVEIAK 73
+ + AK
Sbjct: 64 NIEIVFAK 71
Score = 30.4 bits (68), Expect = 0.16
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L V NL++ V+ + L+ Q G++ + K+ ++ + F+ KA+++++ EL
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKL---ERVKKLKDYAFIHFDERDGAVKAMEEMNGKEL 60
Query: 176 NGRRIRLIEDKP 187
G I ++ KP
Sbjct: 61 EGENIEIVFAKP 72
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 42.2 bits (99), Expect = 1e-04
Identities = 27/81 (33%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 184 EDKPRGGGRGRSRSSSS-----RSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVS 238
D+ R RGR R SS RSR +SR R R +SR R S + + ++S
Sbjct: 5 PDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPR 64
Query: 239 RSPSPSKTRKRSRSRSDSRAR 259
S R R R R SR+
Sbjct: 65 SLRYSSVRRSRDRPRRRSRSV 85
Score = 40.3 bits (94), Expect = 6e-04
Identities = 22/75 (29%), Positives = 29/75 (38%), Gaps = 7/75 (9%)
Query: 188 RGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTR 247
R R S R R + SRS S S RS+ R+S+S S + R
Sbjct: 40 RSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRS-------VRSIEQHR 92
Query: 248 KRSRSRSDSRARKVS 262
+R R RS S +
Sbjct: 93 RRLRDRSPSNQWRKD 107
Score = 38.3 bits (89), Expect = 0.003
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYE 56
++YIG LP + E +++ ++ +G ++ ++K+ G+ F E++D D A+
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356
Query: 57 LNGKSLLGERVTVEIA 72
LNGK ++ V+ A
Sbjct: 357 LNGKDTGDNKLHVQRA 372
Score = 32.9 bits (75), Expect = 0.14
Identities = 22/80 (27%), Positives = 31/80 (38%), Gaps = 13/80 (16%)
Query: 191 GRGRSRSSSSRSRSKSRSRSRS---------SKSRS-PRSRSKSGSPRKSKSKAKSVSRS 240
R RS SR R + R SRS +SR PR RS+ +S + + R
Sbjct: 41 SRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSR---SVRSIEQHRRRLRD 97
Query: 241 PSPSKTRKRSRSRSDSRARK 260
SPS ++ + K
Sbjct: 98 RSPSNQWRKDDKKRSLWDIK 117
Score = 32.9 bits (75), Expect = 0.16
Identities = 26/76 (34%), Positives = 30/76 (39%), Gaps = 12/76 (15%)
Query: 179 RIRLIEDKPRGGGRGRSRSSSS-------RSRSKSRSRSRSSKS-----RSPRSRSKSGS 226
R + +PR R SRS S RSR + R RSRS +S R R RS S
Sbjct: 44 RSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQ 103
Query: 227 PRKSKSKAKSVSRSPS 242
RK K P
Sbjct: 104 WRKDDKKRSLWDIKPP 119
Score = 30.2 bits (68), Expect = 1.2
Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 6/62 (9%)
Query: 201 RSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRARK 260
R R KSR R R S PR RS+ +S+ + R R+ SR R R
Sbjct: 7 REREKSRGRDRDRSSERPRRRSRD------RSRFRDRHRRSRERSYREDSRPRDRRRYDS 60
Query: 261 VS 262
S
Sbjct: 61 RS 62
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element
(TAR) RNA which is synthesized by cellular RNA
polymerase II at the viral long terminal repeat. NELF
is a heterotetrameric protein consisting of NELF A, B,
C or the splice variant D, and E. NELF-E contains an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). It
plays a role in the control of HIV transcription by
binding to TAR RNA. In addition, NELF-E is associated
with the NELF-B subunit, probably via a leucine zipper
motif. .
Length = 75
Score = 39.2 bits (92), Expect = 1e-04
Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 2 VGTKVYIGGLPYGVRERDLEKFVKGYGRIRDV---ILKNGFGFVEFEDYRDADDAVYELN 58
G +Y+ G YG+ E L+K +G I ++ KN GFV FE AD A+ ELN
Sbjct: 3 KGNTLYVHG--YGLTEEILKKAFSPFGNIINISMEKEKNC-GFVTFEKMESADRAIAELN 59
Query: 59 GKSLLGERVTVEIAK 73
G ++ G ++ V +A+
Sbjct: 60 GTTVQGVQLKVSLAR 74
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. hnRNP R is predominantly located
in axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, as well as in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP R binds RNA through its RRM domains. .
Length = 72
Score = 38.9 bits (90), Expect = 1e-04
Identities = 22/68 (32%), Positives = 36/68 (52%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGE 65
+++ L V E LEK +G++ V + FV FE+ A A+ E+NGK + GE
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEERDAAVRAMDEMNGKEIEGE 63
Query: 66 RVTVEIAK 73
+ + +AK
Sbjct: 64 EIEIVLAK 71
Score = 34.2 bits (78), Expect = 0.007
Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L V NL++ V+ + L+ + G++ + K+ ++ V FE +A+D+++ E+
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKL---ERVKKLKDYAFVHFEERDAAVRAMDEMNGKEI 60
Query: 176 NGRRIRLIEDKP 187
G I ++ KP
Sbjct: 61 EGEEIEIVLAKP 72
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 42.4 bits (99), Expect = 2e-04
Identities = 37/191 (19%), Positives = 78/191 (40%), Gaps = 34/191 (17%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVYE 56
+VY+G + + +RE + + +G I+ + + GF FVE+E A A+ +
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 57 LNGKSLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRL 116
+NG+ L G + V + ++Q D + +R+
Sbjct: 169 MNGQMLGGRNIKVGRPSNMPQAQPI---------------------IDMVQEEAKKFNRI 207
Query: 117 IVENLSSRVSWQDLKDFMRQVGEVCY-----ADAHKRHRNEGVVEFESSSDMKKALDKLD 171
V ++ +S D+K GE+ A + H+ G +E+ + +A+ ++
Sbjct: 208 YVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN 267
Query: 172 NAELNGRRIRL 182
+L G+ +R+
Sbjct: 268 LFDLGGQYLRV 278
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAVYELNGKSL 62
++++G LP + E + ++ YG + +V L + GFGF+ + +A+ A EL+G
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMR 62
Query: 63 LGERVTV 69
G ++ V
Sbjct: 63 KGRQLRV 69
Score = 27.6 bits (62), Expect = 1.5
Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEV--CYADAHKRHRNEGVVEFESSSDMKKALDKLDN 172
RL V NL + ++ ++ K+ + GEV + + K G + ++ ++ +KA +LD
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK---GFGFIRLDTRTNAEKAKAELDG 59
Query: 173 AELNGRRIR 181
GR++R
Sbjct: 60 IMRKGRQLR 68
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators.
Unlike other MSSP proteins, RBMS3 is not a
transcriptional regulator. It binds with high affinity
to A/U-rich stretches of RNA, and to A/T-rich DNA
sequences, and functions as a regulator of cytoplasmic
activity. RBMS3 contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and its C-terminal
region is acidic and enriched in prolines, glutamines
and threonines. .
Length = 80
Score = 38.7 bits (89), Expect = 2e-04
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 8/67 (11%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI---RDVILKN-----GFGFVEFEDYRDADDAVY 55
T +YI GLP G ++DL K + YG+I + ++ KN G+GFV+F+ A AV
Sbjct: 5 TNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVA 64
Query: 56 ELNGKSL 62
L +
Sbjct: 65 SLKANGV 71
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 38.5 bits (89), Expect = 3e-04
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYAD---AHKRHRNEGVVEFESSSDMKKALDKLD 171
++ V NL ++WQ LK+ Q G V +A+ + + + G V F+S +KA ++
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACRLMN 60
Query: 172 NAELNGRRIRLIEDK 186
++NGR I + D+
Sbjct: 61 GIKINGREIDVRLDR 75
>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 = 38.0 bits (89), Expect = 3e-04
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 8/68 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
++++ LP+ E +L + + +G I +V L GF FV F A A E
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 57 LNGKSLLG 64
L+G G
Sbjct: 61 LDGSIFQG 68
Score = 31.9 bits (73), Expect = 0.045
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH-------KRHRNEGVVEFESSSDMKKAL 167
RL V NL + ++L++ GE+ ++ H KR + V F KA
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEI--SEVHLPLDKETKRSKGFAFVSFMFPEHAVKAY 58
Query: 168 DKLDNAELNGRRIRL 182
+LD + GR + +
Sbjct: 59 SELDGSIFQGRLLHV 73
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 77
Score = 38.0 bits (89), Expect = 3e-04
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVY 55
++Y+ + + E D++ + +G+I+ L G+GF+E+E+ + A DA+
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Query: 56 ELNGKSLLGERVTVEIA 72
+N L G+++ V A
Sbjct: 61 SMNLFDLGGQQLRVGKA 77
Score = 31.1 bits (71), Expect = 0.091
Identities = 14/73 (19%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYAD-----AHKRHRNEGVVEFESSSDMKKALD 168
+R+ V ++ +S D+K G++ +H+ G +E+E+ + A+
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Query: 169 KLDNAELNGRRIR 181
++ +L G+++R
Sbjct: 61 SMNLFDLGGQQLR 73
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. It functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 38.1 bits (89), Expect = 3e-04
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
V NL +V W+ LK+ + G+V A D + R GVV+FE + +A+ +
Sbjct: 3 VANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFNGQ 62
Query: 174 ELNGRRIRL 182
L R +R+
Sbjct: 63 MLFDRPMRV 71
Score = 29.7 bits (67), Expect = 0.34
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVYELN 58
+++ L Y V + L++ K G++ +K G G V+FE +A A+ N
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60
Query: 59 GKSLLGERVTVEI 71
G+ L + V++
Sbjct: 61 GQMLFDRPMRVKM 73
>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 = 37.9 bits (88), Expect = 4e-04
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--GFGFVEFEDYRDADDAVYELNGKS 61
+++++G LP + E ++ K + YG+ ++ + GFGF+ E A+ A EL+
Sbjct: 2 SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMP 61
Query: 62 LLGERVTV 69
L G+++ V
Sbjct: 62 LRGKQLRV 69
Score = 27.2 bits (60), Expect = 2.4
Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
RL V NL ++ ++++ + G+ HK + G + E+ + + A +LDN
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHK-DKGFGFIRLETRTLAEIAKAELDNMP 61
Query: 175 LNGRRIRL 182
L G+++R+
Sbjct: 62 LRGKQLRV 69
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM2 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 73
Score = 37.7 bits (88), Expect = 4e-04
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 8/70 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYEL 57
+++G L + E + + YG I V L GFG+VEF A A+ L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 58 NGKSLLGERV 67
G LLG V
Sbjct: 61 GGTDLLGRPV 70
Score = 30.8 bits (70), Expect = 0.12
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRIRL 182
G VEF S + ALD L +L GR +RL
Sbjct: 43 GYVEFSSQEAAQAALDALGGTDLLGRPVRL 72
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 37.6 bits (88), Expect = 4e-04
Identities = 26/70 (37%), Positives = 38/70 (54%), Gaps = 7/70 (10%)
Query: 118 VENLSSRVSWQDLKDFMRQVG-----EVCYADAHK-RHRNEGVVEFESSSDMKKALDKLD 171
V LS + +DL++ + G +V Y D R R G V FES D K+A ++L+
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPIEKVQVVY-DQKTGRSRGFGFVYFESVEDAKEAKERLN 62
Query: 172 NAELNGRRIR 181
E++GRRIR
Sbjct: 63 GMEIDGRRIR 72
Score = 34.9 bits (81), Expect = 0.004
Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 10 GLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKS 61
GL ERDL + YG I V + GFGFV FE DA +A LNG
Sbjct: 6 GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65
Query: 62 LLGERVTVEIA 72
+ G R+ V+ +
Sbjct: 66 IDGRRIRVDYS 76
>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 = 37.7 bits (88), Expect = 5e-04
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVYELN 58
++G LP+ + DL+ K ++ V L GF +VEFED +A+ E +
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEAL-EYD 62
Query: 59 GKSLLGERVTVEIA 72
G + V+IA
Sbjct: 63 GALFDDRSLRVDIA 76
Score = 31.5 bits (72), Expect = 0.062
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 155 VEFESSSDMKKALDKLDNAELNGRRIRL 182
VEFE +K+AL+ D A + R +R+
Sbjct: 47 VEFEDVESLKEALE-YDGALFDDRSLRV 73
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in
mRNA stability in mammalian cells. hnRNP A1 is an
abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The hnRNP D subfamily includes hnRNP D0,
hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a
UUAG-specific nuclear RNA binding protein that may be
involved in pre-mRNA splicing and telomere elongation.
hnRNP A/B is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus, plays an
important role in apoB mRNA editing. hnRNP DL (or hnRNP
D-like) is a dual functional protein that possesses
DNA- and RNA-binding properties. It has been implicated
in mRNA biogenesis at the transcriptional and
post-transcriptional levels. All members in this
subfamily contain two putative RRMs and a glycine- and
tyrosine-rich C-terminus. The family also contains
DAZAP1 (Deleted in azoospermia-associated protein 1),
RNA-binding protein Musashi homolog Musashi-1,
Musashi-2 and similar proteins. They all harbor two
RRMs. .
Length = 72
Score = 37.6 bits (88), Expect = 5e-04
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 12/66 (18%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAV---- 54
+IGGL + E L ++ YG + D ++ GFGFV F D D +
Sbjct: 2 FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61
Query: 55 YELNGK 60
+ L+G+
Sbjct: 62 HVLDGR 67
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM2 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 71
Score = 37.2 bits (87), Expect = 5e-04
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 27 YGRIRDVILKNGFG---FVEFEDYRDADDAVYELNGKSLLGERVTVE 70
+G ++D+ FVEF D R A+ A+ LNG+ LG R+ V+
Sbjct: 25 FGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRPFLGGRLKVK 71
Score = 31.4 bits (72), Expect = 0.062
Identities = 21/67 (31%), Positives = 32/67 (47%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L+V NL S +S Q+L+ Q GEV ++ VEF + ALD L+
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNGRPF 63
Query: 176 NGRRIRL 182
G R+++
Sbjct: 64 LGGRLKV 70
>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 = 37.5 bits (87), Expect = 5e-04
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYEL 57
++++GG+ + E DL KF YG +++V + N G+GFV FE DA + E
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEA 63
Query: 58 N 58
N
Sbjct: 64 N 64
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 37.1 bits (86), Expect = 6e-04
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV--CYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
L+V NL VS DL GE+ +KRH +EF + AL L+ +
Sbjct: 4 LVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHK--FIEFYDVRSAEAALKALNRS 61
Query: 174 ELNGRRIRL 182
E+ G+RI+L
Sbjct: 62 EIAGKRIKL 70
Score = 34.4 bits (79), Expect = 0.007
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 15 VRERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVE 70
V DL + YG I+++ K F+EF D R A+ A+ LN + G+R+ +E
Sbjct: 13 VSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNRSEIAGKRIKLE 71
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 37.3 bits (86), Expect = 6e-04
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAVYELNGKSLL 63
VY GG+ G+ E+ + + +G+I +V + G+ FV F + A A+ +NG ++
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFVRFNSHESAAHAIVSVNGTTIE 62
Query: 64 GERV 67
G V
Sbjct: 63 GHVV 66
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 40.4 bits (94), Expect = 6e-04
Identities = 65/270 (24%), Positives = 102/270 (37%), Gaps = 45/270 (16%)
Query: 5 KVYIGGLP-YGVRERDLEKFVKGYGRIRDVIL--------KN-GFGFVEFEDYRDADDAV 54
++++GG+P RE LE+F K + DVI+ KN GF FVE+E +R A A
Sbjct: 140 RLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMAR 199
Query: 55 YEL-NGK-SLLGERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRS 112
+L G+ L G + V+ W ++
Sbjct: 200 RKLMPGRIQLWGHVIAVD---------------------------WAEPEEEVDEDVMAK 232
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDN 172
L V NL + + + ++ + + K+ R+ V FE D KA+D+L+
Sbjct: 233 VKILYVRNLMTTTTEEIIEKSFSEFKPGK-VERVKKIRDYAFVHFEDREDAVKAMDELNG 291
Query: 173 AELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSR----SPRSRSKSGSPR 228
EL G I + KP + + R K R +R S + + RS +
Sbjct: 292 KELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYY- 350
Query: 229 KSKSKAKSVSRSPSPSKTRKRSRSRSDSRA 258
A S+ P R R R + SRA
Sbjct: 351 YHPPYAPSLHFPRMPGPIRGRGRGGAPSRA 380
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 37.7 bits (88), Expect = 7e-04
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L L+ S +D+K+ Q GEV Y D EG V F++ KKAL+K A+L
Sbjct: 4 LKFSGLNKPTSREDIKEAFSQHGEVKYVD-FLEGDKEGYVRFKTPEAAKKALEKATEAKL 62
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 37.2 bits (87), Expect = 7e-04
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKL 170
+L+V NL VS D+K+ + G + A D R V FE +D KA+ +
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQY 61
Query: 171 DNAELNGR 178
+ L+GR
Sbjct: 62 NGVPLDGR 69
>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 = 37.3 bits (87), Expect = 7e-04
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL------KNGFGFVEFEDYRDADDAVYELNG 59
+++G L V + +L + +G+I +V L N F F++FE + A AV N
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65
Query: 60 KSLLGERVTVE 70
L + + V+
Sbjct: 66 SMLKNKTMHVQ 76
Score = 27.3 bits (61), Expect = 2.3
Identities = 11/69 (15%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGV-----VEFESSSDMKKALDKLDN 172
V LS V+ ++L + + G++ + + R ++FE +A++ ++
Sbjct: 8 VGQLSPDVTKEELNERFSRHGKI--LEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65
Query: 173 AELNGRRIR 181
+ L + +
Sbjct: 66 SMLKNKTMH 74
>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 = 37.4 bits (87), Expect = 8e-04
Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 13/78 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------------GFGFVEFEDYRDAD 51
+VYI L Y E DLE+F+K + + +I G + EF A+
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 52 DAVYELNGKSLLGERVTV 69
V +LNGK ++ V
Sbjct: 61 KVVKDLNGKVFKNRKLFV 78
Score = 30.0 bits (68), Expect = 0.24
Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 10/78 (12%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKR---HRNEGV--VEFESSSDMK 164
R+ + NLS S +DL++F++ V R R G+ EF S +
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 165 KALDKLDNAELNGRRIRL 182
K + L+ R++ +
Sbjct: 61 KVVKDLNGKVFKNRKLFV 78
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 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). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 36.8 bits (86), Expect = 0.001
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKL---DN 172
L + + S +DLK+ + GEV + D R + EG V F+ + K+AL+KL N
Sbjct: 4 LHFSGVGEQTSREDLKEAFEEFGEVAWVD-FARGQTEGYVRFKEENAAKEALEKLKEAKN 62
Query: 173 AELNGRRI--RLIE 184
++ G + +L+E
Sbjct: 63 LKIKGSEVTVKLLE 76
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2
of PHIP1. A. thaliana PHIP1 and its homologs represent
a novel class of plant-specific RNA-binding proteins
that may play a unique role in the polarized mRNA
transport to the vicinity of the cell plate. The family
members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 36.6 bits (85), Expect = 0.001
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKG-------YGRIRDVILKNGFGFVEFEDYRDADDAVYELN 58
VYIG L + + E D+ +F KG ++ GFG V+F D D A+ +L+
Sbjct: 2 VYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KLD 60
Query: 59 GKSLLGERVTV 69
G L G + +
Sbjct: 61 GTVLCGRPIRI 71
Score = 26.2 bits (58), Expect = 4.4
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRIRL 182
G V+F + AL KLD L GR IR+
Sbjct: 43 GHVDFADEESLDAAL-KLDGTVLCGRPIRI 71
>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 = 36.6 bits (85), Expect = 0.001
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 11/65 (16%)
Query: 10 GLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVYELNGKS 61
GLP+ E+DL+ + +G + V +K GFGFV F DY +D V L+ +
Sbjct: 6 GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADY---EDQVKVLSQRH 62
Query: 62 LLGER 66
++ R
Sbjct: 63 MIDGR 67
Score = 30.4 bits (69), Expect = 0.16
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKAL 167
LIV L + + QDLKD+ GE+ K + + G V F D K L
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM1 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 36.8 bits (86), Expect = 0.001
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL---KNG----FGFVEFEDYRDADDAVYE 56
+++ + LP V E L + + G + DV + ++G FGFV F+ DA AV
Sbjct: 1 SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60
Query: 57 LNGKSLLGERVTVEIA 72
N + +++VE+A
Sbjct: 61 FNKTFIDTSKISVELA 76
Score = 28.7 bits (65), Expect = 0.60
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAH------KRHRNEGVVEFESSSDMKKALD 168
R+IV+NL V+ L++ GEV D + R G V F+S D ++A+
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEV--TDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVK 59
Query: 169 KLDNAELNGRRI 180
+ ++ +I
Sbjct: 60 YFNKTFIDTSKI 71
>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 = 36.5 bits (85), Expect = 0.001
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 12/65 (18%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN---GFGFVEFEDYRDADDAVYELNGK 60
KV++G L + E DL ++ +G + DV + F FV F D + A +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTF---ADPEVA------Q 51
Query: 61 SLLGE 65
SL GE
Sbjct: 52 SLCGE 56
>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 = 36.6 bits (85), Expect = 0.001
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 8/50 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKNG-------FGFVEFED 46
++++G LP+ + E +L++F K +G + +V I G FGFV F+D
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDD 54
Score = 30.8 bits (70), Expect = 0.12
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 6/78 (7%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRH-----RNEGVVEFESSSDMKKALD 168
H+L V NL ++ +LK+F ++ G V + + N G V F+ ++K L
Sbjct: 4 HQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILA 63
Query: 169 KLDNAELNGRRIRLIEDK 186
R+ +E+K
Sbjct: 64 NKPIYFRGDHRLN-VEEK 80
>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 = 36.8 bits (85), Expect = 0.001
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV---ILKN----GFGFVEFEDYRDADDAVYELN 58
+Y+G L V E L++ + G +++V KN +GFVE+ DA+ A+ LN
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60
Query: 59 GKSLLGERVTVEIA 72
G+ + + V A
Sbjct: 61 GRQIENNEIRVNWA 74
Score = 29.8 bits (67), Expect = 0.28
Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 9/69 (13%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV----CYADAHKRHRNEGVVEFESSSDMKKALDKLD 171
L V NL RV+ LK + G V D + + N G VE+ S D + AL
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQT-- 58
Query: 172 NAELNGRRI 180
LNGR+I
Sbjct: 59 ---LNGRQI 64
>gnl|CDD|218883 pfam06075, DUF936, Plant protein of unknown function (DUF936).
This family consists of several hypothetical proteins
from Arabidopsis thaliana and Oryza sativa. The function
of this family is unknown.
Length = 564
Score = 39.8 bits (93), Expect = 0.001
Identities = 20/84 (23%), Positives = 31/84 (36%)
Query: 177 GRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKS 236
GRR + + RG R + + + K SRS KS S + SP KS + K+
Sbjct: 206 GRRSSIGSRRLRGSASLRKKVAVLSAPRKPGSRSSDCKSSPRARSSSAKSPFKSSIQRKA 265
Query: 237 VSRSPSPSKTRKRSRSRSDSRARK 260
S + S++
Sbjct: 266 TKALSKLSLRASPKDTSKSSKSEV 289
Score = 35.2 bits (81), Expect = 0.032
Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 4/107 (3%)
Query: 160 SSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSP- 218
S D +D++ + R ++ SSRS + S S + S
Sbjct: 145 SWDSSSKSASIDSSPTVIGPRPRSFSELNLTDRTPAKVRSSRSELGAPSPSGGTSCPSSS 204
Query: 219 ---RSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRARKVS 262
RS S R S S K V+ +P K RS S + S
Sbjct: 205 GGRRSSIGSRRLRGSASLRKKVAVLSAPRKPGSRSSDCKSSPRARSS 251
Score = 34.0 bits (78), Expect = 0.076
Identities = 22/95 (23%), Positives = 36/95 (37%), Gaps = 12/95 (12%)
Query: 178 RRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAK-- 235
R L P GG S S RS SR S+ R + + +PRK S++
Sbjct: 185 SRSELGAPSPSGGTSCPSSSGGRRSSIGSRRLRGSASLR--KKVAVLSAPRKPGSRSSDC 242
Query: 236 --------SVSRSPSPSKTRKRSRSRSDSRARKVS 262
S ++SP S ++++ + + S
Sbjct: 243 KSSPRARSSSAKSPFKSSIQRKATKALSKLSLRAS 277
Score = 33.6 bits (77), Expect = 0.096
Identities = 31/135 (22%), Positives = 53/135 (39%), Gaps = 6/135 (4%)
Query: 124 RVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLI 183
R S +L G C + + R + G S+ ++K + L G R
Sbjct: 183 RSSRSELGAPSPSGGTSCPSSSGGRRSSIGSRRLRGSASLRKKVAVLSAPRKPGSRSSDC 242
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSP 243
+ PR +RSSS++S KS + +++K+ S S S SK++ S
Sbjct: 243 KSSPR------ARSSSAKSPFKSSIQRKATKALSKLSLRASPKDTSKSSKSEVAPPKKSE 296
Query: 244 SKTRKRSRSRSDSRA 258
+K S+ +D
Sbjct: 297 AKVPSSSKKWTDGNV 311
Score = 27.5 bits (61), Expect = 9.8
Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 7/84 (8%)
Query: 186 KPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSP-------RKSKSKAKSVS 238
+ + R S S S+S S S + PRS S+ R S+S+ + S
Sbjct: 134 RKKASSAPRRGSWDSSSKSASIDSSPTVIGPRPRSFSELNLTDRTPAKVRSSRSELGAPS 193
Query: 239 RSPSPSKTRKRSRSRSDSRARKVS 262
S S RS +R++
Sbjct: 194 PSGGTSCPSSSGGRRSSIGSRRLR 217
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 92
Score = 36.9 bits (86), Expect = 0.001
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 7 YIGGLPYGVRERD-LEKFVKGYGRIRD--VILKN-----GFGFVEFEDYRDADDAVYELN 58
++ LP R+ L K G+ + + GF FVE+ DA++A LN
Sbjct: 6 FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALN 65
Query: 59 GKSLLGERVTV 69
G SL G + V
Sbjct: 66 GHSLQGSPIRV 76
Score = 28.0 bits (63), Expect = 1.4
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRIR 181
VE+ ++ D ++A L+ L G IR
Sbjct: 47 AFVEYATAEDAEEAQQALNGHSLQGSPIR 75
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 36.6 bits (85), Expect = 0.001
Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR-IRDVILKN------GFGFVEFEDYRDADDAVYE 56
T +YI LP + E+DLE +K YG+ I IL++ G GF E +D + +
Sbjct: 1 TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISK 60
Query: 57 LNGKSLLGE 65
NGK L GE
Sbjct: 61 FNGKYLKGE 69
>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 = 36.6 bits (85), Expect = 0.001
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVYEL 57
VY+GG+PY E ++ + G I ++ L G F+ F+ +A L
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKT-EEAAKRALAL 59
Query: 58 NGKSLLGERVTVE 70
+G+ + G + VE
Sbjct: 60 DGEDMGGRFLKVE 72
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 90
Score = 37.1 bits (85), Expect = 0.001
Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 10/77 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI---RDVI-----LKNGFGFVEFEDYRDADDAVYEL 57
+Y+ GLP + +++LE+ YGRI R ++ + G GF+ F+ +A++A+ L
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67
Query: 58 NGKSLLG--ERVTVEIA 72
NG+ G E +TV+ A
Sbjct: 68 NGQKPPGATEPITVKFA 84
>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 = 36.5 bits (85), Expect = 0.001
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
V NL V +L+ + GE+ + + + VEFE+ +++AL KLD
Sbjct: 4 VSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-KLDRE 62
Query: 174 ELNGR 178
+ GR
Sbjct: 63 LIKGR 67
Score = 31.9 bits (73), Expect = 0.043
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDA 53
V++ L Y V E +L K G I DV ++KN G+ +VEFE+ +A
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEA 56
>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 = 36.5 bits (85), Expect = 0.001
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYEL 57
+++G + YG +L++ K G I + IL + GF ++EF D ++A+ L
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60
Query: 58 NGKSLLGERVTV 69
N G ++ V
Sbjct: 61 NESEFRGRQIKV 72
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells and also regulates the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 36.6 bits (84), Expect = 0.001
Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 10/77 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI---RDVI-----LKNGFGFVEFEDYRDADDAVYEL 57
+Y+ GLP + +++LE+ YGRI R ++ + G GF+ F+ +A++A+ L
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64
Query: 58 NGKSLLG--ERVTVEIA 72
NG+ G E +TV+ A
Sbjct: 65 NGQKPSGAAEPITVKFA 81
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 36.3 bits (84), Expect = 0.001
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 20 LEKFVKGYG---RIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVE 70
L + YG +R+ K FVEF D RDA A+ +NGK + G+ V +E
Sbjct: 18 LRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKEISGKPVVIE 71
Score = 30.6 bits (69), Expect = 0.12
Identities = 18/67 (26%), Positives = 32/67 (47%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L++ NL VS + L+ + G+V R + VEF D KAL ++ E+
Sbjct: 4 LVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKEI 63
Query: 176 NGRRIRL 182
+G+ + +
Sbjct: 64 SGKPVVI 70
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 36.5 bits (84), Expect = 0.001
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 10/77 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
+YI GLP + ++D+E +GRI + L G F+ F+ +A++A+
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62
Query: 58 NGKSLLG--ERVTVEIA 72
NG G E +TV+ A
Sbjct: 63 NGHKPPGSSEPITVKFA 79
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. SKAR is
widely expressed and localizes to the nucleus. It may be
a critical player in the function of S6K1 in cell and
organism growth control by binding the activated,
hyperphosphorylated form of S6K1 but not S6K2.
Furthermore, SKAR functions as a protein partner of the
p50 subunit of DNA polymerase delta. In addition, SKAR
may have particular importance in pancreatic beta cell
size determination and insulin secretion. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 36.1 bits (84), Expect = 0.002
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
RL+V NL V+ D+ + +G + A V + D A+DK +N
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGAL--KRARLVRPGVAEVVYVRKDDALTAIDKYNNR 58
Query: 174 ELNGRRIR 181
EL+G+ ++
Sbjct: 59 ELDGQPMK 66
>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 = 36.0 bits (84), Expect = 0.002
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 9/73 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYEL 57
V++G LP+ + E +L K + G + V I+++ GFG+V F+ +D+ +L
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKT-KDSVALALKL 60
Query: 58 NGKSLLGERVTVE 70
NG L G ++ V+
Sbjct: 61 NGIKLKGRKIRVK 73
Score = 28.3 bits (64), Expect = 0.85
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRIRL 182
G V F++ + AL KL+ +L GR+IR+
Sbjct: 44 GYVLFKTKDSVALAL-KLNGIKLKGRKIRV 72
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is the ubiquitously expressed Hu family member. It
has a variety of biological functions mostly related to
the regulation of cellular response to DNA damage and
other types of stress. Hu proteins perform their
cytoplasmic and nuclear molecular functions by
coordinately regulating functionally related mRNAs. In
the cytoplasm, Hu proteins recognize and bind to
AU-rich RNA elements (AREs) in the 3' untranslated
regions (UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. Also included
in this subfamily is the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 36.1 bits (83), Expect = 0.002
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 10/79 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVI--LKNGFGFVEFEDYRDADDAVY 55
+Y+ GLP + +++LE+ YGRI RD + + G GF+ F+ +A++A+
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Query: 56 ELNGKSLLG--ERVTVEIA 72
LNG+ G E +TV+ A
Sbjct: 61 GLNGQKPEGASEPITVKFA 79
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind
to cytoplasmic proteins. Raver-2 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. Raver-2 binds to PTB through the
SLLGEPP motif only, and binds to RNA through its RRMs.
.
Length = 77
Score = 36.0 bits (83), Expect = 0.002
Identities = 22/68 (32%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 8 IGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNG 59
+ LP + E+ V+ YG I L G+GFVE+ A A EL G
Sbjct: 4 VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63
Query: 60 KSLLGERV 67
K LGE
Sbjct: 64 KQ-LGEST 70
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 36.1 bits (84), Expect = 0.002
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 29 RIRDVI--LKNGFGFVEFEDYRDADDAVYELNGK 60
IR+ G+GFVEF + A+ A+ LNGK
Sbjct: 31 IIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGK 64
>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 = 35.9 bits (83), Expect = 0.002
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 11/75 (14%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYEL 57
+++G L + E +L GRIR V + GF FV+FE+ A +A L
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA---L 57
Query: 58 NGKSLLGERVTVEIA 72
GK L G + VE
Sbjct: 58 KGKHLNGRALRVEYG 72
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 36.0 bits (84), Expect = 0.002
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN------------GFGFVEFEDYRDA 50
T +++ L + E L+K + G +R V I K G+GFVEF+ A
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60
Query: 51 DDAVYELNGKSLLGERVTVEI 71
A+ L G L G + +++
Sbjct: 61 QKALKRLQGTVLDGHALELKL 81
Score = 29.5 bits (67), Expect = 0.36
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRIRL 182
G VEF+S +KAL +L L+G + L
Sbjct: 50 GFVEFKSKEAAQKALKRLQGTVLDGHALEL 79
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved
poly(A) binding protein containing poly(A) tails that
can be attached to the 3'-ends of mRNAs. The yeast PABP
and its homologs may play important roles in the
initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 77
Score = 36.0 bits (84), Expect = 0.002
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERVTV 69
G+GFV FE A A+ ++NG L ++V V
Sbjct: 44 GYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75
Score = 26.7 bits (60), Expect = 3.8
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRI 180
G V FE+ +A++K++ LN +++
Sbjct: 46 GFVHFETEEAAVRAIEKVNGMLLNDKKV 73
>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 = 36.0 bits (84), Expect = 0.002
Identities = 19/80 (23%), Positives = 31/80 (38%), Gaps = 18/80 (22%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNG-------------FGFVEFEDYRDAD 51
++Y+G LP G+ E +L F + G F FVEF R +
Sbjct: 3 RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEF---RTVE 59
Query: 52 DAV--YELNGKSLLGERVTV 69
+A L+G G+ + +
Sbjct: 60 EATAALALDGIIFKGQPLKI 79
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 2 (Musashi-2) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 79
Score = 35.8 bits (82), Expect = 0.002
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 8/49 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFE 45
K+++GGL D++++ + +G++ D +L GFGFV FE
Sbjct: 5 KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53
Score = 26.9 bits (59), Expect = 2.8
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKKALD 168
++ V LS+ +D+K + Q G+V + RHR G V FE+ ++K +
Sbjct: 5 KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 35.7 bits (82), Expect = 0.003
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFEDYRDADDAVYE 56
K++IGGL + ++DL +++ +G + D +K GFGFV F+D D V E
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASV-DKVLE 59
Query: 57 LNGKSLLGERVTVEIAK 73
L L G+ + + AK
Sbjct: 60 LKEHKLDGKLIDPKRAK 76
>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 = 35.5 bits (82), Expect = 0.003
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVYE 56
+VY+G + + + E + + +G I+ + + GF FVE+E A A+ +
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61
Query: 57 LNGKSLLGERVTV 69
+NG L G + V
Sbjct: 62 MNGVMLGGRNIKV 74
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 35.4 bits (82), Expect = 0.003
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 6/70 (8%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVC----YADAH-KRHRNEGVVEFESSSDMKKALDKL 170
L V NL + +DL + G D + + VEF+++ M KAL KL
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-KL 61
Query: 171 DNAELNGRRI 180
+ L GR+I
Sbjct: 62 HHTLLKGRKI 71
Score = 33.5 bits (77), Expect = 0.014
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 9/73 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYEL 57
+++G LPY DL K G V L G FVEF+ A+ +L
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-KL 61
Query: 58 NGKSLLGERVTVE 70
+ L G ++ VE
Sbjct: 62 HHTLLKGRKINVE 74
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions
as a translational regulator that activates translation
in an mRNA-specific manner. DAZAP1 was initially
identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 82
Score = 35.6 bits (82), Expect = 0.003
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 8/50 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRD-VILKN-------GFGFVEFED 46
K+++GGL + + L ++ YG + D VI+K+ GFGFV+F+D
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM1 of the majority of family
members that include polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. Rod1 is
a mammalian polypyrimidine tract binding protein (PTB)
homolog of a regulator of differentiation in the
fission yeast Schizosaccharomyces pombe, where the nrd1
gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It might play a role controlling
differentiation in mammals. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. In addition, this family also includes
RNA-binding motif protein 20 (RBM20) that is an
alternative splicing regulator associated with dilated
cardiomyopathy (DCM) and contains only one RRM. .
Length = 74
Score = 35.3 bits (82), Expect = 0.003
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFG--FVEFEDYRDA 50
+++ LP V E DL V +G++ +V+L G VE + A
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDSVESA 48
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 38.6 bits (90), Expect = 0.003
Identities = 29/88 (32%), Positives = 35/88 (39%), Gaps = 4/88 (4%)
Query: 176 NGRRIRLIEDKPRGGGRGRSRS---SSSRSRSK-SRSRSRSSKSRSPRSRSKSGSPRKSK 231
NG R R RS S SS S S R+ SS S S S S S S
Sbjct: 276 NGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSES 335
Query: 232 SKAKSVSRSPSPSKTRKRSRSRSDSRAR 259
S+ +VS PSPS++ SR +
Sbjct: 336 SRGAAVSPGPSPSRSPSPSRPPPPADPS 363
Score = 37.1 bits (86), Expect = 0.010
Identities = 24/70 (34%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 191 GRGRSRSSSSRSR-SKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKR 249
S + S R S S S SR S S S S S+S S S SRSPSPS+
Sbjct: 301 SSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAV-SPGPSPSRSPSPSRPPPP 359
Query: 250 SRSRSDSRAR 259
+ S +
Sbjct: 360 ADPSSPRKRP 369
Score = 36.7 bits (85), Expect = 0.011
Identities = 20/68 (29%), Positives = 29/68 (42%)
Query: 192 RGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSR 251
S ++ S S SRS S P + S R S+A S + + TR+R+R
Sbjct: 332 SSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRAR 391
Query: 252 SRSDSRAR 259
+ RAR
Sbjct: 392 AAVAGRAR 399
Score = 36.3 bits (84), Expect = 0.014
Identities = 26/89 (29%), Positives = 30/89 (33%), Gaps = 13/89 (14%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSK------------ 231
+ G SR + S S R RS S SP S SPR S
Sbjct: 269 IWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSS 328
Query: 232 -SKAKSVSRSPSPSKTRKRSRSRSDSRAR 259
S + SR + S SRS S SR
Sbjct: 329 TSSSSESSRGAAVSPGPSPSRSPSPSRPP 357
Score = 35.5 bits (82), Expect = 0.025
Identities = 20/78 (25%), Positives = 26/78 (33%), Gaps = 9/78 (11%)
Query: 191 GRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKS---------GSPRKSKSKAKSVSRSP 241
R SSSS S S SR + SRS S S + + + SP
Sbjct: 319 SSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSP 378
Query: 242 SPSKTRKRSRSRSDSRAR 259
+ S R R + A
Sbjct: 379 AASAGRPTRRRARAAVAG 396
Score = 35.5 bits (82), Expect = 0.028
Identities = 21/69 (30%), Positives = 24/69 (34%), Gaps = 1/69 (1%)
Query: 192 RGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSP-RKSKSKAKSVSRSPSPSKTRKRS 250
SR SSS S S S SR + S S+S SP R S R S
Sbjct: 318 SSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSS 377
Query: 251 RSRSDSRAR 259
+ S R
Sbjct: 378 PAASAGRPT 386
Score = 35.5 bits (82), Expect = 0.030
Identities = 30/90 (33%), Positives = 36/90 (40%), Gaps = 3/90 (3%)
Query: 176 NGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAK 235
R P G S +SS S S S S S+ S S SR + SP S S++
Sbjct: 292 RERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSP 351
Query: 236 SVSRSPS---PSKTRKRSRSRSDSRARKVS 262
S SR P PS RKR R + S
Sbjct: 352 SPSRPPPPADPSSPRKRPRPSRAPSSPAAS 381
Score = 33.6 bits (77), Expect = 0.11
Identities = 12/67 (17%), Positives = 20/67 (29%), Gaps = 1/67 (1%)
Query: 188 RGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKA-KSVSRSPSPSKT 246
R R + S + R R + S S + R + A ++ R +
Sbjct: 349 RSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGRFP 408
Query: 247 RKRSRSR 253
R R
Sbjct: 409 AGRPRPS 415
Score = 31.3 bits (71), Expect = 0.60
Identities = 16/73 (21%), Positives = 21/73 (28%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSP 243
+ P + + S S S S + SP S S S SP
Sbjct: 253 NECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSP 312
Query: 244 SKTRKRSRSRSDS 256
+ S SR S
Sbjct: 313 RASSSSSSSRESS 325
Score = 30.5 bits (69), Expect = 0.94
Identities = 14/73 (19%), Positives = 23/73 (31%)
Query: 187 PRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKT 246
RS S+ + S + + RS+ + S S S S S + P P
Sbjct: 202 ASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPA 261
Query: 247 RKRSRSRSDSRAR 259
+R +
Sbjct: 262 PITLPTRIWEASG 274
Score = 27.8 bits (62), Expect = 8.1
Identities = 10/42 (23%), Positives = 19/42 (45%)
Query: 187 PRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPR 228
PR R SS + + +R R+ + + R+R + + R
Sbjct: 365 PRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGR 406
Score = 27.4 bits (61), Expect = 9.3
Identities = 20/92 (21%), Positives = 26/92 (28%), Gaps = 16/92 (17%)
Query: 187 PRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPR---------------SRSKSGSPRKSK 231
R SSS S S+S ++ P S S R
Sbjct: 225 GRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGP 284
Query: 232 SKAKSVSRSPSPSKTRKRSRSRS-DSRARKVS 262
+ + S R SPS + S S R S
Sbjct: 285 ASSSSSPRERSPSPSPSSPGSGPAPSSPRASS 316
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM, but
unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might share
similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 35.0 bits (81), Expect = 0.003
Identities = 22/71 (30%), Positives = 28/71 (39%), Gaps = 5/71 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNE-----GVVEFESSSDMKKALDKL 170
L V LSS DLK + G+V A R+ G V S + K + L
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 171 DNAELNGRRIR 181
EL+GR I
Sbjct: 62 HRTELHGRVIS 72
Score = 32.3 bits (74), Expect = 0.038
Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 8/73 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
+++ GL + DL++ YG++ FGFV +A + L
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 58 NGKSLLGERVTVE 70
+ L G ++VE
Sbjct: 62 HRTELHGRVISVE 74
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and four hnRNP K homology (KH) domains. .
Length = 76
Score = 35.0 bits (81), Expect = 0.003
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 5/72 (6%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRD---VILKNGFG--FVEFEDYRDADDAVYELN 58
K+ I +P VR DL+ + YG +++ V K+ V +E A AV +LN
Sbjct: 1 RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLN 60
Query: 59 GKSLLGERVTVE 70
G G ++ V
Sbjct: 61 GHEYEGSKLKVS 72
Score = 28.8 bits (65), Expect = 0.72
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVE--FESSSDMKKALDKLDN 172
++ + N+ V W+DL + G V + V +ES ++A++KL+
Sbjct: 2 KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLNG 61
Query: 173 AELNGRRIR 181
E G +++
Sbjct: 62 HEYEGSKLK 70
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2,
Smad3 and Smad4, and stimulates Smad-mediated
transactivation. Cpo may play an important role in
regulating normal function of the nervous system,
whereas mutations in Mec-8 affect mechanosensory and
chemosensory neuronal function. All members contain a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). Some uncharacterized family members contain
two RRMs; this subfamily includes their RRM1. Their
RRM2 shows high sequence homology to the RRM of yeast
proteins scw1, Whi3, and Whi4.
Length = 79
Score = 35.3 bits (82), Expect = 0.003
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 11/64 (17%)
Query: 6 VYIGGLPYGVRERDLE---KFVKGYGRIRDVILKNG-------FGFVEFEDYRDADDAVY 55
+++ GLP V+ER+L + GY R ++ K GFV+F + A A+
Sbjct: 3 LFVSGLPSDVKERELAHLFRPFPGYEASR-LVFKEKKGGEKQPVGFVDFSSAQCAAAAMD 61
Query: 56 ELNG 59
L G
Sbjct: 62 ALQG 65
>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 = 34.9 bits (81), Expect = 0.004
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERVTVE 70
FGFV +++ A A+ +NG + G+R+ V+
Sbjct: 41 CFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM3 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 73
Score = 35.0 bits (80), Expect = 0.004
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRD--VILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
VY GG+ G+ E+ + + +G+I + V + G+ F+ F + A A+ +NG ++
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEKGYSFIRFSTHESAAHAIVSVNGTTIE 62
Query: 64 GERV 67
G V
Sbjct: 63 GHVV 66
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 83
Score = 35.2 bits (81), Expect = 0.004
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 8/76 (10%)
Query: 5 KVYIGGLPYGVRE-RDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYE 56
K+ I LP+ +++ L+K YG++R+ + GF FV + ++A+ A+
Sbjct: 2 KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALEN 61
Query: 57 LNGKSLLGERVTVEIA 72
NG + G V V+ A
Sbjct: 62 TNGLEIDGRPVAVDWA 77
>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 = 35.2 bits (81), Expect = 0.005
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 18/76 (23%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV---ILKN------------GFGFVEFEDYRDA 50
+YI LP + +LE + YG +R V LK GF F+ + +A
Sbjct: 3 LYISNLPPDTTQLELESWFTQYG-VRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEA 61
Query: 51 DDAVYELNGKSLLGER 66
+A+ LNG+ LGER
Sbjct: 62 MEAL-ALNGR-CLGER 75
>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 = 34.9 bits (81), Expect = 0.005
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 10/77 (12%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYAD-----AHKRHRNEGVVEFESSSDMKKALDKL 170
+ + NL + ++LK+ Q GEV YA + V+F++ +K L+
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62
Query: 171 DNAE-----LNGRRIRL 182
DNAE L+GRR+ +
Sbjct: 63 DNAEDSGLSLDGRRLIV 79
Score = 30.3 bits (69), Expect = 0.21
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 13/80 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-KN-------GFGFVEFEDYRDADDAVYEL 57
V+I LP+ E +L++ +G ++ + K+ G FV+F+ A +
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62
Query: 58 NGKS-----LLGERVTVEIA 72
+ L G R+ V +A
Sbjct: 63 DNAEDSGLSLDGRRLIVTLA 82
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in yeast.
Yra2p belongs to the evolutionarily conserved REF (RNA
and export factor binding proteins) family of hnRNP-like
proteins. It is a major component of endogenous Yra1p
complexes. It interacts with Yra1p and functions as a
negative regulator of Yra1p. Yra2p consists of two
highly conserved N- and C-terminal boxes and a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 34.6 bits (80), Expect = 0.005
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYAD--AHKRHRNEGVVEFESSSDMKKALDKLDN 172
RL + N+ VS ++D +++ GE Y+ HK R V EFE S ++K ++K +
Sbjct: 2 RLRITNIPLDVSDYTIEDLIKEFGEPVYSKFYDHKDSRT-AVFEFEDPSILEKVVEKYNG 60
Query: 173 AELNGRRI 180
ELNG +I
Sbjct: 61 KELNGAKI 68
Score = 30.4 bits (69), Expect = 0.19
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYG-----RIRDVILKNG-FGFVEFEDYRDADDAVYEL 57
++ I +P V + +E +K +G + D K+ EFED + V +
Sbjct: 1 KRLRITNIPLDVSDYTIEDLIKEFGEPVYSKFYD--HKDSRTAVFEFEDPSILEKVVEKY 58
Query: 58 NGKSLLGERVTVEI 71
NGK L G ++ VEI
Sbjct: 59 NGKELNGAKIEVEI 72
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2
protein homolog beta (TRA-2 beta) and similar proteins.
This subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 35.0 bits (80), Expect = 0.006
Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 10 GLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKS 61
GL ERDL + YG I DV + GF FV FE+ DA +A NG
Sbjct: 16 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 75
Query: 62 LLGERVTVEIA 72
L G R+ V+ +
Sbjct: 76 LDGRRIRVDFS 86
Score = 31.5 bits (71), Expect = 0.100
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGE-----VCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V LS + +DL++ + G + Y +R R V FE+ D K+A ++
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71
Query: 171 DNAELNGRRIRL 182
+ EL+GRRIR+
Sbjct: 72 NGMELDGRRIRV 83
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
in the middle and an RGG box rich in glycine and
arginine residues in the C-terminal part. Each of RRMs
can bind solely to the UUAG sequence specifically. .
Length = 74
Score = 34.6 bits (79), Expect = 0.006
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 12/67 (17%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV--- 54
++IGGL + ++DL+ + +G + D LK GFGFV F++ D +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 55 -YELNGK 60
++LNGK
Sbjct: 61 EHKLNGK 67
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells, and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1) and has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
It represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 34.6 bits (79), Expect = 0.006
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GGL D++++ + +G++ D +L GFGFV FE D + V E
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCE 59
Query: 57 LN 58
++
Sbjct: 60 IH 61
Score = 29.6 bits (66), Expect = 0.33
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEV-----CYADAHKRHRNEGVVEFESSSDMKK 165
++ V LS + +D+K + Q G+V + RHR G V FES ++K
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK 56
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the
RRM of Star-PAP, also termed RNA-binding motif protein
21 (RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs
to the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both,
the poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione
S-transferase (GST)-PIPKIalpha. Star-PAP preferentially
uses ATP as a nucleotide substrate and possesses PAP
activity that is stimulated by PtdIns4,5P2. It contains
an N-terminal C2H2-type zinc finger motif followed by
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), a
split PAP domain linked by a proline-rich region, a PAP
catalytic and core domain, a PAP-associated domain, an
RS repeat, and a nuclear localization signal (NLS). .
Length = 74
Score = 34.3 bits (79), Expect = 0.006
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 4/67 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGKSL 62
V++ G G E L + +G + +VI+ K + VEF+ ++ D V +L
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDS-KEGVDKVLSEPQHTL 63
Query: 63 LGERVTV 69
G R+ V
Sbjct: 64 NGHRLRV 70
Score = 27.0 bits (60), Expect = 2.5
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 4/73 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
+ V S + L D+ G V K +VEF+S + K L + L
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGVYAIVEFDSKEGVDKVLSE-PQHTL 63
Query: 176 NGRRIRLIEDKPR 188
NG R+R+ +PR
Sbjct: 64 NGHRLRV---RPR 73
>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 = 34.7 bits (79), Expect = 0.006
Identities = 15/34 (44%), Positives = 23/34 (67%)
Query: 39 FGFVEFEDYRDADDAVYELNGKSLLGERVTVEIA 72
+ FVEF ++RDA A+ +NG+ +LG+ V V A
Sbjct: 41 YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA 74
>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 = 34.6 bits (80), Expect = 0.007
Identities = 30/81 (37%), Positives = 44/81 (54%), Gaps = 12/81 (14%)
Query: 4 TKVYIGGLP-YGVRERDLEKFVKGYGRIRDVIL--------KN-GFGFVEFEDYRDADDA 53
++++GG+P +E LE+F K + DVI+ KN GF FVE+E +R A A
Sbjct: 2 CRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMA 61
Query: 54 VYEL-NGKSLL-GERVTVEIA 72
+L G+ LL G V V+ A
Sbjct: 62 RRKLVPGRILLWGHEVAVDWA 82
>gnl|CDD|221825 pfam12877, DUF3827, Domain of unknown function (DUF3827). This
family contains the human KIAA1549 protein which has
been found to be fused fused to BRAF gene in many cases
of pilocytic astrocytomas. The fusion is due mainly to a
tandem duplication of 2 Mb at 7q34. Although nothing is
known about the function of KIAA1549 protein, the BRAF
protein is a well characterized oncoprotein. It is a
serine/threonine protein kinase which is implicated in
MAP/ERK signalling, a critical pathway for the
regulation of cell division, differentiation and
secretion.
Length = 684
Score = 37.2 bits (86), Expect = 0.007
Identities = 19/58 (32%), Positives = 29/58 (50%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSR 251
+S+SS S +K R R R S S S S R S+ K+ S +PS + +K ++
Sbjct: 366 KSKSSQDGSSNKKRRRGRKSPSDGDSEGSSVISNRSSREKSGRPSTTPSVTAQQKPTK 423
Score = 29.1 bits (65), Expect = 2.5
Identities = 15/64 (23%), Positives = 24/64 (37%)
Query: 192 RGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSR 251
RGR S S S +RSS+ +S R + + K + + P+P
Sbjct: 381 RGRKSPSDGDSEGSSVISNRSSREKSGRPSTTPSVTAQQKPTKEEGRKKPAPPSGTDEQL 440
Query: 252 SRSD 255
S +
Sbjct: 441 SSAS 444
>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 = 34.6 bits (80), Expect = 0.007
Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 117 IVENLSSRVSWQDLKDFMRQVGEVCY---ADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
V NL + L +F Q GEV Y A + VEF + + AL KL+ A
Sbjct: 8 YVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINAL-KLNGA 66
Query: 174 ELNGRRIRLI 183
GR +++
Sbjct: 67 MFGGRPLKVN 76
>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 = 34.2 bits (79), Expect = 0.008
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 6 VYIGGLPYGVRERDL-EKFVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVYEL 57
+++G L V E L E F++ G + V I K+ F FV F+ A+ L
Sbjct: 4 LFVGNLDARVTEEILYELFLQA-GPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLL 62
Query: 58 NGKSLLGERVTVE 70
NG L G + ++
Sbjct: 63 NGIRLFGRELRIK 75
Score = 32.3 bits (74), Expect = 0.031
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEV----CYADAHKRHRNEGVVEFESSSDMKKALD 168
D L V NL +RV+ + L + Q G + D + + ++ V F+ + A+
Sbjct: 1 DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60
Query: 169 KLDNAELNGRRIRL 182
L+ L GR +R+
Sbjct: 61 LLNGIRLFGRELRI 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 = 34.5 bits (80), Expect = 0.008
Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 4 TKVYIGGLPYGVR----ERDLEKF--VKGYGRIRDVILKN--GFGFVEFEDYRDADDAVY 55
T V++G +P GV + LEK V + R++D FGF EFED A A+
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60
Query: 56 ELNGKSLLGERVTV 69
LNG L G+++ V
Sbjct: 61 LLNGLELGGKKLLV 74
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 33.7 bits (78), Expect = 0.009
Identities = 18/63 (28%), Positives = 31/63 (49%)
Query: 120 NLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRR 179
N+S V+ + +K F ++G +VEFES SD KA L+ ++ G+
Sbjct: 7 NVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEGALVEFESPSDAGKASLSLNGSQFGGKT 66
Query: 180 IRL 182
I++
Sbjct: 67 IKI 69
Score = 26.8 bits (60), Expect = 3.4
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 7/53 (13%)
Query: 20 LEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGKSLLGERVTV 69
EK +R + L G VEFE DA A LNG G+ + +
Sbjct: 21 FEKIG---PDVRKIELFPDHEG-ALVEFESPSDAGKASLSLNGSQFGGKTIKI 69
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 34.2 bits (79), Expect = 0.009
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 29 RIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
R + G+ FVEF D A+ +++LNGK + G
Sbjct: 34 RNKLTGGPAGYCFVEFADEATAERCLHKLNGKPIPG 69
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate
RNA-binding Raly-like protein (RALYL). This subgroup
corresponds to the RRM of RALYL, also termed
heterogeneous nuclear ribonucleoprotein C-like 3, or
hnRNP core protein C-like 3, a putative RNA-binding
protein that shows high sequence homology with Raly, an
RNA-binding protein playing a critical role in
embryonic development. The biological role of RALYL
remains unclear. Like Raly, RALYL contains two distinct
domains, an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal auxiliary
domain. .
Length = 69
Score = 33.8 bits (77), Expect = 0.009
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 4 TKVYIGGLPYG-VRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
++V+IG L V++ D+E YG+I + G+ FV++ R A AV N + +
Sbjct: 2 SRVFIGNLNTAIVKKADIEAIFAKYGKIVGCSVHKGYAFVQYISERHARAAVAGENARII 61
Query: 63 LGE 65
G+
Sbjct: 62 AGQ 64
>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 = 33.9 bits (78), Expect = 0.009
Identities = 22/68 (32%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAVYE 56
+++I L Y E DLEK YG + +V L GF FV + A A E
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63
Query: 57 LNGKSLLG 64
L+G G
Sbjct: 64 LDGTVFQG 71
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living
cells. RRM2/3 are implicated in ACF interaction with
APOBEC-1. .
Length = 78
Score = 34.2 bits (78), Expect = 0.009
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVY 55
G +++IG LP + E +L + G+I ++ + G+ FV F + ++A +A+
Sbjct: 1 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIK 60
Query: 56 ELNGKSLLGERV 67
+LN + R+
Sbjct: 61 QLNNYEIRNGRL 72
>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 = 34.1 bits (79), Expect = 0.009
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV--------ILKNGFGFVEFE 45
+++GGL V E DLE+ +G + DV GF +++
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B shows high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 34.0 bits (78), Expect = 0.010
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 10/68 (14%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYELN 58
V++ GLPY E D+++F G + DVI NG V+F ++DA +A+
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGL-DVEDVIFLKRHNGRNNGNAIVKFATFQDAKEALKR-- 58
Query: 59 GKSLLGER 66
+ L+G R
Sbjct: 59 HRELMGSR 66
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear
molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 33.8 bits (78), Expect = 0.010
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
G +++ LP E L + +G + +V ++++ G+GFV +Y +A A+
Sbjct: 1 GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60
Query: 55 YELNGKSLLGERV 67
LNG LG RV
Sbjct: 61 ASLNG-YRLGGRV 72
>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 = 33.7 bits (78), Expect = 0.014
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 8/63 (12%)
Query: 7 YIGGLPYGVRE---RDLEKFVKGYGRIRDVILKNGFG---FVEFEDYRDADDAVYELNGK 60
++ L E R L G+ R++ + G G FVEFED A A+ L G
Sbjct: 6 FVANLGPNTTEEELRQLFSRQPGFRRLK--MHNKGGGPVCFVEFEDVSFATQALNSLQGA 63
Query: 61 SLL 63
L
Sbjct: 64 VLS 66
>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 = 33.6 bits (77), Expect = 0.014
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV--ILKNGFGFVEFEDYRDADDAVYEL 57
VYIG LP E +L + ++ +G I + + + FV F +A V L
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLSIANAIKVVTTL 59
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 36.4 bits (83), Expect = 0.014
Identities = 25/55 (45%), Positives = 29/55 (52%)
Query: 206 SRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRARK 260
S RS SS S S S S S S R S+S S+S SPSP + RSRS R +
Sbjct: 1812 SAGRSSSSSSSSSSSSSSSPSSRPSRSATPSLSPSPSPPRRAPVDRSRSGRRRER 1866
Score = 30.6 bits (68), Expect = 0.90
Identities = 25/59 (42%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 198 SSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDS 256
SSS S S S S S S SR RS + S SP S + V RS S R+R R R +
Sbjct: 1816 SSSSSSSSSSSSSSSPSSRPSRSATPSLSPSPSPPRRAPVDRSRS---GRRRERDRPSA 1871
Score = 29.4 bits (65), Expect = 2.1
Identities = 27/79 (34%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 173 AELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKS 232
A+ + R R + R GG+ SSSS S S RS S SS+ R R S+ R +
Sbjct: 1544 ADRHADRRRSTKGPQRPGGKRPRSSSSSSSASHDRSPSSSSRRRDGRPSSRRRPSR--RM 1601
Query: 233 KAKSVSRSPSPSKTRKRSR 251
A+ SR P+ R R
Sbjct: 1602 SARPPSRPPAAVILRASWR 1620
Score = 29.4 bits (65), Expect = 2.6
Identities = 28/79 (35%), Positives = 35/79 (44%), Gaps = 19/79 (24%)
Query: 190 GGRGRSRSSSSRSRSKSRSRSRSSKS-------------RSPRSRSKSGSPRKSKSKAKS 236
GR S SSSS S S S SR S+S R+P RS+SG R+
Sbjct: 1813 AGRSSSSSSSSSSSSSSSPSSRPSRSATPSLSPSPSPPRRAPVDRSRSGRRRERDRP--- 1869
Query: 237 VSRSPSPSKTRKRSRSRSD 255
S +P + R RSR+D
Sbjct: 1870 ---SANPFRWAPRQRSRAD 1885
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM1 in hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 78
Score = 33.5 bits (77), Expect = 0.014
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDA 53
K++IGGL Y + L+ + +G I D ++ GFGFV F + D A
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAA 57
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 33.1 bits (75), Expect = 0.015
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
+L V N+SS + Q+L+ + G V D K + V E + D +A+ LDN E
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKDY---AFVHMERAEDAVEAIRGLDNTE 58
Query: 175 LNGRRI 180
G+R+
Sbjct: 59 FQGKRM 64
Score = 30.0 bits (67), Expect = 0.23
Identities = 16/67 (23%), Positives = 33/67 (49%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL 63
TK+++G + ++L + YG + + + + FV E DA +A+ L+
Sbjct: 1 TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQ 60
Query: 64 GERVTVE 70
G+R+ V+
Sbjct: 61 GKRMHVQ 67
>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509). This
family consists of several uncharacterized viral
proteins from the Marek's disease-like viruses. Members
of this family are typically around 400 residues in
length. The function of this family is unknown.
Length = 377
Score = 36.2 bits (83), Expect = 0.015
Identities = 21/51 (41%), Positives = 26/51 (50%)
Query: 190 GGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRS 240
G R R + S SRS+SRSRS S + R R R G +S+ VS S
Sbjct: 323 GERRGRRRNRSESRSRSRSRSGSRRYRRRRGRGVPGRRSESRQDTVLVSSS 373
Score = 32.7 bits (74), Expect = 0.16
Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSP 243
ED G R S S + R S+SRS RSRS+SGS R + + + V S
Sbjct: 304 EDSAGGSHHTMRRPPHSTSGERRGRRRNRSESRS-RSRSRSGSRRYRRRRGRGVPGRRSE 362
Query: 244 SK 245
S+
Sbjct: 363 SR 364
Score = 29.6 bits (66), Expect = 1.6
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 3/72 (4%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPR---KSKSKAKSVSRSPSPSKTRKRS 250
R+ + S S S + S SG R +++S+++S SRS S S+ +R
Sbjct: 292 RAGTPDDGSAISEDSAGGSHHTMRRPPHSTSGERRGRRRNRSESRSRSRSRSGSRRYRRR 351
Query: 251 RSRSDSRARKVS 262
R R R S
Sbjct: 352 RGRGVPGRRSES 363
>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 = 32.9 bits (76), Expect = 0.017
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK--NGFGFVEFEDYRDADDAVYELNGKSL- 62
+++GGL +LE+ +G IR + + ++E+E A A L G L
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLG 60
Query: 63 -LGERVTVEIAK 73
G R+ V+ A
Sbjct: 61 GPGRRLRVDFAD 72
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 33.4 bits (77), Expect = 0.017
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 9 GGLPYGVRERDLEKFVKGYGRIRDVILKNG--FGFVEFEDYRDADDAVYELNGKSL 62
GGL GV +L + + YG + D+++ G + FV + DA A LNGK L
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVMPPGKPYCFVSYSSIEDAAAAYDALNGKEL 64
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0 is a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. hnRNP A/B has also been
identified as an APOBEC1-binding protein that interacts
with apolipoprotein B (apoB) mRNA transcripts around
the editing site and thus plays an important role in
apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 33.3 bits (76), Expect = 0.018
Identities = 17/67 (25%), Positives = 36/67 (53%), Gaps = 12/67 (17%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDADDAV--- 54
+++GGL + ++DL+++ +G + D +K GFGFV F+D + +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 55 -YELNGK 60
++L+G+
Sbjct: 61 EHKLDGR 67
Score = 27.1 bits (60), Expect = 2.6
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV--CYADAHK---RHRNEGVVEFESSSDMKKALDKL 170
+ V LS + +DLK++ + GEV C R R G V F+ ++ ++K LD+
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 171 DNAELNGRRI 180
++ +L+GR I
Sbjct: 61 EH-KLDGRVI 69
>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 = 33.3 bits (76), Expect = 0.018
Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 111 RSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGV--VEFESSSDMKKALD 168
R L V+NL ++ +LK+ ++ + K ++G+ +EF++ ++ +KAL+
Sbjct: 1 RDARTLFVKNLPYNITVDELKEVFEDAVDI-RLPSGKDGSSKGIAYIEFKTEAEAEKALE 59
Query: 169 KLDNAELNGRRI 180
+ AE++GR I
Sbjct: 60 EKQGAEVDGRSI 71
>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 = 33.0 bits (75), Expect = 0.018
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--NGFGFVEFEDYRDADDAVYELNGKSL 62
++++G LP + E D +K + YG +V + GFGF+ E A+ A EL+G ++
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDG-TI 61
Query: 63 LGER 66
L R
Sbjct: 62 LKNR 65
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 33.3 bits (77), Expect = 0.021
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSL 62
G+ FVEF +A +AV LNG L
Sbjct: 51 GYAFVEFATPEEAKEAVKALNGYKL 75
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 36.1 bits (83), Expect = 0.021
Identities = 26/114 (22%), Positives = 40/114 (35%)
Query: 143 ADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRS 202
A K+ ++ E SS +K + + ++ ++ RL E S S S
Sbjct: 729 LSAPKKQTSKTASEKSSSKGKRKHKNDEEADKIESKKQRLEEKSSSCSPSSSSSHHHSSS 788
Query: 203 RSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDS 256
+SR SR+ + S S S K + S R T S S S
Sbjct: 789 NKESRKSSRNKEEEMLPSPSSPLSSSSPKPEHPSRKRPRRQEDTSSSSGPFSAS 842
Score = 30.7 bits (69), Expect = 1.0
Identities = 35/165 (21%), Positives = 48/165 (29%), Gaps = 9/165 (5%)
Query: 101 DRDDRYGPPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESS 160
D P + + E SS+ + + E K+ R E S
Sbjct: 724 AEKDSLSAPKKQTSKTASEKSSSKGKRK------HKNDEEADKIESKKQRLEEKSSSCSP 777
Query: 161 SDMKKALDKLDNAELNGRRIRLIED---KPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRS 217
S N E E+ P S SR + R + +S S
Sbjct: 778 SSSSSHHHSSSNKESRKSSRNKEEEMLPSPSSPLSSSSPKPEHPSRKRPRRQEDTSSSSG 837
Query: 218 PRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRARKVS 262
P S S + S KS S +K S T K + S K S
Sbjct: 838 PFSASSTKSSSKSSSTSKHRKTEGKGSSTSKEHKGSSGDTPNKAS 882
Score = 29.9 bits (67), Expect = 1.4
Identities = 13/69 (18%), Positives = 22/69 (31%)
Query: 191 GRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRS 250
G R+ S + GS + S K S P+ K + +S
Sbjct: 550 GDERTGLRPESEPGTLPYGSSVQTPPDRPKAATKGSRKPSPRKEPKSSVPPAAEKRKYKS 609
Query: 251 RSRSDSRAR 259
S+ ++R
Sbjct: 610 PSKIVPKSR 618
>gnl|CDD|223025 PHA03253, PHA03253, UL35; Provisional.
Length = 609
Score = 35.7 bits (82), Expect = 0.021
Identities = 21/64 (32%), Positives = 30/64 (46%)
Query: 181 RLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRS 240
++IE GR SR+S S S S S +P S + +P +S S++ SVS S
Sbjct: 454 QVIERLNVNEGRSSSRASPSHSTSTIPYSPPQSGRSTPTSILRQRTPIRSNSRSSSVSFS 513
Query: 241 PSPS 244
S
Sbjct: 514 QGDS 517
Score = 28.8 bits (64), Expect = 3.7
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 202 SRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDS 256
+ ++ RS SR+S S S + S P+ +S S+ R +P RS SRS S
Sbjct: 460 NVNEGRSSSRASPSHSTSTIPYS-PPQSGRSTPTSILRQRTPI----RSNSRSSS 509
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 33.1 bits (76), Expect = 0.022
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGE---RVTVEIAK 73
G+GFV F D + A+ E+ G S LG RV++ I K
Sbjct: 44 GYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLAIPK 82
Score = 28.4 bits (64), Expect = 0.93
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 113 DHRLIVENLSSRVSWQDLKDFMRQVGEVCYA-----DAHKRHRNEGVVEFESSSDMKKAL 167
+ L V +L+ V L +F + C D + R G V F S+ K+AL
Sbjct: 1 EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRAL 60
Query: 168 DKLDNAE-LNGRRIRL 182
++ A L G+ IR+
Sbjct: 61 TEMQGASGLGGKPIRV 76
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in
muscle differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 32.8 bits (75), Expect = 0.024
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 30 IRDVILKN--GFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIA 72
IRD + G+GFV + D DA+ A+ LNG L + + V A
Sbjct: 34 IRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSYA 78
>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 = 33.0 bits (75), Expect = 0.025
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 5 KVYIGGLPYGVRERDLEKFV--KGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSL 62
K+YIG L V DL + + V+LK+G+ FV++ D A A+ L+GK
Sbjct: 3 KLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62
Query: 63 LGERV 67
L +V
Sbjct: 63 LHGKV 67
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B).
This subgroup corresponds to the RRM of Setd1B, also
termed SET domain-containing protein 1B (Set1B), or
lysine N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits
high homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone
H3 at Lys4. Set1B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), an N- SET
domain, and a C-terminal catalytic SET domain followed
by a post-SET domain. .
Length = 93
Score = 33.1 bits (75), Expect = 0.025
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 15 VRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYELNGKSLLGER 66
+RE L K YG + +V IL N G V F + A DAV L+ S++G
Sbjct: 14 IRENFLTDMCKKYGEVEEVEILYNPKNKKHLGIAKVVFATVKGAKDAVQHLHNTSVMGNI 73
Query: 67 VTVEI-AKGIDR 77
+ VE+ KG R
Sbjct: 74 IHVELDTKGETR 85
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM3 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 83
Score = 33.1 bits (75), Expect = 0.025
Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 29 RIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAKGID 76
+IRD + FV F + DA DA+ LNGK + G + V +AK +D
Sbjct: 42 KIRD------YAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAKPVD 83
>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 = 32.7 bits (74), Expect = 0.025
Identities = 22/72 (30%), Positives = 30/72 (41%), Gaps = 1/72 (1%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
L V NL S +K Q C + K+ R+ V F S D A++ L+ EL
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGC-VERVKKIRDYAFVHFTSREDAVHAMNNLNGTEL 62
Query: 176 NGRRIRLIEDKP 187
G I + KP
Sbjct: 63 EGSCIEVTLAKP 74
Score = 29.6 bits (66), Expect = 0.32
Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 29 RIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAK 73
+IRD + FV F DA A+ LNG L G + V +AK
Sbjct: 35 KIRD------YAFVHFTSREDAVHAMNNLNGTELEGSCIEVTLAK 73
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 77
Score = 32.6 bits (75), Expect = 0.025
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--KNGFGFVEFEDYRDADDAVYELNGKSLL 63
V++ GL V E+ L + YG + V++ + G V F+ A AV E+ G+ L
Sbjct: 10 VWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQAAVNEMKGRKLG 69
Query: 64 GERVTV 69
G ++ V
Sbjct: 70 GRKLQV 75
>gnl|CDD|240972 cd12528, RRM2_MEI2_fungi, RNA recognition motif 2 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM2 of fungal Mei2-like proteins.The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
In the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its
C-terminal RRM motif. .
Length = 81
Score = 32.8 bits (75), Expect = 0.026
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKNGFG-----FVEFEDYRDADDAVYELNG 59
V + + L+ + +G ++ L + EF D RDAD+AV ELNG
Sbjct: 11 VQGDSHNSDLVKNSLQNLLSTFGDLKAFKSLPSQQDNVKEFICEFFDTRDADNAVDELNG 70
Query: 60 KSL 62
+ +
Sbjct: 71 RVV 73
>gnl|CDD|216205 pfam00937, Corona_nucleoca, Coronavirus nucleocapsid protein.
Length = 346
Score = 35.1 bits (81), Expect = 0.026
Identities = 25/73 (34%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 198 SSSRSRSKSRSRSRSSKSRSP-RSRSKSGSP-RKSKSK----------AKSVSRSPSPSK 245
RSRS SRS SRS+ SR P R S++ S R S S + S
Sbjct: 152 FRGRSRSSSRSSSRSN-SRGPSRGSSRNNSRNRNSSSPDDLVAAVLAALAKLGFGKQKSS 210
Query: 246 TRKRSRSRSDSRA 258
++K SR S A
Sbjct: 211 SKKPSRVTKKSAA 223
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein
1 (RBMS1), or suppressor of CDC2 with RNA-binding motif
2 (SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 86
Score = 32.9 bits (74), Expect = 0.027
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI---RDVILKN-----GFGFVEFEDYRDADDAVY 55
T +YI GLP ++DL K + YG+I + ++ K G+GFV+F+ A AV
Sbjct: 8 TNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVS 67
Query: 56 ELNGKSL 62
L +
Sbjct: 68 ALKASGV 74
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 32.3 bits (74), Expect = 0.027
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 20 LEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGKSLLGERVTV 69
LE +G + DV L KN +G+ ++ D A+ A+ L+GK + G ++ V
Sbjct: 16 LEDVFCRFGGLIDVYLVPGKN-YGYAKYADRESAERAITTLHGKEVNGVKLKV 67
>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 = 32.8 bits (75), Expect = 0.027
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 21 EKFVKGYGRIRDVILKNG--FGFVEFEDYRDADDAVYELNGKSLLGERVTVEIA 72
E F K ++DV + + FG+V+FE D + A+ EL GK LLG + +E A
Sbjct: 23 EFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKAL-ELTGKKLLGNEIKLEKA 75
Score = 29.0 bits (65), Expect = 0.62
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 18/73 (24%)
Query: 116 LIVENLSSRVSWQDLKDFMR--------QVGEVCYADAHKRHRNEGVVEFESSSDMKKAL 167
L V NL+ + +LK + V +V + K G V+FES+ D++KAL
Sbjct: 3 LFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKF----GYVDFESAEDLEKAL 58
Query: 168 DKLDNAELNGRRI 180
EL G+++
Sbjct: 59 ------ELTGKKL 65
>gnl|CDD|227367 COG5034, TNG2, Chromatin remodeling protein, contains PhD zinc
finger [Chromatin structure and dynamics].
Length = 271
Score = 34.9 bits (80), Expect = 0.027
Identities = 27/104 (25%), Positives = 37/104 (35%), Gaps = 13/104 (12%)
Query: 163 MKKALDKLDNAELNGRRIRLIEDK-----------PRGGGRGRSRSSSSRSRSKSRSRSR 211
K+ D D AE RR R + D R + S R+ S +R
Sbjct: 82 QKEKSDLADRAEKLLRRHRKLLDDRIAKRPHEKVAARIENCHDAVSRLERNSYSSAARRS 141
Query: 212 SSKSRSPRSRSKSGSP--RKSKSKAKSVSRSPSPSKTRKRSRSR 253
S + RS S S +K K+ RSP S R+ S +
Sbjct: 142 SGEHRSAASSQGSRHTKLKKRKNIHNLKRRSPELSSKREVSFTL 185
>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM2 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein
2 (RBMS2), or suppressor of CDC2 with RNA-binding motif
3 (SCR3). MSSP-2 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence T(C/A)TT, and stimulates DNA
replication in the system using SV40 DNA. MSSP-2 is
identical with Scr3, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-2 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-2 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 86
Score = 33.1 bits (75), Expect = 0.028
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR-IRDVILKN------GFGFVEFEDYRDADDAVYE 56
T +YI LP + E++LE +K +G+ I IL++ G GF E + +
Sbjct: 1 TNLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITH 60
Query: 57 LNGK 60
NGK
Sbjct: 61 FNGK 64
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 32.7 bits (74), Expect = 0.029
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYG------RIRDVILKNGFGFVEFEDYRDADDAVYELNG 59
+Y+G L V E + + G I D + + FVEF ++R A ++ +NG
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMNG 61
Query: 60 KSLLGERVTVEIA 72
+ ++G+ V V A
Sbjct: 62 RKIMGKEVKVNWA 74
>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM1 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. IGF2BP1 promotes mRNA
stabilization; it functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD and stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus
(HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and
enhancing HCV internal ribosome entry site
(IRES)-mediated translation initiation via the 3'-UTR.
IGF2BP1 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. It also
contains two putative nuclear export signals (NESs) and
a putative nuclear localization signal (NLS). .
Length = 77
Score = 32.7 bits (74), Expect = 0.029
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIR---DVILKNGFGFVEFEDYRDADDAVYELNGK- 60
K+YIG L V DLEK + + +I ++K+G+ FV+ D + A A+ +GK
Sbjct: 3 KLYIGNLNESVTPADLEKVFEDH-KISYSGQFLVKSGYAFVDCPDEQWAMKAIETFSGKV 61
Query: 61 SLLGERVTVE 70
L G+R+ +E
Sbjct: 62 ELHGKRLEIE 71
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe
CD corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 79
Score = 32.6 bits (75), Expect = 0.029
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 7/77 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVY 55
G +Y+ L + + L + +G I + GFGFV F +A AV
Sbjct: 1 GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60
Query: 56 ELNGKSLLGERVTVEIA 72
E+NG+ + G+ + V +A
Sbjct: 61 EMNGRIIGGKPLYVALA 77
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 32.3 bits (74), Expect = 0.030
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYEL 57
+++G L + L +G I D ++K+ G+GFV F DA++A+ +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 58 NGKSLLGERV 67
NG+ L G +
Sbjct: 62 NGQWLGGRAI 71
Score = 32.3 bits (74), Expect = 0.034
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHK-RHRNEGVVEFESSSDMKKALDKL 170
+ V +LS + + L+ GE+ A D + + G V F D + A+ +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 171 DNAELNGRRIR 181
+ L GR IR
Sbjct: 62 NGQWLGGRAIR 72
>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 = 32.5 bits (74), Expect = 0.031
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 9/79 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
K+++GGL + L + YG++ + ++ GFGF+ F +AD+A+
Sbjct: 2 LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
Query: 55 YELNGKSLLGERVTVEIAK 73
E S+ G ++ ++ AK
Sbjct: 62 -EAQPHSIDGNQIELKRAK 79
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein
2 (RBMS2), or suppressor of CDC2 with RNA-binding motif
3 (SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in
the system using SV40 DNA. MSSP-2 is identical with
Scr3, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product
of protooncogene c-myc. MSSP-2 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 75
Score = 32.4 bits (73), Expect = 0.032
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI---RDVILKN-----GFGFVEFEDYRDADDAVY 55
T +YI GL G ++DL K + YG+I + ++ K G+GFV+F+ A AV
Sbjct: 2 TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61
Query: 56 ELNGKSL 62
L +
Sbjct: 62 ALKASGV 68
>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3). This subgroup corresponds to the RRM2 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators.
Unlike other MSSP proteins, RBMS3 is not a
transcriptional regulator. It binds with high affinity
to A/U-rich stretches of RNA, and to A/T-rich DNA
sequences, and functions as a regulator of cytoplasmic
activity. RBMS3 contain two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and its C-terminal
region is acidic and enriched in prolines, glutamines
and threonines. .
Length = 88
Score = 32.8 bits (74), Expect = 0.032
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 7/66 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR-IRDVILKN------GFGFVEFEDYRDADDAVYE 56
T +YI LP + E++LE +K +G I IL++ G GF E + +
Sbjct: 2 TNLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQH 61
Query: 57 LNGKSL 62
NGK L
Sbjct: 62 FNGKYL 67
>gnl|CDD|234428 TIGR03979, His_Ser_Rich, His-Xaa-Ser repeat protein HxsA. Members
of this protein share two defining regions. One is a
histidine/serine-rich cluster, typically
H-R-S-H-S-S-H-R-S-H-S-S-H. Members are found always in
the context of a pair of radical SAM proteins, HxsB and
HxsC, and a fourth protein HxsD. The system is predicted
to perform peptide modifications, likely in the
His-Xaa-Ser region, to produce some uncharacterized
natural product.
Length = 186
Score = 34.1 bits (78), Expect = 0.033
Identities = 28/101 (27%), Positives = 36/101 (35%), Gaps = 14/101 (13%)
Query: 167 LDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSG- 225
++ A LN D P RS SS S S S + S S S S
Sbjct: 34 PTDVELAPLN-------VDIPNLLAGHRSHSSHRSHSSHSSHYSGAGGSYSVPSGDTSTY 86
Query: 226 -----SPRKSKSKAKSVSRSPSPSKTRKRS-RSRSDSRARK 260
SP S S S+ PS + R +S ++S RK
Sbjct: 87 SYPVPSPSYSPSPGSSIQSLPSTTGVRPQSSAENANSEKRK 127
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 32.6 bits (74), Expect = 0.033
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 13/80 (16%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEV------------CYAD-AHKRHRNEGVVEFESSSD 162
+ V+ L V+ + + D+ +Q+G + Y D + + E V F+
Sbjct: 5 IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64
Query: 163 MKKALDKLDNAELNGRRIRL 182
K A+D D E +G I++
Sbjct: 65 AKAAIDWFDGKEFSGNPIKV 84
>gnl|CDD|217373 pfam03115, Astro_capsid, Astrovirus capsid protein precursor. This
product is encoded by astrovirus ORF2, one of the three
astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein
undergoes an intracellular cleavage to form a 79kD
protein. Subsequently, extracellular trypsin cleavage
yields the three proteins forming the infectious virion.
Length = 787
Score = 35.1 bits (81), Expect = 0.035
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 11/53 (20%)
Query: 191 GRGRSRSSSSRSRSKSRSRSRS--------SKSRSPRSRSKSGSPRKSKSKAK 235
GR RS+S R+RS+SR R RS +K R R+K S ++ ++
Sbjct: 17 GRSRSKS---RARSQSRGRGRSVKITVNSRNKGRRQNGRNKYQSNQRVRNIVN 66
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads and is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 83
Score = 32.8 bits (74), Expect = 0.035
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + +L+ G I RD I G+GFV + D +DA+ A+
Sbjct: 5 TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 65 TLNGLRLQTKTIKVSYAR 82
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 34.8 bits (80), Expect = 0.036
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 2/68 (2%)
Query: 176 NGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAK 235
NGR+ R RG G GR + R + ++S S+K SR + + + +
Sbjct: 389 NGRQQR--GGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRR 446
Query: 236 SVSRSPSP 243
R P+
Sbjct: 447 RRPRKPAA 454
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM2 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA). However, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 75
Score = 32.1 bits (73), Expect = 0.037
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSL 62
G+GFV F +DA++A+ E+NGK L
Sbjct: 42 GYGFVSFRSQQDAENAINEMNGKWL 66
Score = 28.2 bits (63), Expect = 0.90
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 148 RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
R R G V F S D + A+++++ L R IR
Sbjct: 39 RSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIR 72
>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 = 32.2 bits (74), Expect = 0.038
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 6 VYIGGLPYGVRERDL-EKFVKGYGRIRDVILKN-----GFGFVEFEDYRDADDAVYELNG 59
+Y+ LP+ + +L + F K YG IR + + N G FV +ED DA +A L+G
Sbjct: 5 LYVRNLPFKISSEELYDLFGK-YGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHLSG 63
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a specific
inhibitory effect on oestrogen action, SLTM is shown to
exert a generalized inhibitory effect on gene expression
associated with induction of apoptosis in a wide range
of cell lines. .
Length = 74
Score = 32.3 bits (73), Expect = 0.040
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEG-----VVEFESSSDMKKALDKL 170
L V LSS DLK+ + G+V A R+ G +V SS+++ + + L
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61
Query: 171 DNAELNGRRI 180
EL+G++I
Sbjct: 62 HRTELHGQQI 71
>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 = 32.1 bits (73), Expect = 0.040
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI-RDVILKN-------GFGFVEFEDYRDADDAVYEL 57
VY+G + YG +LE G G I R IL + G+ ++EF RD+ +A L
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFAT-RDSVEAAVAL 60
Query: 58 NGKSLLGERVTV 69
+ S G + V
Sbjct: 61 DESSFRGRVIKV 72
>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 = 32.2 bits (73), Expect = 0.040
Identities = 15/47 (31%), Positives = 31/47 (65%), Gaps = 5/47 (10%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNG-----FGFVEFED 46
++++G LP+ V + +L++F + YG + ++ + +G FGFV F+D
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGKLPNFGFVVFDD 51
Score = 26.4 bits (58), Expect = 4.8
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 114 HRLIVENLSSRVSWQDLKDFMRQVGEVC--YADAHKRHRNEGVVEFESSSDMKKAL 167
H+L V NL V +LK+F +Q G V ++ + N G V F+ S ++K L
Sbjct: 4 HQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGKLPNFGFVVFDDSEPVQKIL 59
>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM2 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein
1 (RBMS1), or suppressor of CDC2 with RNA-binding motif
2 (SCR2). MSSP-1 is a double- and single-stranded DNA
binding protein that belongs to the c-myc single-strand
binding proteins (MSSP) family. It specifically
recognizes the sequence CT(A/T)(A/T)T, and stimulates
DNA replication in the system using SV40 DNA. MSSP-1 is
identical with Scr2, a human protein which complements
the defect of cdc2 kinase in Schizosaccharomyces pombe.
MSSP-1 has been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with c-MYC, the product
of protooncogene c-myc. MSSP-1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
both of which are responsible for the specific DNA
binding activity as well as induction of apoptosis. .
Length = 85
Score = 32.4 bits (73), Expect = 0.044
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 7/64 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR-IRDVILKN------GFGFVEFEDYRDADDAVYE 56
T +YI LP + E++LE +K +G+ I IL++ G GF E + +
Sbjct: 1 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISH 60
Query: 57 LNGK 60
NGK
Sbjct: 61 FNGK 64
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 32.0 bits (73), Expect = 0.046
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNE--GVVEFESSSDMKKALDKLDNA 173
L + NL ++ DL++ + GE+ D K+ N +++ + + KA+ K+D
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDGE 64
Query: 174 ELNGRRIRL 182
L R++L
Sbjct: 65 YLGNNRVKL 73
Score = 28.1 bits (63), Expect = 0.96
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRIRDVILK-----NGFGFVEFEDYRDADDAVYELNGKS 61
+IG L DL + + +G I D+ +K + F+++ D A+ +++G+
Sbjct: 6 FIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKMDGEY 65
Query: 62 LLGERVTV 69
L RV +
Sbjct: 66 LGNNRVKL 73
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced
transcripts of c-src, HIV, GRIN1, and beta-tropomyosin.
hnRNP A1 can shuttle between the nucleus and the
cytoplasm. Thus, it may be involved in transport of
cellular RNAs, including the packaging of pre-mRNA into
hnRNP particles and transport of poly A+ mRNA from the
nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has
high affinity with AU-rich elements, whereas the
nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 31.9 bits (72), Expect = 0.049
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GG+ E L + + YG+I + + K GF FV F+D+ D V +
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family
of histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes
Set1A and Set1B that are ubiquitously expressed
vertebrates histone methyltransferases exhibiting high
homology to yeast Set1. Set1A and Set1B proteins
exhibit a largely non-overlapping subnuclear
distribution in euchromatic nuclear speckles, strongly
suggesting that they bind to a unique set of target
genes and thus make non-redundant contributions to the
epigenetic control of chromatin structure and gene
expression. With the exception of the catalytic
component, the subunit composition of the Set1A and
Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The
genomic targeting of these complexes is determined by
the identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast
to Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 32.3 bits (74), Expect = 0.051
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL----KN----GFGFVEFEDYRDADDAVYEL 57
V L + E L+ K YG + +V + K G V F+ + A V +L
Sbjct: 5 VTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKL 64
Query: 58 NGKSLLGERVTVEI 71
N S++G+ + V +
Sbjct: 65 NQTSVMGKIIKVFL 78
Score = 31.9 bits (73), Expect = 0.064
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 120 NLSSRVSWQDLKDFMRQVGEVC-----YADAHKRHRNEGVVEFESSSDMKKALDKLDNAE 174
NL+ + LKD ++ GEV + +H V F+S K+ ++KL+
Sbjct: 9 NLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTS 68
Query: 175 LNGRRIR 181
+ G+ I+
Sbjct: 69 VMGKIIK 75
>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777). This is
a family of eukaryotic proteins of unknown function.
Some of the proteins in this family are putative nucleic
acid binding proteins.
Length = 158
Score = 33.3 bits (76), Expect = 0.052
Identities = 30/75 (40%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 186 KPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSK 245
+ R R R RSRS+ R R R S+SRSP +S SPR+ +S+ SRSPS +
Sbjct: 15 RGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRSR----SRSPSRRR 70
Query: 246 TRKRSRSRSDSRARK 260
RKR R + +K
Sbjct: 71 DRKRERDKDAREPKK 85
Score = 27.9 bits (62), Expect = 3.5
Identities = 32/72 (44%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 191 GRGRSRS-SSSRSRSKSRSRSRSSKSRS-PRSRSKSGSPRKSKSKAKSVSRSPSPSKTRK 248
GR RSRS SR R +SRSR R + R RSR + R RS SP + R
Sbjct: 2 GRSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRS 61
Query: 249 RSRSRSDSRARK 260
RSRS S R RK
Sbjct: 62 RSRSPSRRRDRK 73
>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 = 31.7 bits (72), Expect = 0.054
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAVYEL 57
V++G +PY E L+ G + R+ G+GF E++D A A+ L
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 58 NGKSLLGERVTVEIA 72
NG L G ++ V+ A
Sbjct: 61 NGYELNGRQLRVDNA 75
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 80
Score = 32.0 bits (72), Expect = 0.055
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 8/70 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYEL 57
V++G L + D++ +GRI D ++K+ G+GFV F + DA++A+ ++
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 58 NGKSLLGERV 67
G+ L G ++
Sbjct: 64 GGQWLGGRQI 73
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly
development. Cabeza contains one RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 32.0 bits (73), Expect = 0.055
Identities = 19/83 (22%), Positives = 30/83 (36%), Gaps = 16/83 (19%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI----------------RDVILKNGFGFVEFEDYRD 49
V++ LP E+DL + G I +D G V ++D
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 50 ADDAVYELNGKSLLGERVTVEIA 72
A A+ N K +G + V +A
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVSLA 83
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM1 of RBM40, also known
as RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of
the U12 small nuclear RNA (snRNA). The proline-rich
region might be involved in protein-protein
interactions. .
Length = 73
Score = 31.8 bits (73), Expect = 0.056
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 8 IGGLPYGVRERDLEKFVKGYGRIRDVILKNGFG------FVEFEDYRDADDAVYELNGKS 61
+ LP + E D E +K +G V + + G F F++ + A A+ L+
Sbjct: 4 VRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQLK 62
Query: 62 LLGERVTVEIA 72
+LG+R+ VE A
Sbjct: 63 ILGKRLVVEYA 73
Score = 30.7 bits (70), Expect = 0.15
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVG--EVCYADAHKRHRNEGVVEFESSSDMKKALDKLDN 172
L+V +L +S D +D ++ G V + +N F++ +AL +L
Sbjct: 1 TLLVRHLPPELSEDDKEDLLKHFGASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQ 60
Query: 173 AELNGRRI 180
++ G+R+
Sbjct: 61 LKILGKRL 68
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 31.9 bits (72), Expect = 0.061
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GG+ E L + + YG+I + + K GF FV F+D+ D V +
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 34.3 bits (79), Expect = 0.062
Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 4/79 (5%)
Query: 186 KPRGGG---RGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPS 242
PR G R +++ + + R + + P S + K K+ K ++
Sbjct: 730 APRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKK 789
Query: 243 PS-KTRKRSRSRSDSRARK 260
PS KT+K + + RA K
Sbjct: 790 PSAKTQKIAAATKAKRAAK 808
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. Structurally related CFIm68 and
CFIm59, also termed cleavage and polyadenylation
specificity factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59), are functionally redundant. Both contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. Their N-terminal RRM mediates the interaction
with CFIm25, and also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 76
Score = 31.5 bits (72), Expect = 0.062
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 128 QDLKDFMRQVGEVCYAD----AHK---RHRNEGVVEFESSSDMKKALDKLDNAELNGRR 179
+DL+ + + G V HK + + VEF S + +KL+ E NG++
Sbjct: 13 EDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGKK 71
Score = 29.6 bits (67), Expect = 0.32
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 10/74 (13%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK----------NGFGFVEFEDYRDADDAVY 55
+Y+G L + + DLE + G + +K GF +VEF A
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 56 ELNGKSLLGERVTV 69
+L G+ G++ V
Sbjct: 61 KLEGREFNGKKCVV 74
>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 = 31.5 bits (72), Expect = 0.064
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 8/66 (12%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRI-RDVILKN-------GFGFVEFEDYRDADDAVYELN 58
+G LP + + V +G + R ++ + G+GFVE+ A A +L+
Sbjct: 3 CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62
Query: 59 GKSLLG 64
GK + G
Sbjct: 63 GKQIGG 68
Score = 30.7 bits (70), Expect = 0.12
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVC-----YADAHKRHRNEGVVEFESSSDMKKALDKL 170
L V NL + + ++ + G V Y+++ + G VE+ S + KA ++L
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61
Query: 171 DNAELNGRRIR 181
D ++ GR+++
Sbjct: 62 DGKQIGGRKLQ 72
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 31.6 bits (72), Expect = 0.065
Identities = 20/61 (32%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL---KN-----GFGFVEFEDYRDADDAVYEL 57
VY+ LP L+ YG + V L K+ GF F+EFE +A A L
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 58 N 58
N
Sbjct: 62 N 62
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 84
Score = 32.0 bits (72), Expect = 0.066
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 30 IRDVILKN--GFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAK 73
+RD I G+GFV + D DAD A+ LNG L + + V A+
Sbjct: 36 VRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYAR 81
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM2 domain in the Spen (split end) protein family
which includes RNA binding motif protein 15 (RBM15),
putative RNA binding motif protein 15B (RBM15B), and
similar proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possess mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also termed one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 31.6 bits (72), Expect = 0.070
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVYELNG 59
++G L + E +L + + YG + DV +K N + FV+F + A A ++G
Sbjct: 6 FVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMSG 65
Query: 60 KSL 62
+ +
Sbjct: 66 QYI 68
>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 = 31.5 bits (72), Expect = 0.075
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 9/76 (11%)
Query: 6 VYIGGLPYGVRERDL-EKFVKGYGRIRD--VILKN------GFGFVEFEDYRDADDAVYE 56
+++G L V + L E F Y +R V++ G+GFV F D + D A+ E
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Query: 57 LNGKSLLGERVTVEIA 72
+NG + V A
Sbjct: 64 MNGVYCSSRPMRVSPA 79
>gnl|CDD|218107 pfam04484, DUF566, Family of unknown function (DUF566). Family of
related proteins that is plant specific.
Length = 313
Score = 33.8 bits (77), Expect = 0.077
Identities = 24/76 (31%), Positives = 28/76 (36%), Gaps = 1/76 (1%)
Query: 188 RGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSP-SPSKT 246
S SS R S S +S S PR + SP S + S S SK
Sbjct: 8 GSTSGDASSPRSSSRRRLSSSFLSTSASSRPRRLNAPASPPSSSPARNTSSSSSFGLSKQ 67
Query: 247 RKRSRSRSDSRARKVS 262
R S SR +R VS
Sbjct: 68 RPSSLSRGRLSSRFVS 83
Score = 32.2 bits (73), Expect = 0.24
Identities = 23/80 (28%), Positives = 28/80 (35%), Gaps = 3/80 (3%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRK---SKSKAKSVSRS 240
R SR S S + + SR + +P S S R S S S R
Sbjct: 10 TSGDASSPRSSSRRRLSSSFLSTSASSRPRRLNAPASPPSSSPARNTSSSSSFGLSKQRP 69
Query: 241 PSPSKTRKRSRSRSDSRARK 260
S S+ R SR S SR
Sbjct: 70 SSLSRGRLSSRFVSPSRGSP 89
Score = 31.8 bits (72), Expect = 0.33
Identities = 23/81 (28%), Positives = 32/81 (39%), Gaps = 5/81 (6%)
Query: 183 IEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSK-----SRSPRSRSKSGSPRKSKSKAKSV 237
PR R R SS + + SR R ++ S R+ S S S SK + S+
Sbjct: 13 DASSPRSSSRRRLSSSFLSTSASSRPRRLNAPASPPSSSPARNTSSSSSFGLSKQRPSSL 72
Query: 238 SRSPSPSKTRKRSRSRSDSRA 258
SR S+ SR + A
Sbjct: 73 SRGRLSSRFVSPSRGSPSAAA 93
Score = 29.5 bits (66), Expect = 1.7
Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 2/79 (2%)
Query: 181 RLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRS 240
RL R R ++ + S S +R++ S S SK S S+ + SR
Sbjct: 24 RLSSSFLSTSASSRPRRLNAPASPPSSSPARNTSSSSSFGLSKQRP--SSLSRGRLSSRF 81
Query: 241 PSPSKTRKRSRSRSDSRAR 259
SPS+ + + +
Sbjct: 82 VSPSRGSPSAAASLNGSLA 100
Score = 29.5 bits (66), Expect = 1.9
Identities = 16/69 (23%), Positives = 28/69 (40%)
Query: 188 RGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTR 247
R R S++ S + S + + +S S SP ++ S S SV + K
Sbjct: 80 RFVSPSRGSPSAAASLNGSLATASTSGSSSPSRSRRTTSSDLSSGNGPSVLSFMADVKRG 139
Query: 248 KRSRSRSDS 256
K+ S+ +
Sbjct: 140 KKGPSKIED 148
Score = 28.0 bits (62), Expect = 4.7
Identities = 21/66 (31%), Positives = 27/66 (40%), Gaps = 2/66 (3%)
Query: 193 GRSRSSSSRSRSKSRSRSR-SSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSR 251
S S+ R S SR R SS+ SP SR + + S S S S +R R
Sbjct: 58 SSSSFGLSKQRPSSLSRGRLSSRFVSP-SRGSPSAAASLNGSLATASTSGSSSPSRSRRT 116
Query: 252 SRSDSR 257
+ SD
Sbjct: 117 TSSDLS 122
>gnl|CDD|220662 pfam10265, DUF2217, Uncharacterized conserved protein (DUF2217).
This is a family of conserved proteins of from 500 - 600
residues found from worms to humans. Its function is not
known.
Length = 515
Score = 33.6 bits (77), Expect = 0.086
Identities = 23/85 (27%), Positives = 30/85 (35%), Gaps = 7/85 (8%)
Query: 178 RRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSV 237
RR R + K G G R S + S R RS S+ + S + SK S
Sbjct: 37 RRRRG-KRKMEGEQLGTRRPLSRKIGKCSSRRVRSPSSKPNDTLSGAS------SKLSSK 89
Query: 238 SRSPSPSKTRKRSRSRSDSRARKVS 262
S S R+ S S + S
Sbjct: 90 HSGSSHSLASVSDRNSSSSGSCANS 114
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 33.7 bits (77), Expect = 0.087
Identities = 28/114 (24%), Positives = 43/114 (37%), Gaps = 1/114 (0%)
Query: 144 DAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSR 203
D H H ++ ++ K A KL E+ + +S+S S
Sbjct: 261 DHHHSHNHQHHSIGINNHHSKHADSKLQTIEVIENHSNKSRPSSSSTNGSKETTSNSSSA 320
Query: 204 SKSRSRSRSSKSRSPRSRSKS-GSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDS 256
+ S+SSKS +R+KS SP+ S SV S K+ R+ S
Sbjct: 321 AAGSIGSKSSKSAKHSNRNKSNSSPKSHSSANGSVPSSSVSDNESKQKRASKSS 374
Score = 31.8 bits (72), Expect = 0.42
Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 1/81 (1%)
Query: 169 KLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRS-KSGSP 227
+ ++ NG + G S+SS S S + S KS S + S S S
Sbjct: 301 RPSSSSTNGSKETTSNSSSAAAGSIGSKSSKSAKHSNRNKSNSSPKSHSSANGSVPSSSV 360
Query: 228 RKSKSKAKSVSRSPSPSKTRK 248
++SK K S+S S ++ K
Sbjct: 361 SDNESKQKRASKSSSGARDSK 381
>gnl|CDD|219061 pfam06495, Transformer, Fruit fly transformer protein. This family
consists of transformer proteins from several Drosophila
species and also from Ceratitis capitata (Mediterranean
fruit fly). The transformer locus (tra) produces an RNA
processing protein that alternatively splices the
doublesex pre-mRNA in the sex determination hierarchy of
Drosophila melanogaster.
Length = 182
Score = 33.1 bits (75), Expect = 0.089
Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 179 RIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVS 238
R+R + + R + R+RS+SRS+S S R RS+S S +S S+
Sbjct: 35 RVRNLRQRKTQSTRPTTSHRGRRTRSRSRSQSAERNSCQRRHRSRSRSRNRSDSR----H 90
Query: 239 RSPSPSKTRKRSRSRS 254
RS S ++ R+RSRSRS
Sbjct: 91 RSTSSTERRRRSRSRS 106
Score = 31.6 bits (71), Expect = 0.23
Identities = 27/64 (42%), Positives = 40/64 (62%), Gaps = 4/64 (6%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSR 253
R +S R++SRSRS+S++ S + R +S +S+S+ +S SR S S T +R RSR
Sbjct: 48 RPTTSHRGRRTRSRSRSQSAERNSCQRRHRS----RSRSRNRSDSRHRSTSSTERRRRSR 103
Query: 254 SDSR 257
S SR
Sbjct: 104 SRSR 107
Score = 26.9 bits (59), Expect = 7.8
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 192 RGRSRS-SSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSK 245
R RSRS S+ R+ + R RSRS SR +S S + + +++S SR +
Sbjct: 59 RSRSRSQSAERNSCQRRHRSRSRSRNRSDSRHRSTSSTERRRRSRSRSRYSRTPR 113
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the
RRM of TRMT2A, also known as HpaII tiny fragments locus
9c protein (HTF9C), a novel cell cycle regulated
protein. It is an independent biologic factor expressed
in tumors associated with clinical outcome in HER2
expressing breast cancer. The function of TRMT2A
remains unclear although by sequence homology it has a
RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
related to RNA methyltransferases. .
Length = 79
Score = 31.1 bits (71), Expect = 0.090
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYG----RIRDVILKNG-FGFVEFEDYRDADDAVYELN 58
KV I LP + + L+KF+K +I+ +LK F FV F + A+ L+
Sbjct: 6 FKVEIKNLPKYIGFKQLKKFLKKQLFKPHKIK--LLKRQDFAFVTFRSEEERQKALEILD 63
Query: 59 GKSLLGERVTVEIAKG 74
G G ++ +AK
Sbjct: 64 GFKWKGRVLSARLAKP 79
Score = 26.8 bits (60), Expect = 3.5
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK----RHRNEGVVEFESSSDMKKALDKL 170
++ ++NL + ++ LK F+++ HK + ++ V F S + +KAL+ L
Sbjct: 7 KVEIKNLPKYIGFKQLKKFLKKQL----FKPHKIKLLKRQDFAFVTFRSEEERQKALEIL 62
Query: 171 DNAELNGRRIRLIEDKP 187
D + GR + KP
Sbjct: 63 DGFKWKGRVLSARLAKP 79
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM2 of FCA, a gene
controlling flowering time in Arabidopsis, which
encodes a flowering time control protein that functions
in the posttranscriptional regulation of transcripts
involved in the flowering process. The flowering time
control protein FCA contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 31.4 bits (71), Expect = 0.091
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYEL 57
K+++G L E+++E+ YGR+ D+ + G FV++ A A+ L
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60
Query: 58 NG 59
NG
Sbjct: 61 NG 62
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM2 of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Overexpression of hnRNP A2/B1 has been described in
many cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 31.2 bits (70), Expect = 0.099
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GG+ E L + + YG+I + + K GFGFV F+D+ D V +
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0, a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. It has also been identified
as an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 31.2 bits (71), Expect = 0.099
Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 12/61 (19%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++GGL E + ++ +G I ++ L + GF F+ F D+++ V +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITF----DSEEPVKK 56
Query: 57 L 57
+
Sbjct: 57 I 57
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12
small nuclear ribonucleoprotein 35 kDa protein
(U11/U12-35K) and similar proteins. This subfamily
corresponds to the RRM of U11/U12-35K, also termed
protein HM-1, or U1 snRNP-binding protein homolog, and
is one of the components of the U11/U12 snRNP, which is
a subunit of the minor (U12-dependent) spliceosome
required for splicing U12-type nuclear pre-mRNA
introns. U11/U12-35K is highly conserved among
bilateria and plants, but lacks in some organisms, such
as Saccharomyces cerevisiae and Caenorhabditis elegans.
Moreover, U11/U12-35K shows significant sequence
homology to U1 snRNP-specific 70 kDa protein (U1-70K or
snRNP70). It contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5'
splice site recognition in the minor spliceosome and
play a role in exon bridging, interacting with
components of the major spliceosome bound to the
pyrimidine tract of an upstream U2-type intron. The
family corresponds to the RRM of U11/U12-35K that may
directly contact the U11 or U12 snRNA through the RRM
domain.
Length = 93
Score = 31.5 bits (72), Expect = 0.10
Identities = 27/89 (30%), Positives = 37/89 (41%), Gaps = 22/89 (24%)
Query: 17 ERDLEKFVKGYGRI------RDVI--LKNGFGFVEFEDYRDADDAVYELNGKSLL-GERV 67
E L + YG I RD++ G+ FVE+E RDA A Y K ++ G +
Sbjct: 17 EETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA-YRDAHKLVIDGSEI 75
Query: 68 TVEIAKGIDRSQERGRRGYGSYRAPPPRR 96
V D +ER G+ PRR
Sbjct: 76 FV------DFERERTLPGW------IPRR 92
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM1 of SXL which governs sexual
differentiation and X chromosome dosage compensation in
Drosophila melanogaster. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 31.2 bits (71), Expect = 0.10
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAK 73
GFGFV+++ DA A+ LNG L +R+ V A+
Sbjct: 43 GFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYAR 78
Score = 27.0 bits (60), Expect = 3.3
Identities = 11/37 (29%), Positives = 24/37 (64%)
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRG 189
G V+++S+ D ++A+ L+ +L +RI++ +P G
Sbjct: 45 GFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYARPGG 81
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast
RNA-binding protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or
modifier of damage tolerance Mdt1, a novel
phosphothreonine (pThr)-containing protein that
specifically interacts with the pThr-binding site of
the Rad53 FHA1 domain. It is encoded by gene MDT1
(YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is
involved in normal G2/M cell cycle progression in the
absence of DNA damage and functions as a novel target
of checkpoint-dependent cell cycle arrest pathways. It
contains an N-terminal RRM, a nuclear localization
signal, a coiled coil, and a total of 15 SQ/TQ motifs.
cip1 (Csx1-interacting protein 1) and cip2
(Csx1-interacting protein 2) are novel cytoplasmic
RRM-containing proteins that counteract Csx1 function
during oxidative stress. They are not essential for
viability in fission yeast Schizosaccharomyces pombe.
Both cip1 and cip2 contain one RRM. Like PIN4, Cip2
also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 31.3 bits (71), Expect = 0.11
Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIR--------DVILKNGFGFVEFEDYRDADDAVY 55
T + I +P+ +R+ L ++ G D + G F F +A V
Sbjct: 2 TAIVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVE 61
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG + G R+ VE +
Sbjct: 62 ALNGYEISGRRLRVEYKR 79
Score = 27.8 bits (62), Expect = 1.3
Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGV------VEFESSSDMKKALDK 169
++++N+ + + L D + +G + A H + GV F S + + ++
Sbjct: 4 IVIKNIPFSLRKEQLLDIIEDLG-IPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVEA 62
Query: 170 LDNAELNGRRIRL 182
L+ E++GRR+R+
Sbjct: 63 LNGYEISGRRLRV 75
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 31.1 bits (70), Expect = 0.11
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 7/63 (11%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL------KN-GFGFVEFEDYRDADDAVY 55
G +V++G +P V E +L + GRI ++ L KN G+ FV + +A AV
Sbjct: 1 GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVR 60
Query: 56 ELN 58
ELN
Sbjct: 61 ELN 63
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 85
Score = 31.2 bits (70), Expect = 0.11
Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 30 IRDVILKN--GFGFVEFEDYRDADDAVYELNGKSLLGERV 67
IRD GFGFV +Y +A A+ LNG LG+RV
Sbjct: 34 IRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYR-LGDRV 72
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 33.1 bits (76), Expect = 0.11
Identities = 16/45 (35%), Positives = 20/45 (44%)
Query: 177 GRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSR 221
R R R G RGRSR S R S+ S R+ + + R R
Sbjct: 17 RRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDR 61
Score = 33.1 bits (76), Expect = 0.12
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 188 RGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKA---KSVSRSPS 242
R R R SR +SR RSR SR +R + + ++ SPS
Sbjct: 17 RRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDRYRAYFAYLASSPS 74
Score = 32.4 bits (74), Expect = 0.22
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 188 RGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTR 247
RS SS RSR +R R + SR +S + +S +S +R + T
Sbjct: 2 DDLALRRSSSSLRRSRRAARRSRRDGRV---GSRGRSRYRSRRRSSRRSSTRRAELADTE 58
Query: 248 KRSRSR 253
R R R
Sbjct: 59 -RDRYR 63
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. The family
also includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 31.1 bits (71), Expect = 0.11
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
L V+NLS VS + L+ Q GEV A D R EG+VEF + A+ +
Sbjct: 2 LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKR 59
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM2 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal, highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 80
Score = 31.2 bits (70), Expect = 0.11
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 8/70 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYEL 57
V++G L + D++ +G+I D ++K+ G+GFV F + DA++A+ +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 58 NGKSLLGERV 67
G+ L G ++
Sbjct: 64 GGQWLGGRQI 73
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily corresponds
to the RRM2 of La and LARP7. La is a highly abundant
nuclear phosphoprotein and well conserved in eukaryotes.
It specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. LARP7
is an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
of 7SK RNA. It is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP), intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. LARP7 plays an essential role in the inhibition
of positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
Both La and LARP7 contain an N-terminal La motif (LAM),
followed by two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 30.7 bits (70), Expect = 0.12
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 125 VSWQDLKDFMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDK 169
V+ +D+K Q GEV Y D + G + F++ +KA +
Sbjct: 13 VTREDIKAVFAQFGEVKYVD-FTEGADTGYIRFKTPEAAQKAREA 56
>gnl|CDD|227430 COG5099, COG5099, RNA-binding protein of the Puf family,
translational repressor [Translation, ribosomal
structure and biogenesis].
Length = 777
Score = 33.6 bits (77), Expect = 0.12
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 199 SSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKA---KSVSRSPSPSKTRKRSRSRSD 255
S+ SR+KS S S++ + S S + S + S K +P+ S + ++S S
Sbjct: 110 STSSRNKSNSALSSTQQGNANS-SVTLSSSTASSMFNSNKLPLPNPNHSNSATTNQSGSS 168
Query: 256 S 256
Sbjct: 169 F 169
>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 = 31.0 bits (70), Expect = 0.13
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVI--LKNGFGFVEFEDYRDADDAVY 55
T +Y+ LP + E +L K + YG I RD L G FV ++ +A A+
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
Query: 56 ELNG 59
LNG
Sbjct: 61 SLNG 64
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline-
and glutamine-rich splicing factor, or 100 kDa
DNA-pairing protein (POMp100), or 100 kDa subunit of
DNA-binding p52/p100 complex, a multifunctional protein
that mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the
formation of D-loops in superhelical duplex DNA, and is
involved in cell proliferation. PSF can also interact
with multiple factors. It is an RNA-binding component
of spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions,
such as DNA recombination and RNA synthesis,
processing, and transport. PSF contains two conserved
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which are responsible for interactions with RNA and for
the localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. .
Length = 71
Score = 30.7 bits (69), Expect = 0.13
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--GFGFVEFEDYRDADDAVYELNGKSL 62
++++G LP + E + +K YG +V + GFGF++ E A+ A EL+ +
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPM 62
Query: 63 LGERVTV 69
G ++ V
Sbjct: 63 RGRQLRV 69
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 31.1 bits (71), Expect = 0.13
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL-----KNGFGFVEFEDYRDADDAV 54
+Y+G +P +L + + +G I ++ L + +GFV + DA A+
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAI 58
>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 = 30.5 bits (69), Expect = 0.13
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--NGFGFVEFEDYRDADDAVYELNG 59
T VY+G +P + DL + +G I + + GF FV+ + + A A+ +L G
Sbjct: 1 TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQG 58
>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 = 30.7 bits (69), Expect = 0.14
Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 118 VENLSSRVSWQDLKDFMRQVG-----EVCYADAHKRHRNEGVVEFESSSDMKKALDKLDN 172
V LS + +DL++ + G V Y R R V FE D K+A++ +
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63
Query: 173 AELNGRRIRL 182
EL+GRRIR+
Sbjct: 64 MELDGRRIRV 73
Score = 28.8 bits (64), Expect = 0.76
Identities = 23/69 (33%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 10 GLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKS 61
GL ERDL + YG + V + GF FV FE D+ +A+ NG
Sbjct: 6 GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGME 65
Query: 62 LLGERVTVE 70
L G R+ V+
Sbjct: 66 LDGRRIRVD 74
>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 = 30.6 bits (70), Expect = 0.14
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 10 GLPYGVRERDLE----KFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGE 65
LP + LE +F G+ +R ++ + G FVEFE A A+ L G +
Sbjct: 9 NLPEETTKEMLEMLFNQF-PGFKEVR-LVPRRGIAFVEFETEEQATVALQALQGFKITPG 66
Score = 29.8 bits (68), Expect = 0.28
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 7/62 (11%)
Query: 114 HRLIVENLSSRVSWQDLKD-FMRQVG--EVCYADAHKRHRNEGVVEFESSSDMKKALDKL 170
L ++NL + + L+ F + G EV R VEFE+ AL L
Sbjct: 3 KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR----RGIAFVEFETEEQATVALQAL 58
Query: 171 DN 172
Sbjct: 59 QG 60
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 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 = 75
Score = 30.5 bits (69), Expect = 0.15
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 8/65 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVI--------LKNGFGFVEFEDYRDADDAVY 55
T V + LP+ ++ F GY I + G V F+ +R+A AV
Sbjct: 1 TCVKVQNLPFTATIEEILDFFYGYRVIPGSVSLLYNDNGAPTGEATVAFDTHREAMAAVR 60
Query: 56 ELNGK 60
ELNG+
Sbjct: 61 ELNGR 65
>gnl|CDD|132358 TIGR03315, Se_ygfK, putative selenate reductase, YgfK subunit.
Members of this protein family are YgfK, predicted to be
one subunit of a three-subunit, molybdopterin-containing
selenate reductase. This enzyme is found, typically, in
genomic regions associated with xanthine dehydrogenase
homologs predicted to belong to the selenium-dependent
molybdenum hydroxylases (SDMH). Therefore, the selenate
reductase is suggested to play a role in furnishing
selenide for SelD, the selenophosphate synthase.
Length = 1012
Score = 32.8 bits (75), Expect = 0.17
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 13 YGVRERDLEKFVK------GYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGER 66
Y + E+ L FVK GY +RD + + GF ++ ++ + D YE + ++L
Sbjct: 229 YLLEEKGLHTFVKLNPTLLGYKFVRDTMDEMGFDYIVLKEESFSHDLQYE-DAVAMLQRL 287
Query: 67 VTVEIAKGI 75
+ KG+
Sbjct: 288 QLLAKEKGL 296
>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 = 30.6 bits (70), Expect = 0.17
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 13/76 (17%)
Query: 10 GLPYGVRERDLEKFVKGYGR--IRDV-ILKN-------GFGFVEF---EDYRDADDAVYE 56
GL E D+ + + I+DV ++++ GF FVEF ED DA+
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68
Query: 57 LNGKSLLGERVTVEIA 72
L+ + G V V A
Sbjct: 69 LDPFVIDGRVVRVSYA 84
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long C-terminal glycine-rich
domain that contains a potential ATP/GTP binding loop.
.
Length = 75
Score = 30.3 bits (68), Expect = 0.17
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 8/55 (14%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILK--------NGFGFVEFEDYRDAD 51
K+++GGL + ++DL+ + +G + D +K GFGF+ F+D +
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVE 55
Score = 26.5 bits (58), Expect = 4.9
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-----RHRNEGVVEFESSSDMKKALDK 169
++ V LS S +DLKD+ + GEV R R G + F+ +S ++K L++
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 170 LDNAELNGRRI 180
++ L+GR I
Sbjct: 61 KEH-RLDGRLI 70
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
family also includes polypyrimidine tract binding
protein homolog 3 (PTBPH3) found in plant. Although its
biological roles remain unclear, PTBPH3 shows
significant sequence similarity to polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Like PTB, PTBPH3
contains four RRMs.
Length = 71
Score = 30.2 bits (69), Expect = 0.18
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 27 YG---RIRDVILKN--GFGFVEFEDYRDADDAVYELNGKSLLGERVTV 69
YG RI+ LK+ G V+ D + A+ A+ LNG L G+++ V
Sbjct: 24 YGNVLRIK--FLKSKPGTAMVQMGDPQAAERAIEYLNGVVLFGQKLEV 69
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 30.4 bits (69), Expect = 0.18
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 14 GVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYELNGKSL 62
V E DL + +G I+D+ ++K+ G +V+F A A+ E+NGK L
Sbjct: 13 SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCL 69
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar
proteins. This subfamily corresponds to the RRM1 of
RBM19 and MRD1. RBM19, also termed RNA-binding domain-1
(RBD-1), is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 77
Score = 30.3 bits (69), Expect = 0.19
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 4 TKVYIGGLPYGVRERDLEK-FVKGYGRIRDV-ILKN------GFGFVEFEDYRDADDAVY 55
+++ + LP + E +L++ F K G I DV +L+ F+ ++ +A A
Sbjct: 1 SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60
Query: 56 ELNGKSLLGERVTVEIA 72
N + +++VE A
Sbjct: 61 YFNNTYINTSKISVEFA 77
Score = 25.7 bits (57), Expect = 8.6
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 115 RLIVENLSSRVSWQDLKD-FMRQVGEV--CY--ADAHKRHRNEGVVEFESSSDMKKALDK 169
RLIV+NL + ++ +LK+ F + GE+ + R + +++ + +KA D
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDY 61
Query: 170 LDNAELNGRRI 180
+N +N +I
Sbjct: 62 FNNTYINTSKI 72
>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 = 30.2 bits (68), Expect = 0.19
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 9/72 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRI-RDVILKN-------GFGFVEFEDYRDADDAVYEL 57
VY+G + YG +LE G G + R IL + GF ++EF D +++ L
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTALAL 60
Query: 58 NGKSLLGERVTV 69
+ G ++ V
Sbjct: 61 DESLFRGRQIKV 72
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 2 (Musashi-2 ) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 76
Score = 30.4 bits (68), Expect = 0.20
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV-- 54
K++IGGL + L + +G IR+ ++ GFGFV F D D +
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 55 --YELNGKSL 62
+EL+ K++
Sbjct: 61 PHHELDSKTI 70
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the
RRM of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). This
family also includes yeast eIF3-p33, a homolog of
vertebrate eIF-3G, plays an important role in the
initiation phase of protein synthesis in yeast. It
binds both, mRNA and rRNA, fragments due to an RRM near
its C-terminus. .
Length = 77
Score = 30.2 bits (69), Expect = 0.21
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 15 VRERDLEKFVKGYGRIRDVIL-KN-------GFGFVEFEDYRDADDAVYELNG 59
E DL + + +G I V L K+ GF FV F DA+ A+ +LNG
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding
protein 34 (RBM34) and similar proteins. This
subfamily corresponds to the RRM1 of RBM34, a putative
RNA-binding protein containing two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). Although the
function of RBM34 remains unclear currently, its RRM
domains may participate in mRNA processing. RBM34 may
act as an mRNA processing-related protein. .
Length = 91
Score = 30.3 bits (69), Expect = 0.22
Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 26/89 (29%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYG-----RIRDVILKNGF--------------------G 40
V++G LP +++DL+K K +G R R V +K
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62
Query: 41 FVEFEDYRDADDAVYELNGKSLLGERVTV 69
+V F++ A+ A+ +LNG G + V
Sbjct: 63 YVVFKEEESAEKAL-KLNGTEFEGHHIRV 90
>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM1 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 70
Score = 30.1 bits (68), Expect = 0.22
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVG-EVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNA 173
R+++ NL + V+ Q++ D + + C D KR V + +A+ KL +
Sbjct: 1 RIVIRNLPADVTKQEVHDLLSDYQVKYCDVDKSKR---TAQVTLLNGDQASRAIAKLHQS 57
Query: 174 ELNGRRI 180
R+I
Sbjct: 58 SYKERKI 64
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional
and post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus.
.
Length = 75
Score = 30.0 bits (67), Expect = 0.22
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFED 46
KV++GGL E ++++ +G I ++ L + GF FV + D
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTD 50
>gnl|CDD|221931 pfam13136, DUF3984, Protein of unknown function (DUF3984). This
family of proteins is functionally uncharacterized. This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 393 and 442 amino
acids in length.
Length = 301
Score = 32.4 bits (74), Expect = 0.22
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 200 SRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRAR 259
S SRS SRSR K S RS + K+KS + TR RS+S + +
Sbjct: 57 SHSRSPSRSRLHKRKKSSRRSP-----MSDTLLKSKSSAHLLHHQSTRSHRRSKSGTTSP 111
Score = 28.5 bits (64), Expect = 3.6
Identities = 14/43 (32%), Positives = 19/43 (44%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGS 226
E + SR +S R RS + S + R RS S+ GS
Sbjct: 166 EREAAREREHSSRRASRRGRSGYSTPSAALSRRGSRSASRRGS 208
>gnl|CDD|240932 cd12488, RRM2_hnRNPR, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM2 of hnRNP R, a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. hnRNP R is predominantly located
in axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, as well as in retinal development and
light-elicited cellular activities. It contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif. hnRNP R binds RNA through its RRM domains. .
Length = 85
Score = 30.5 bits (68), Expect = 0.24
Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 12/80 (15%)
Query: 5 KVYIGGLPYG-VRERDLEKFVKGYGRIRDVIL---------KNGFGFVEFEDYRDADDAV 54
++++G +P +E LE+F K + DVIL GF F+E+ED++ A A
Sbjct: 4 RLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQAR 63
Query: 55 YEL-NGK-SLLGERVTVEIA 72
L +GK + G VTVE A
Sbjct: 64 RRLMSGKVKVWGNVVTVEWA 83
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells, as well as the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 30.1 bits (67), Expect = 0.25
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRI------RDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + + G I RD I G+GFV + D +DA+ A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 30.1 bits (68), Expect = 0.26
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL---------KNGFGFVEFEDYRDADDAV 54
+K+ + +P+ ++L + +G ++ V L GFGFV+F +DA A
Sbjct: 1 SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60
Query: 55 YELNGKS-LLGERVTVEIA 72
L + L G R+ +E A
Sbjct: 61 KALCHSTHLYGRRLVLEWA 79
Score = 29.7 bits (67), Expect = 0.31
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEVCY------ADAHKRHRNEGVVEFESSSDMKKALD 168
+++V N+ + ++L++ GE+ HR G V+F + D K+A
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61
Query: 169 KL-DNAELNGRRIRL 182
L + L GRR+ L
Sbjct: 62 ALCHSTHLYGRRLVL 76
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 31.7 bits (72), Expect = 0.31
Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 3/60 (5%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSP 243
+ GG S S + + R+S+SR + SP ++ S+A
Sbjct: 29 NPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWED---SPWRTVSRAPGDETPEKA 85
Score = 27.8 bits (62), Expect = 6.2
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPS 242
+D + R+ R KSR+ +R R S+S + S ++VSR+P
Sbjct: 21 DDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDR-NSQSRDRKWEDSPWRTVSRAPG 78
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM
of some eukaryotic DnaJ homolog subfamily C member 17
and similar proteins. DnaJ/Hsp40 (heat shock protein
40) proteins are highly conserved and play crucial
roles in protein translation, folding, unfolding,
translocation, and degradation. They act primarily by
stimulating the ATPase activity of Hsp70s, an important
chaperonine family. Members in this family contains an
N-terminal DnaJ domain or J-domain, which mediates the
interaction with Hsp70. They also contains a RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
C-terminus, which may play an essential role in RNA
binding. .
Length = 74
Score = 29.5 bits (67), Expect = 0.34
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 17 ERDLEKFVKGYGRIRDVIL---KNGFGFVEFEDYRDADDAVYELNGK 60
E +L K YG + DV++ K G VEF + A+ AV G
Sbjct: 18 EDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAVENECGL 64
>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 = 29.9 bits (68), Expect = 0.35
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 14/81 (17%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-----GFGF---------VEFEDYRDAD 51
VY G LP V + DL +F K Y I + V + D
Sbjct: 5 VYCGKLPKKVTDEDLREFFKDYNPQEIWIFRTRKSKRNPLQLHRHFTAALVTLDTEETLD 64
Query: 52 DAVYELNGKSLLGERVTVEIA 72
+ + L K L G++++++ A
Sbjct: 65 EIIESLKSKKLNGKKISLKPA 85
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 32.0 bits (72), Expect = 0.40
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 196 RSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSD 255
R+S + +S R+ S + + + SK+ S +K K K + SP K+ KR R +
Sbjct: 31 RASPTNEDQRSSGRNSPSAASTSSNDSKAESTKKPNKKIKE--EATSPLKSTKRQREKPA 88
Query: 256 SRA 258
S
Sbjct: 89 SDT 91
>gnl|CDD|215814 pfam00242, DNA_pol_viral_N, DNA polymerase (viral) N-terminal
domain.
Length = 379
Score = 31.3 bits (71), Expect = 0.41
Identities = 21/124 (16%), Positives = 36/124 (29%), Gaps = 9/124 (7%)
Query: 142 YADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGR---RIRLIEDKPRGGGRGRSRSS 198
Y+ + G + ++ + R R SRS
Sbjct: 178 YSWEQEYLLQHGGQQHSHLQRHGDEPFGAQSSGILSRSENRRTRNLANNTSRKSDTSRSV 237
Query: 199 SSRSRSK---SRSRSRSSKS---RSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRS 252
+S+ SR ++++ + RS S RK + + PS S S
Sbjct: 238 GPVRQSQIQRSRLGLQANQGKLAHGQQGRSGSIRGRKHSTTRRPFGVEPSSSGVTTNRAS 297
Query: 253 RSDS 256
S S
Sbjct: 298 SSSS 301
Score = 29.0 bits (65), Expect = 2.9
Identities = 17/80 (21%), Positives = 24/80 (30%), Gaps = 7/80 (8%)
Query: 187 PRGG-GRGRSRSSSSRSRSKSRSRSRS-----SKSRSPRSRSKSGSPRKSKSKAKSVSR- 239
+G G R R S+ R S S S S +S + S + R
Sbjct: 263 QQGRSGSIRGRKHSTTRRPFGVEPSSSGVTTNRASSSSSCFHQSAVRETAYSSLSTSERH 322
Query: 240 SPSPSKTRKRSRSRSDSRAR 259
S S RS ++
Sbjct: 323 SSSGHAVELRSIPGGSVSSQ 342
Score = 28.2 bits (63), Expect = 4.7
Identities = 12/64 (18%), Positives = 20/64 (31%), Gaps = 1/64 (1%)
Query: 195 SRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRS 254
SSS + S S S +S R + S + + S + S S
Sbjct: 284 VEPSSSGVTTNRASSSSSCFHQSA-VRETAYSSLSTSERHSSSGHAVELRSIPGGSVSSQ 342
Query: 255 DSRA 258
++
Sbjct: 343 NAGP 346
>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 = 29.7 bits (66), Expect = 0.42
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERV 67
GFGFV +Y +A A+ LNG LG+RV
Sbjct: 46 GFGFVTMTNYDEAAMAIASLNGYR-LGDRV 74
>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 = 29.2 bits (66), Expect = 0.43
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNG------FGFVEFEDYRDADDAVYELNG 59
+++GG+ + E DL++F G + V L F FVEF D A A+ L+G
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSAL-NLSG 61
Query: 60 KSLLGERVTVEIAK 73
L G + V +K
Sbjct: 62 TLLGGHPLRVSPSK 75
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 78
Score = 29.2 bits (65), Expect = 0.45
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 153 GVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRG 189
G V+F S D K A + +++ E++G ++ L KP+G
Sbjct: 42 GFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAKPKG 78
Score = 28.4 bits (63), Expect = 0.98
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 31 RDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAK 73
RD GFGFV+F DA A + + G +VT++ AK
Sbjct: 33 RDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAK 75
>gnl|CDD|240707 cd12261, RRM1_3_MRN1, RNA recognition motif 1 and 3 in
RNA-binding protein MRN1 and similar proteins. This
subfamily corresponds to the RRM1 and RRM3 of MRN1,
also termed multicopy suppressor of RSC-NHP6 synthetic
lethality protein 1, or post-transcriptional regulator
of 69 kDa, which is an RNA-binding protein found in
yeast. Although its specific biological role remains
unclear, MRN1 might be involved in translational
regulation. Members in this family contain four copies
of conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 73
Score = 29.1 bits (66), Expect = 0.46
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGF--GFVEFEDYRDAD 51
VY+G LP RD+ ++G G + + L V F D A+
Sbjct: 2 TVYLGNLPEDTTIRDILSAIRG-GPLESIKLLPTKNSATVSFLDEAAAE 49
>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM2 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 = 89
Score = 29.7 bits (66), Expect = 0.47
Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 12/81 (14%)
Query: 5 KVYIGGLP-YGVRERDLEKFVKGYGRIRDVI--------LKN-GFGFVEFEDYRDADDAV 54
+++IGG+P RE LE+ K + DVI +KN GF FVE+E +R A A
Sbjct: 3 RLFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62
Query: 55 YEL-NGK-SLLGERVTVEIAK 73
+L G+ L G ++ V+ A+
Sbjct: 63 RKLMPGRIQLWGHQIAVDWAE 83
>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export
factor BR1 family. It has been shown that the 104
N-terminal amino acids of the maize streak virus coat
protein bind DNA non- specifically. This family also
includes various geminivirus movement proteins that are
nuclear export factors or shuttles. One member BR1
facilitates the export of both ds and ss DNA form the
nucleus.
Length = 244
Score = 31.1 bits (71), Expect = 0.47
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 188 RGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSP 227
R R+R+ + RS +K R S+ R RS SP
Sbjct: 6 FDSRRSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRSP 45
>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 = 29.2 bits (66), Expect = 0.47
Identities = 12/49 (24%), Positives = 27/49 (55%), Gaps = 8/49 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFE 45
K+++G LP+ V ++L+++ +G+++ + G+GFV F
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFS 49
Score = 28.0 bits (63), Expect = 1.3
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGEV--CYADAHK---RHRNEGVVEFESSSDMKKALDK 169
+L V NL V ++LK++ Q G+V C K + G V F S ++ AL K
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 170 ----LDNAELN 176
L+ +L
Sbjct: 61 QKHILEGNKLQ 71
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family. This subfamily corresponds to the RRM2
of hnRNP H protein family which includes hnRNP H (also
termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP
H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA
only in the presence of cap-binding proteins.
Furthermore, hnRNP H and hnRNP H2 are almost identical;
both have been found to bind nuclear-matrix proteins.
hnRNP H activates exon inclusion by binding G-rich
intronic elements downstream of the 5' splice site in
the transcripts of c-src, human immunodeficiency virus
type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences
exons when bound to exonic elements in the transcripts
of beta-tropomyosin, HIV-1, and alpha-tropomyosin.
hnRNP H2 has been implicated in pre-mRNA 3' end
formation. hnRNP H3 may be involved in the splicing
arrest induced by heat shock. Most family members
contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and they
play an important role in efficiently silencing the
exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction
with the exonic GGG motifs. The lack of RRM1 could
account for the reduced silencing activity within hnRNP
H3. In addition, the family members have an extensive
glycine-rich region near the C-terminus, which may
allow them to homo- or heterodimerize. .
Length = 77
Score = 29.3 bits (66), Expect = 0.50
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDA 53
V + GLP+G + ++ +F G + + I G +V+F A+ A
Sbjct: 3 VRLRGLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERA 58
>gnl|CDD|220401 pfam09786, CytochromB561_N, Cytochrome B561, N terminal. Members
of this family are found in the N terminal region of
cytochrome B561, as well as in various other putative
uncharacterized proteins.
Length = 559
Score = 31.3 bits (71), Expect = 0.50
Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 1/67 (1%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKT-RKRSRS 252
SS S S S+S S SR S +S +P + S +SPS S + + S
Sbjct: 137 PGHSSFSDSPSRSASPSRKFSPSSTIQQSPQLTPSNKPASPSSSYQSPSYSSSLGPVNSS 196
Query: 253 RSDSRAR 259
+ S R
Sbjct: 197 GNRSNLR 203
Score = 29.7 bits (67), Expect = 1.8
Identities = 22/94 (23%), Positives = 39/94 (41%), Gaps = 2/94 (2%)
Query: 165 KALDKLDNAELNGRRIRLIEDKPRGGGRGR-SRSSSSRSRSKSRSRSRSSKSRSPRSRSK 223
K L D L+ R++ L+ K + S++ S SK+ + +S+ P S
Sbjct: 83 KYLFTSDQLVLSERQLGLLGVKAKDSQFTVVSQAKKSPPASKTSTPMNTSEPLVPGHSSF 142
Query: 224 SGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSR 257
S SP +S S ++ S S S + + +
Sbjct: 143 SDSPSRSASPSRKFSPS-STIQQSPQLTPSNKPA 175
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 29.3 bits (65), Expect = 0.51
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 15 VRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKSLLGER 66
+R RDLE+F G++RDV + G +VEF D A+ L G+ +LG
Sbjct: 13 IRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI-GLTGQRVLGVP 71
Query: 67 VTVEIAKG 74
+ V+ ++
Sbjct: 72 IIVQASQA 79
>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 = 29.3 bits (65), Expect = 0.56
Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERV 67
GFGFV +Y +A A+ LNG LG+RV
Sbjct: 46 GFGFVTMTNYDEAAMAIASLNGYR-LGDRV 74
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44
(RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 29.1 bits (65), Expect = 0.57
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 118 VENLSSRVSWQDLKDFMR--QVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
V LS VS DL+ + QV + + F+ +SD A+ K++ L
Sbjct: 4 VGGLSPSVSEGDLRSHFQKYQVSVISLCKLSNY--RYASLHFDRASDALLAVKKMNGGVL 61
Query: 176 NGRRIRLIEDK 186
+G I++ K
Sbjct: 62 SGLSIKVRMVK 72
Score = 27.9 bits (62), Expect = 1.1
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL----KNGFGFVEFEDYRDADDAVYELNGKS 61
V++GGL V E DL + Y ++ + L + + F+ DA AV ++NG
Sbjct: 2 VHVGGLSPSVSEGDLRSHFQKY-QVSVISLCKLSNYRYASLHFDRASDALLAVKKMNGGV 60
Query: 62 LLGERVTVEIAK 73
L G + V + K
Sbjct: 61 LSGLSIKVRMVK 72
>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 = 29.2 bits (65), Expect = 0.58
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 8/50 (16%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVILKN--------GFGFVEFED 46
++++G LP+ + E +L++F +G + ++ + FGFV F+D
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDD 56
>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 = 29.0 bits (65), Expect = 0.58
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHK-RHRNEGVVEFESSSDMKKA 166
PPT+ H V NL S V+ +D+ + + + G + + + + +VEF + +A
Sbjct: 5 PPTKMIH---VSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATEEQATEA 61
Query: 167 LDKLDNAELNGRRIRL 182
L + LNG IRL
Sbjct: 62 LACKHASSLNGSTIRL 77
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 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 = 89
Score = 29.1 bits (66), Expect = 0.59
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 10/45 (22%)
Query: 16 RERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGK 60
R V G G++ FVEF D DA A L G+
Sbjct: 45 RPEAEGVDVPGVGKV----------FVEFADVEDAQKAQLALAGR 79
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM3 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2
(also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR),
both of which belong to the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) family of
RNA-binding proteins that have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contain
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are important for localization in
the cytoplasm. The splicing activation or repression
activity of CELF-2 on some specific substrates is
mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2,
can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 29.3 bits (65), Expect = 0.59
Identities = 19/85 (22%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAV 54
G ++I LP ++DL + +G + + L FGFV +++ A A+
Sbjct: 7 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 66
Query: 55 YELNGKSLLGERVTVEIAKGIDRSQ 79
+NG + +R+ V++ + + S+
Sbjct: 67 QAMNGFQIGMKRLKVQLKRSKNDSK 91
>gnl|CDD|215556 PLN03064, PLN03064, alpha,alpha-trehalose-phosphate synthase
(UDP-forming); Provisional.
Length = 934
Score = 31.3 bits (71), Expect = 0.59
Identities = 17/73 (23%), Positives = 27/73 (36%)
Query: 174 ELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSK 233
EL + + G + S SRS S++S+ + RS S + +
Sbjct: 813 ELPSDSPAIARSRSPDGLKSSGDRRPSGKLPSSRSNSKNSQGKKQRSLLSSAKSGVNHAA 872
Query: 234 AKSVSRSPSPSKT 246
+ R PSP K
Sbjct: 873 SHGSDRRPSPEKI 885
Score = 28.6 bits (64), Expect = 3.7
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 198 SSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSR 257
S + +RS+S +SS R P + S S+ K S +K + + S
Sbjct: 818 SPAIARSRSPDGLKSSGDRRPSGKLPSSRSNSKNSQGKKQRSLLSSAK-SGVNHAASHGS 876
Query: 258 ARKVS 262
R+ S
Sbjct: 877 DRRPS 881
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 28.8 bits (64), Expect = 0.62
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 4/74 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHK----RHRNEGVVEFESSSDMKKALDKLD 171
+ V NL +V W+ LK+ G V AD + + R G V FE + +A+ +
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62
Query: 172 NAELNGRRIRLIED 185
L R + + D
Sbjct: 63 GQFLFDRPMHVKMD 76
>gnl|CDD|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 3
(IGF2BP3). This subgroup corresponds to the RRM1 of
IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also
termed KH domain-containing protein overexpressed in
cancer (KOC), or VICKZ family member 3, an RNA-binding
protein that plays an important role in the
differentiation process during early embryogenesis. It
is known to bind to and repress the translation of IGF2
leader 3 mRNA. IGF2BP3 also acts as a
Glioblastoma-specific proproliferative and proinvasive
marker acting through IGF2 resulting in the activation
of oncogenic phosphatidylinositol
3-kinase/mitogen-activated protein kinase (PI3K/MAPK)
pathways. IGF2BP3 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 = 28.8 bits (64), Expect = 0.67
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRI---RDVILKNGFGFVEFEDYRDADDAVYELNGK- 60
K+YIG L DLE K +I ++K+G+ FV+ D A A+ L+GK
Sbjct: 3 KLYIGNLSENASPLDLESIFKDS-KIPFSGPFLVKSGYAFVDCPDESWAMKAIDTLSGKV 61
Query: 61 SLLGERVTVE 70
L G+ + VE
Sbjct: 62 ELHGKVIEVE 71
>gnl|CDD|219916 pfam08580, KAR9, Yeast cortical protein KAR9. The KAR9 protein in
Saccharomyces cerevisiae is a cytoskeletal protein
required for karyogamy, correct positioning of the
mitotic spindle and for orientation of cytoplasmic
microtubules. KAR9 localises at the shmoo tip in mating
cells and at the tip of the growing bud in anaphase.
Length = 626
Score = 31.0 bits (70), Expect = 0.68
Identities = 20/66 (30%), Positives = 24/66 (36%), Gaps = 1/66 (1%)
Query: 192 RGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSR 251
R S + SR SR S S S R S SGS VSR + + RS
Sbjct: 507 PLSPRQSIITLPTPSRPASRIS-SLSLRLGSYSGSIVSPPPYPTLVSRKGAAGLSFNRSV 565
Query: 252 SRSDSR 257
S +
Sbjct: 566 SDIEGE 571
>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 = 29.0 bits (65), Expect = 0.68
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 1 MVGTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDA 53
++ V++GG+ + E ++ F YG +++V + G+GFV F D D
Sbjct: 3 IMPNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKI 62
Query: 54 V 54
V
Sbjct: 63 V 63
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 28.8 bits (64), Expect = 0.70
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHK----RHRNEGVVEFESSSDMKKALDKLD 171
+ V NL +V W+ LK+ G V AD + + R G V FE + +A+ +
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFN 62
Query: 172 NAELNGR 178
L R
Sbjct: 63 GQLLFDR 69
>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 = 28.8 bits (64), Expect = 0.70
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRI--------RDVILKNGFGFVEFEDYRDADDAV 54
G ++I LP + DL + +G + + L FGFV +++ A A+
Sbjct: 4 GCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAI 63
Query: 55 YELNGKSLLGERVTVE 70
+NG + +R+ V+
Sbjct: 64 QAMNGFQIGTKRLKVQ 79
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate
probable RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 28.9 bits (64), Expect = 0.73
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 9/68 (13%)
Query: 15 VRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNGKSLLGER 66
+R RDLE F G++RDV + G +VEF + + A+ L G+ LLG
Sbjct: 13 IRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVP 71
Query: 67 VTVEIAKG 74
+ V+ ++
Sbjct: 72 IIVQASQA 79
>gnl|CDD|240698 cd12252, RRM_DbpA, RNA recognition motif in the DbpA subfamily of
prokaryotic DEAD-box rRNA helicases. This subfamily
corresponds to the C-terminal RRM homology domain of
dbpA proteins implicated in ribosome biogenesis. They
bind with high affinity and specificity to RNA
substrates containing hairpin 92 of 23S rRNA (HP92),
which is part of the ribosomal A-site. The majority of
dbpA proteins contain two N-terminal ATPase catalytic
domains and a C-terminal RNA binding domain, an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain). The catalytic domains bind to nearby regions
of RNA to stimulate ATP hydrolysis and disrupt RNA
structures. The C-terminal domain is responsible for
the high-affinity RNA binding. Several members of this
family lack specificity for 23S rRNA. These proteins
can generally be distinguished by a basic region that
extends beyond the C-terminal domain.
Length = 71
Score = 28.3 bits (64), Expect = 0.76
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 14 GVRERDLEKFVKGYG-----RIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVT 68
G+ RDL + G I D+ + + F FVE + A+ + LNGK + G++V
Sbjct: 11 GIDPRDLVGAICRAGGIPGRDIGDIDIFDKFSFVEVPE-EVAEKVIEALNGKKIKGKKVR 69
Query: 69 VE 70
VE
Sbjct: 70 VE 71
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 31.1 bits (70), Expect = 0.76
Identities = 13/72 (18%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 178 RRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSP-RSRSKSGSPRKSKSKAKS 236
+ ++LI +K + +G + +S + + SSK+++ ++++ + SK+K S
Sbjct: 640 KSLKLIIEKLKINEQGGQKKNSKKEYMNPAQTTTSSKAKTHSKTKNDHNKSKTSKNKEPS 699
Query: 237 VSRSPSPSKTRK 248
+ K +
Sbjct: 700 STSFLQDVKKKS 711
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in
Saccharomyces cerevisiae protein Nrd1,
Schizosaccharomyces pombe Rpb7-binding protein seb1 and
similar proteins. This subfamily corresponds to the
RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous
nuclear ribonucleoprotein (hnRNP)-like RNA-binding
protein encoded by gene NRD1 (for nuclear pre-mRNA
down-regulation) from yeast S. cerevisiae. It is
implicated in 3' end formation of small nucleolar and
small nuclear RNAs transcribed by polymerase II, and
plays a critical role in pre-mRNA metabolism. Nrd1
contains an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a short arginine-, serine-, and glutamate-rich
segment similar to the regions rich in RE and RS
dipeptides (RE/RS domains) in many metazoan splicing
factors, and a proline- and glutamine-rich C-terminal
domain (P+Q domain) similar to domains found in several
yeast hnRNPs. Disruption of NRD1 gene is lethal to
yeast cells. Its N-terminal domain is sufficient for
viability, which may facilitate interactions with RNA
polymerase II where Nrd1 may function as an auxiliary
factor. By contrast, the RRM, RE/RS domains, and P+Q
domain are dispensable. Seb1 is an RNA-binding protein
encoded by gene seb1 (for seven binding) from fission
yeast S. pombe. It is essential for cell viability and
bound directly to Rpb7 subunit of RNA polymerase II.
Seb1 is involved in processing of polymerase II
transcripts. It also contains one RRM motif and a
region rich in arginine-serine dipeptides (RS domain).
Length = 79
Score = 28.7 bits (64), Expect = 0.77
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNGF--GFVEFEDYRDADDA 53
++ GG+ + + E DL +G ++ IL N FV+ + RDA++A
Sbjct: 6 LFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMYNRRDAENA 55
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 28.8 bits (64), Expect = 0.78
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
L V+NLS VS + L+ Q G V A D R +G VEF + +KAL++
Sbjct: 2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALER 59
>gnl|CDD|220710 pfam10351, Apt1, Golgi-body localisation protein domain. This is
the C-terminus of a family of proteins conserved from
plants to humans. The plant members are localised to the
Golgi proteins and appear to regulate membrane
trafficking, as they are required for rapid vesicle
accumulation at the tip of the pollen tube. The
C-terminus probably contains the Golgi localisation
signal and it is well-conserved.
Length = 451
Score = 30.7 bits (70), Expect = 0.78
Identities = 23/63 (36%), Positives = 26/63 (41%), Gaps = 5/63 (7%)
Query: 195 SRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSK-----TRKR 249
S SS SR S + S SS S S S S KSK K S+ S S +
Sbjct: 319 SSSSGSRRSSSTSRSSSSSSSLLSSSSILSKSSDKSKDKRFSLKLSKSEKEESDDLEEMI 378
Query: 250 SRS 252
SRS
Sbjct: 379 SRS 381
Score = 28.4 bits (64), Expect = 4.6
Identities = 25/74 (33%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 177 GRRIRLIEDKPRGGGRGRSR--SSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKA 234
GR L E+ R SSSS S S+ S + S S S S S KS K+
Sbjct: 295 GRDSSLSEEDSDSSKREEDSDISSSSSSGSRRSSSTSRSSSSSSSLLSSSSILSKSSDKS 354
Query: 235 KSVSRSPSPSKTRK 248
K S SK+ K
Sbjct: 355 KDKRFSLKLSKSEK 368
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1)
is a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation,
and tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator
of the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 75
Score = 28.6 bits (64), Expect = 0.79
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 12/68 (17%)
Query: 7 YIGGLPYGVRERDLEKFVKGYGRIRD-VILKN-------GFGFVEFEDYRDAD----DAV 54
+IGGL + L ++ +G I++ +++++ GFGFV F D D
Sbjct: 2 FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGP 61
Query: 55 YELNGKSL 62
+EL+GK +
Sbjct: 62 HELDGKKI 69
>gnl|CDD|114474 pfam05750, Rubella_Capsid, Rubella capsid protein. Rubella virus
is an enveloped positive-strand RNA virus of the family
Togaviridae. Virions are composed of three structural
proteins: a capsid and two membrane-spanning
glycoproteins, E2 and E1. During virus assembly, the
capsid interacts with genomic RNA to form nucleocapsids.
It has been discovered that capsid phosphorylation
serves to negatively regulate binding of viral genomic
RNA. This may delay the initiation of nucleocapsid
assembly until sufficient amounts of virus glycoproteins
accumulate at the budding site and/or prevent
non-specific binding to cellular RNA when levels of
genomic RNA are low. It follows that at a late stage in
replication, the capsid may undergo dephosphorylation
before nucleocapsid assembly occurs.
Length = 300
Score = 30.6 bits (68), Expect = 0.79
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 197 SSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRK-----SKSKAKSVSRSPSPSKTRKRSR 251
+ +S+SR R R S + S SG PR+ + + K SR+P P + R+ SR
Sbjct: 29 AGASQSRRPRPPRQRDSSTSGDDSGRDSGGPRRRRGNRGRGQRKDWSRAPPPPEERQESR 88
Query: 252 SRS 254
S++
Sbjct: 89 SQT 91
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM1 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and it is highly conserved between
plants and fungi. Up to date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 77
Score = 28.4 bits (64), Expect = 0.79
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 13 YGVRERDLEKFVKGYGRIR---DVILKNGFGFVEFEDYRDADDAVYELNGKSLLG 64
V + +L + +G IR GF V + D R A A L G L G
Sbjct: 11 SNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTELGG 65
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 28.9 bits (64), Expect = 0.83
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 38 GFGFVEFEDYRDADDAVYELNGKSLLGERV 67
GFGFV +Y +A A+ LNG LG+++
Sbjct: 44 GFGFVTMTNYEEAAMAIASLNGYR-LGDKI 72
>gnl|CDD|219947 pfam08639, SLD3, DNA replication regulator SLD3. The SLD3 DNA
replication regulator is required for loading and
maintenance of Cdc45 on chromatin during DNA
replication.
Length = 437
Score = 30.6 bits (69), Expect = 0.83
Identities = 12/71 (16%), Positives = 24/71 (33%), Gaps = 3/71 (4%)
Query: 189 GGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVS---RSPSPSK 245
S ++ + S+ ++ S S + + + V R S +
Sbjct: 232 KPSMKISPLKKKKTGTLKSSKPEPGTPLKRQTSPASSSQKSRRRSLQRVLTDERKSSSRR 291
Query: 246 TRKRSRSRSDS 256
T RSR++S
Sbjct: 292 TPSLLRSRTNS 302
Score = 28.2 bits (63), Expect = 4.6
Identities = 18/79 (22%), Positives = 28/79 (35%)
Query: 181 RLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRS 240
L KP G + ++S + S KSR RS R S +P +S+ S
Sbjct: 247 TLKSSKPEPGTPLKRQTSPASSSQKSRRRSLQRVLTDERKSSSRRTPSLLRSRTNSSLIE 306
Query: 241 PSPSKTRKRSRSRSDSRAR 259
++ + SR
Sbjct: 307 FLKRESSENLLPSLSSRTS 325
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing (RBP-MS).
This subfamily corresponds to the RRM of RBP-MS, also
termed heart and RRM expressed sequence (hermes), an
RNA-binding proteins found in various vertebrate
species. It contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). RBP-MS physically interacts
with Smad2, Smad3 and Smad4 and plays a role in
regulation of Smad-mediated transcriptional activity.
In addition, RBP-MS may be involved in regulation of
mRNA translation and localization during Xenopus laevis
development. .
Length = 76
Score = 28.5 bits (63), Expect = 0.96
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 6 VYIGGLPYGVRERDLE---KFVKGY-GRIRDVILKNGFGFVEFEDYRDADDAVYELNG 59
+++ GLP ++ R+L + KGY G + + K GFV F+ +A+ A LNG
Sbjct: 4 LFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG 61
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed
RNA-binding motif, single-stranded-interacting protein
4, an RNA-binding protein that is essential for
maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. For instance, DND1
binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and
cell cycle regulator and tumor suppressor, LATS2 (large
tumor suppressor, homolog 2 of Drosophila). It helps
maintain their protein expression through blocking the
inhibitory function of microRNAs (miRNA) from these
transcripts. DND1 may also impose another level of
translational regulation to modulate expression of
critical factors in embryonic stem (ES) cells. DND1
interacts specifically with apolipoprotein B editing
complex 3 (APOBEC3), a multi-functional protein
inhibiting retroviral replication. The DND1-APOBEC3
interaction may play a role in maintaining viability of
germ cells and for preventing germ cell tumor
development. DND1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 78
Score = 28.2 bits (63), Expect = 0.97
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVY 55
G++V+IG +P V E L + G + + L GF + ++ D R A A+
Sbjct: 1 GSEVFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIA 60
Query: 56 ELNG 59
L+
Sbjct: 61 TLHN 64
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 75
Score = 28.2 bits (63), Expect = 1.0
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKNGFG------FVEFEDYRDADDA 53
+++G LP VRE + + K YGR+ V IL FV+F D + A A
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA 56
>gnl|CDD|144738 pfam01254, TP2, Nuclear transition protein 2.
Length = 132
Score = 29.3 bits (65), Expect = 1.0
Identities = 23/64 (35%), Positives = 31/64 (48%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSR 253
R +S + S S S+SR RSRS S SP +S + S+SPSPS K ++
Sbjct: 20 RPQSHTCNQCSCSHHCQSCSQSRGSRSRSSSQSPAGHRSSSGHQSQSPSPSPPPKHHKTT 79
Query: 254 SDSR 257
S
Sbjct: 80 MHSH 83
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response element
(IGFRE). Moreover, PSF functions as a transcriptional
repressor interacting with Sin3A and mediating silencing
through the recruitment of histone deacetylases (HDACs)
to the DNA binding domain (DBD) of nuclear hormone
receptors. PSF is an essential pre-mRNA splicing factor
and is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. PSF
forms a heterodimer with the nuclear protein p54nrb,
also known as non-POU domain-containing octamer-binding
protein (NonO). The PSF/p54nrb complex displays a
variety of functions, such as DNA recombination and RNA
synthesis, processing, and transport. PSF contains two
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which are responsible for interactions with
RNA and for the localization of the protein in speckles.
It also contains an N-terminal region rich in proline,
glycine, and glutamine residues, which may play a role
in interactions recruiting other molecules. .
Length = 80
Score = 28.1 bits (62), Expect = 1.1
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
L V NLS VS + L++ Q G V A D R +G+VEF S +KA ++
Sbjct: 2 LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFER 59
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein
42 (RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 83
Score = 28.3 bits (64), Expect = 1.1
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 38 GFGFVEFEDYRDADDAVYELNGK 60
G+GFV F D D A+ E+NGK
Sbjct: 49 GYGFVSFSDPNDYLKAMKEMNGK 71
>gnl|CDD|218190 pfam04651, Pox_A12, Poxvirus A12 protein.
Length = 188
Score = 29.8 bits (67), Expect = 1.1
Identities = 16/39 (41%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 191 GRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRK 229
G+ + +SSS+S+ S S + +K S SRS+SG+PR+
Sbjct: 58 GKRVTSASSSKSKRCSTS-TSKTKPCSRSSRSRSGAPRR 95
>gnl|CDD|222011 pfam13257, DUF4048, Domain of unknown function (DUF4048). This
presumed domain is functionally uncharacterized. This
domain family is found in eukaryotes, and is typically
between 228 and 257 amino acids in length.
Length = 242
Score = 29.7 bits (67), Expect = 1.1
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVS 238
RSR S SRS S+SR R + S S+S + + + S S S
Sbjct: 126 RSRRSGSRSTSRSRLRLQGGSL-SSSRSSRSSTSKGATSGKDSKS 169
Score = 29.0 bits (65), Expect = 2.0
Identities = 12/47 (25%), Positives = 17/47 (36%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRS 240
SR+ +S SRS S + S S S S +K +
Sbjct: 118 ESRTVPPPRSRRSGSRSTSRSRLRLQGGSLSSSRSSRSSTSKGATSG 164
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 30.2 bits (68), Expect = 1.1
Identities = 44/173 (25%), Positives = 71/173 (41%), Gaps = 21/173 (12%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKNG--FGFVEFEDYRDADDAVYELNGKSLL 63
V++ LP V E DL + + +G + V++ G VEFED A V N +
Sbjct: 5 VHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACV---NFAT-- 59
Query: 64 GERVTVEIAKGIDRSQERGRRGYGSYRAPPPRRGWGHDRDDRYGPPTRSDHRLIVENLSS 123
V + I RG+ + +Y + G+ D GP R+IVEN
Sbjct: 60 --SVPIYI---------RGQPAFFNYSTSQEIKRDGNSDFDSAGP--NKVLRVIVENPMY 106
Query: 124 RVSWQDLKDFMRQVGEVC-YADAHKRHRNEGVVEFESSSDMKKALDKLDNAEL 175
++ L G+V K + + +VEFES + + A L+ A++
Sbjct: 107 PITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNSAQHAKAALNGADI 159
Score = 30.2 bits (68), Expect = 1.3
Identities = 35/157 (22%), Positives = 53/157 (33%), Gaps = 24/157 (15%)
Query: 86 YGSYRAPPPRRGWGHDRDD-----------RYGPPTRSDHR-LIVENLS-SRVSWQDLKD 132
G R PP R YGP L+V L +V+ L +
Sbjct: 236 AGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFN 295
Query: 133 FMRQVGEVCYADAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDK------ 186
G V K + ++E + AL L+ +L G+ +R+ K
Sbjct: 296 LFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQP 355
Query: 187 PRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSK 223
PR G +S K S SR+ + + P S +K
Sbjct: 356 PREGQLDDGLTS-----YKDYSSSRNHRFKKPGSANK 387
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 86
Score = 28.2 bits (63), Expect = 1.2
Identities = 14/34 (41%), Positives = 17/34 (50%)
Query: 148 RHRNEGVVEFESSSDMKKALDKLDNAELNGRRIR 181
R R V+F + D K AL K L+GR IR
Sbjct: 43 RQRPYAFVQFTNDDDAKNALAKGQGTILDGRHIR 76
>gnl|CDD|215191 PLN02333, PLN02333, glucose-6-phosphate 1-dehydrogenase.
Length = 604
Score = 30.3 bits (68), Expect = 1.2
Identities = 19/57 (33%), Positives = 27/57 (47%)
Query: 198 SSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRS 254
SSS S +RS S S S S S P +S S ++ + +P+K RS+ S
Sbjct: 5 SSSHSCPYARSYSYSLSPSSSSSHSSVVDPHRSLSFLSAIPQGLNPAKLCVRSQRNS 61
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to
the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contain three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. On the other hand, both RRM1 and RRM2 of
CELF-4 can activate cardiac troponin T (cTNT) exon 5
inclusion. CELF-5, expressed in brain, is also known as
bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein
6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent
manner and can activate inclusion via multiple copies
of a single element, MSE2. CELF-6 also promotes
skipping of exon 11 of insulin receptor, a known target
of CELF activity that is expressed in kidney. In
additiona to three highly conserved RRMs, CELF-6 also
possesses numerous potential phosphorylation sites, a
potential nuclear localization signal (NLS) at the C
terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 28.1 bits (63), Expect = 1.3
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVY 55
K+++G +P + E+DL + +G+I ++ +LK+ G F+ + A A
Sbjct: 6 IKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQS 65
Query: 56 ELNGKSLL 63
L+ + L
Sbjct: 66 ALHEQKTL 73
>gnl|CDD|218612 pfam05501, DUF755, Domain of unknown function (DUF755). This
family is predominated by ORFs from Circoviridae. The
function of this family remains to be determined.
Length = 122
Score = 28.9 bits (65), Expect = 1.3
Identities = 15/58 (25%), Positives = 23/58 (39%)
Query: 195 SRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRS 252
R + +S + + KSR SRS K + ++ S S S S S + S
Sbjct: 65 QRKRKEQQKSSQTHKKKRKKSRHVSSRSAKKISAKKRRRSSSSSSSSSSSSSSSSESS 122
Score = 27.0 bits (60), Expect = 5.6
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 181 RLIEDKPRGGGRGRSRSSSSRSRSKSRS-RSRSSKSRSPRSRSKSGSPRKSKSKAKSVSR 239
+L + + + + +S + + R KSR SRS+K S + R +S S S S + S S
Sbjct: 60 QLQQPQRKRKEQQKSSQTHKKKRKKSRHVSSRSAKKISAKKRRRSSSSSSSSSSSSSSSS 119
Query: 240 SPS 242
S
Sbjct: 120 ESS 122
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 30.0 bits (67), Expect = 1.3
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV 54
GT + + LP + +R+L + G I I+++ G+ FV+F D+ A+
Sbjct: 107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI 166
Query: 55 YELNGKSLLGERVTVEIAK 73
LNG ++ +R+ V A+
Sbjct: 167 KNLNGITVRNKRLKVSYAR 185
>gnl|CDD|113196 pfam04415, DUF515, Protein of unknown function (DUF515). Family of
hypothetical Archaeal proteins.
Length = 416
Score = 29.9 bits (67), Expect = 1.4
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 195 SRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSP---RKSKSKAKSVSRSPSPSKTRKRSR 251
S S S S+S+S S S SS + S S S S SP S+ + S S S++ S
Sbjct: 275 SSISVSESQSQSTSTSSSSSTSSSESSSTSYSPGDASIQNSQRSQLQSSTSQSESESASS 334
Query: 252 SRSDS 256
S S S
Sbjct: 335 SYSYS 339
>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen. The core
antigen of hepatitis viruses possesses a carboxyl
terminus rich in arginine. On this basis it was
predicted that the core antigen would bind DNA. There is
some experimental evidence to support this.
Length = 182
Score = 29.4 bits (66), Expect = 1.4
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 214 KSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSK 245
+ RSPR R+ S R+S+S + S+SPS
Sbjct: 151 RGRSPRRRTPSPRRRRSQSPRRRRSQSPSSQC 182
Score = 27.8 bits (62), Expect = 4.0
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRK 229
R R S R R+ S R RS R R RS+S S +
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPR--RRRSQSPSSQC 182
Score = 26.7 bits (59), Expect = 9.8
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 192 RGRSRSSSSRSRSKSRSRSRSSKSRSPRSRS 222
R R RS R+ S R RS+S + R +S S
Sbjct: 149 RRRGRSPRRRTPSPRRRRSQSPRRRRSQSPS 179
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to
the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p,
also termed cleavage factor IB (CFIB), is a
sequence-specific trans-acting factor that is essential
for mRNA 3'-end formation in yeast Saccharomyces
cerevisiae. It can be UV cross-linked to RNA and
specifically recognizes the (UA)6 RNA element required
for both, the cleavage and poly(A) addition, steps.
Moreover, Hrp1p can shuttle between the nucleus and the
cytoplasm, and play an additional role in the export of
mRNAs to the cytoplasm. Hrp1p also interacts with
Rna15p and Rna14p, two components of CF1A. In addition,
Hrp1p functions as a factor directly involved in
modulating the activity of the nonsense-mediated mRNA
decay (NMD) pathway. It binds specifically to a
downstream sequence element (DSE)-containing RNA and
interacts with Upf1p, a component of the surveillance
complex, further triggering the NMD pathway. Hrp1p
contains two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an
arginine-glycine-rich region harboring repeats of the
sequence RGGF/Y. .
Length = 76
Score = 27.9 bits (62), Expect = 1.4
Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 11/66 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAV--- 54
++IGGL + + L ++ +G + D ++++ GFGF+ F+ + ++ +
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60
Query: 55 YELNGK 60
+ L+GK
Sbjct: 61 HILDGK 66
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1),
a ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response; it binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
Meanwhile, HuR also has pro-apoptotic function by
promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Like other Hu proteins, HuR contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 81
Score = 28.1 bits (62), Expect = 1.4
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 4 TKVYIGGLPYGVRERDLEKFVKGYGR------IRDVILKN--GFGFVEFEDYRDADDAVY 55
T + + LP + + +L G IRD + + G+GFV + + +DA+ A+
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61
Query: 56 ELNGKSLLGERVTVEIAK 73
LNG L + + V A+
Sbjct: 62 TLNGLRLQSKTIKVSYAR 79
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 27.9 bits (63), Expect = 1.5
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 7 YIGGLPYGVRERDLEK----FVKGYGRIRDVI-LKN----GFGFVEFEDYRDADDAVYEL 57
YI L +++ +L++ +G + D++ K G FV F+D A +A+ L
Sbjct: 3 YINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALRAL 62
Query: 58 NGKSLLGERVTVEIAK 73
G + + ++ AK
Sbjct: 63 QGFPFYDKPMRIQYAK 78
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise role
of PPIase remains unclear. PPIase contains a conserved
N-terminal peptidyl-prolyl cistrans isomerase (PPIase)
motif, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 28.0 bits (63), Expect = 1.5
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 108 PPTRSDHRLIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHR-----NEGVVEFESSSD 162
PP ++ L V L+ + +DL+ + G++ + + + +EFE+ D
Sbjct: 1 PP---ENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKED 57
Query: 163 MKKALDKLDNAELNGRRI 180
++A K+DN ++ RRI
Sbjct: 58 CEEAYFKMDNVLIDDRRI 75
Score = 25.7 bits (57), Expect = 9.4
Identities = 11/51 (21%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 17 ERDLEKFVKGYGRIRDV-ILKN-------GFGFVEFEDYRDADDAVYELNG 59
+ DLE +G+I+ ++++ + F+EFE D ++A ++++
Sbjct: 17 DEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDN 67
>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572). Family of
eukaryotic proteins with undetermined function.
Length = 321
Score = 29.7 bits (67), Expect = 1.6
Identities = 29/115 (25%), Positives = 41/115 (35%), Gaps = 3/115 (2%)
Query: 144 DAHKRHRNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSS-SSRS 202
+R + E E E + K+L RR ED + S S S
Sbjct: 175 ALFRREKKEEEEEEEEDEALIKSL-SFGPETEEDRRRADDEDSEDDEEDNDNTPSPKSGS 233
Query: 203 RSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPS-KTRKRSRSRSDS 256
S ++ S KS + RS + S S K S+ R S RK++ S S
Sbjct: 234 SSPAKPTSILKKSAAKRSEAPSSSKAKKNSRGIPKPRDALSSLVVRKKAAPESTS 288
>gnl|CDD|240716 cd12270, RRM_MTHFSD, RNA recognition motif in vertebrate
methenyltetrahydrofolate synthetase domain-containing
proteins. This subfamily corresponds to
methenyltetrahydrofolate synthetase domain (MTHFSD), a
putative RNA-binding protein found in various
vertebrate species. It contains an N-terminal
5-formyltetrahydrofolate cyclo-ligase domain and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The biological role of MTHFSD remains unclear. .
Length = 74
Score = 27.7 bits (62), Expect = 1.6
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 13/77 (16%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDV----ILKNGFGFVEFEDYRD-----ADDAVYE 56
V +G + +R DL K R R V I G F + D AD A+
Sbjct: 2 VKVGNISRNLRVSDL----KSALRERGVKPLRITWQGARGKAFLHFPDKDAADADSALAS 57
Query: 57 LNGKSLLGERVTVEIAK 73
L S+ G +TVE+AK
Sbjct: 58 LQQLSIGGNTLTVELAK 74
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small
nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa
subunit (U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer
composed of large and small subunits; this family
includes the small subunit of U2AF (U2AF35 or U2AF1)
and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35
directly binds to the 3' splice site of the conserved
AG dinucleotide and performs multiple functions in the
splicing process in a substrate-specific manner. It
promotes U2 snRNP binding to the branch-point sequences
of introns through association with the large subunit
of U2AF (U2AF65 or U2AF2). Although the biological role
of U2AF35B remains unclear, it shows high sequence
homolgy to U2AF35, which contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR) -rich segment interrupted by
glycines. In contrast to U2AF35, U2AF35B has a
plant-specific conserved C-terminal region containing
SERE motif(s), which may have an important function
specific to higher plants. .
Length = 102
Score = 28.4 bits (64), Expect = 1.6
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 25 KGYGRIRDVILK-------NGFGFVEFEDYRDADDAVYELNGKSLLGERVTVE 70
+G I D+++ G +V+FE DA+ A+ LNG+ G + E
Sbjct: 47 SRFGEIEDLVVCDNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPE 99
>gnl|CDD|220402 pfam09787, Golgin_A5, Golgin subfamily A member 5. Members of this
family of proteins are involved in maintaining Golgi
structure. They stimulate the formation of Golgi stacks
and ribbons, and are involved in intra-Golgi retrograde
transport. Two main interactions have been
characterized: one with RAB1A that has been activated by
GTP-binding and another with isoform CASP of CUTL1.
Length = 509
Score = 29.8 bits (67), Expect = 1.6
Identities = 18/68 (26%), Positives = 25/68 (36%), Gaps = 1/68 (1%)
Query: 159 SSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSP 218
SS + + A N R R + P G S SS + + SRS S +
Sbjct: 37 SSPVGSISWSVRETASSNKARSRSEKWNPDQPGSRVSSPSSKKDGT-SRSLSSQVDDLAS 95
Query: 219 RSRSKSGS 226
S+S S
Sbjct: 96 AVSSQSSS 103
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 29.9 bits (67), Expect = 1.7
Identities = 18/82 (21%), Positives = 28/82 (34%), Gaps = 4/82 (4%)
Query: 178 RRIRLIEDKPRGGGRGRSRSSSSRSR-SKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKS 236
R R E++ RGGGR S R + PR R K PR +
Sbjct: 422 REQRAAEEQRRGGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRPRRK---PRVEGEADAA 478
Query: 237 VSRSPSPSKTRKRSRSRSDSRA 258
+ + +P +++ A
Sbjct: 479 AAGAETPVVAAAAAQAPGVVAA 500
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or
CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3,
or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1
and ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
family of RNA-binding proteins that have been
implicated in regulation of pre-mRNA splicing, and
control of mRNA translation and deadenylation. CELF-1
is strongly expressed in all adult and fetal tissues
tested. The human CELF-1 is a nuclear and cytoplasmic
RNA-binding protein that regulates multiple aspects of
nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element
involved in translational control of oskar mRNA in
Drosophila, and share sequence similarity to Bruno, the
Drosophila protein that mediates this process. The
Xenopus homolog embryo deadenylation element-binding
protein (EDEN-BP) mediates sequence-specific
deadenylation of Eg5 mRNA. It binds specifically to the
EDEN motif in the 3'-untranslated regions of maternal
mRNAs and targets these mRNAs for deadenylation and
translational repression. CELF-1 contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. This
subgroup also includes Drosophila melanogaster Bruno
protein, which plays a central role in regulation of
Oskar (Osk) expression in flies. It mediates repression
by binding to regulatory Bruno response elements (BREs)
in the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 84
Score = 27.8 bits (62), Expect = 1.7
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 11/71 (15%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDV-ILKN---------GFGFVEFEDYRDADDAV 54
K+++G +P E+DL + + YG + + +L++ G FV F + A +A
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62
Query: 55 YEL-NGKSLLG 64
L N K+L G
Sbjct: 63 NALHNMKTLPG 73
>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains. .
Length = 85
Score = 27.8 bits (61), Expect = 1.7
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 10/59 (16%)
Query: 5 KVYIGGLPYG-VRERDLEKFVKGYGRIRDVIL---------KNGFGFVEFEDYRDADDA 53
++++G +P +E+ +E+F K + DVIL GF F+E+ED++ A A
Sbjct: 4 RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQA 62
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 27.6 bits (62), Expect = 1.8
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 41 FVEFEDYRDADDAVYELNGKSLLGERVTVE 70
FVEF D +A AV LNG+ G +VT
Sbjct: 53 FVEFSDADEAIKAVRALNGRFFGGRKVTAR 82
>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 = 27.5 bits (61), Expect = 1.9
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 35 LKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIA 72
L GFGFV F+ A A+ ++G L G + V+ +
Sbjct: 45 LSMGFGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFS 82
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM2 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 27.7 bits (61), Expect = 1.9
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYA----DAHKRHRNEGVVEFESSSDMKKALDK 169
L V+NL VS + L++ G+V A D R +G+VEF +KALD+
Sbjct: 2 LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDR 59
>gnl|CDD|221745 pfam12737, Mating_C, C-terminal domain of homeodomain 1. Mating in
fungi is controlled by the loci that determine the
mating type of an individual, and only individuals with
differing mating types can mate. Basidiomycete fungi
have evolved a unique mating system, termed tetrapolar
or bifactorial incompatibility, in which mating type is
determined by two unlinked loci; compatibility at both
loci is required for mating to occur. The multi-allelic
tetrapolar mating system is considered to be a novel
innovation that could have only evolved once, and is
thus unique to the mushroom fungi. This domain is
C-terminal to the homeodomain transcription factor
region.
Length = 418
Score = 29.4 bits (66), Expect = 2.0
Identities = 30/105 (28%), Positives = 38/105 (36%), Gaps = 13/105 (12%)
Query: 168 DKLDNA---ELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKS 224
KLD A + +L ++K R R S R+ S RS S R S S
Sbjct: 30 AKLDVAVKDMTPDLKEQLKDEKRRRRQTPRQSRRSKRAAHAYPSPERSPALSSERLLSPS 89
Query: 225 GS-----PRKSKSKAKSVSRSPSPS-----KTRKRSRSRSDSRAR 259
S P + + RS SPS R R RSDS +
Sbjct: 90 PSVLDLSPVLASPQTGKRRRSSSPSDDEDEAERPSKRPRSDSISS 134
Score = 27.8 bits (62), Expect = 6.0
Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 194 RSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRS-PSPSKTRKRSRS 252
S + R RS S S R P R +S S S S AK PSP+ + + S
Sbjct: 100 ASPQTGKRRRSSSPSDDEDEAER-PSKRPRSDSISSSSSPAKPPEACLPSPAASTQDELS 158
Query: 253 RSDS 256
+ +
Sbjct: 159 EASA 162
Score = 27.8 bits (62), Expect = 6.5
Identities = 25/90 (27%), Positives = 32/90 (35%), Gaps = 24/90 (26%)
Query: 192 RGRSRSSSSRS-------RSKSRSRSRSSKS-RSPRSRSKSGSPRKSKS-----KAKSVS 238
G+ R SSS S R R RS S S SP ++ P + S S +
Sbjct: 104 TGKRRRSSSPSDDEDEAERPSKRPRSDSISSSSSPAKPPEACLPSPAASTQDELSEASAA 163
Query: 239 RSPSPS-----------KTRKRSRSRSDSR 257
P+PS + KR R SD
Sbjct: 164 PLPTPSLSPPHTPTDTAPSGKRKRRLSDGF 193
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to
the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15)
family of RNA-binding proteins. This ubiquitously
expressed family of similarly structured proteins
predominantly localizing to the nuclear, includes FUS
(also known as TLS or Pigpen or hnRNP P2), EWS (also
known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N
or RPB56), and Drosophila Cabeza (also known as SARFH).
The corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a
degenerate hexapeptide repeat motif at the N-terminus.
The C-terminal region consists of a conserved nuclear
import and retention signal (C-NLS), a putative
zinc-finger domain, and a conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 27.3 bits (61), Expect = 2.1
Identities = 20/80 (25%), Positives = 28/80 (35%), Gaps = 15/80 (18%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIR---------------DVILKNGFGFVEFEDYRDA 50
+YI GLP V E L + G G I+ G V ++D A
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60
Query: 51 DDAVYELNGKSLLGERVTVE 70
A+ NG G ++ V
Sbjct: 61 QAAIEWFNGYEFRGNKIKVS 80
Score = 25.7 bits (57), Expect = 8.4
Identities = 13/75 (17%), Positives = 26/75 (34%), Gaps = 12/75 (16%)
Query: 118 VENLSSRVSWQDLKDFMRQVGEV------------CYADAHKRHRNEGVVEFESSSDMKK 165
+ L V+ L + +G + Y D + E V ++ S +
Sbjct: 3 ISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAAQA 62
Query: 166 ALDKLDNAELNGRRI 180
A++ + E G +I
Sbjct: 63 AIEWFNGYEFRGNKI 77
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 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), 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. The
research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 98
Score = 27.8 bits (62), Expect = 2.2
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 155 VEFESSSDMKKALDKLDNAELNGRRIR 181
VEF S+ +KA+ L+ GR+++
Sbjct: 57 VEFSLPSEAEKAIQALNGRWFGGRKVK 83
Score = 26.6 bits (59), Expect = 5.7
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 32 DVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEI 71
++I+K FVEF +A+ A+ LNG+ G +V E+
Sbjct: 50 EIIVKI---FVEFSLPSEAEKAIQALNGRWFGGRKVKAEL 86
>gnl|CDD|203875 pfam08206, OB_RNB, Ribonuclease B OB domain. This family
includes the N-terminal OB domain found in ribonuclease
B proteins in one or two copies.
Length = 58
Score = 26.7 bits (60), Expect = 2.3
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 8/52 (15%)
Query: 36 KNGFGFVEFEDYRDADDAVY----ELNGKSLLGERVTVEIAKGIDRSQERGR 83
K GFGF+ +D + DD ++ ++ K++ G+RV V I KG R + GR
Sbjct: 7 KKGFGFLIPDD--EEDD-IFIPPEQMK-KAMHGDRVLVRITKGDRRGRREGR 54
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 of MRD1. RBM19, also termed RNA-binding
domain-1 (RBD-1), is a nucleolar protein conserved in
eukaryotes involved in ribosome biogenesis by processing
rRNA and is essential for preimplantation development.
It has a unique domain organization containing 6
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). MRD1 is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well conserved in
yeast and its homologues exist in all eukaryotes. MRD1
is present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 27.2 bits (61), Expect = 2.3
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 11/60 (18%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKR-----HRNEGVVEFESSSDMKKALDKL 170
++V+NL + ++L++ + G + R R +VEF SD +KA L
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSL------GRLLLPPSRTIALVEFLEPSDARKAFKSL 56
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 28.7 bits (64), Expect = 2.8
Identities = 12/85 (14%), Positives = 32/85 (37%), Gaps = 2/85 (2%)
Query: 180 IRLIEDKPRGGGRGRSRSSSSRS-RSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVS 238
+ K + S ++KS ++ S K + + S + + + AK
Sbjct: 194 VGAANAKKAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAK 253
Query: 239 RSPSPS-KTRKRSRSRSDSRARKVS 262
++ + K ++ ++ +A K +
Sbjct: 254 KTAKKALKKAAKAVKKAAKKAAKAA 278
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 98
Score = 27.6 bits (61), Expect = 2.8
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 154 VVEFESSSDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRS 195
VVE+E++ ++ +D + G RI+L P G GRS
Sbjct: 48 VVEYETAEQAEEVQLAMDGTTIKGSRIQLSFCAP--GAPGRS 87
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 28.9 bits (64), Expect = 2.9
Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 1/80 (1%)
Query: 182 LIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSP 241
L ED + ++ + + K + + S +SK+ + SKS +K +
Sbjct: 111 LEEDDSKDDMEFKANPNEAGKPGKPKGNQGEGLASSSDGKSKASAKSGSKSASKHGESNS 170
Query: 242 SPSKTRKRSRSRSDSRARKV 261
S S S S A V
Sbjct: 171 SDESATD-SGKASASVAGIV 189
Score = 28.1 bits (62), Expect = 6.0
Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 13/75 (17%)
Query: 195 SRSSSSRSRSKSRSRSRSSKSRSPR-------------SRSKSGSPRKSKSKAKSVSRSP 241
S + + + +SR RS+ + + + +++G P K K S
Sbjct: 87 SENGDASKKGHGKSRVRSASAAAILEEDDSKDDMEFKANPNEAGKPGKPKGNQGEGLASS 146
Query: 242 SPSKTRKRSRSRSDS 256
S K++ ++S S S
Sbjct: 147 SDGKSKASAKSGSKS 161
>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 = 27.0 bits (60), Expect = 3.0
Identities = 24/76 (31%), Positives = 34/76 (44%), Gaps = 9/76 (11%)
Query: 5 KVYIGGLPYGVRERDL-EKFVKGYGRIRDVILK-------NGFGFVEFEDYRDADDAVYE 56
KV + LP V E + E FV G I+ V+L G + F+ DA A +
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60
Query: 57 LNGKSLLGER-VTVEI 71
NG+ G R + VE+
Sbjct: 61 FNGRIDDGNRKMKVEV 76
Score = 26.2 bits (58), Expect = 5.3
Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 115 RLIVENLSSRVSWQDLKD-FMRQVGEV--CYADAHKRHRNEGV--VEFESSSDMKKALDK 169
++IV NL V+ +++ F+ Q+G + ++ ++ G+ + F+ + D KA DK
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60
Query: 170 LDNAELNGRR 179
+ +G R
Sbjct: 61 FNGRIDDGNR 70
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 29.1 bits (65), Expect = 3.0
Identities = 24/103 (23%), Positives = 37/103 (35%), Gaps = 11/103 (10%)
Query: 161 SDMKKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSR---- 216
S+ K++ K + R S+ + S S + S SS +
Sbjct: 57 SESKESFGKYALGHQIFSSFSSSPKLFQ-----RRNSAGPITHSPSATSSTSSLNSNDGD 111
Query: 217 --SPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSR 257
SP S S S +P ++S+ S SP + RK S S
Sbjct: 112 QFSPASDSLSFNPSSTQSRKDSGPGDGSPVQKRKNPLLPSSST 154
>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein.
Length = 582
Score = 28.7 bits (64), Expect = 3.5
Identities = 16/85 (18%), Positives = 29/85 (34%), Gaps = 6/85 (7%)
Query: 177 GRRIRLI--EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKA 234
G+ IR + D+ R RGR R R + ++ R +S ++
Sbjct: 432 GQSIRFLPQSDQQRPVSRGRGRGQRGPRSQPQNQRRQQNRGR----QSSQPPRQQQNRSN 487
Query: 235 KSVSRSPSPSKTRKRSRSRSDSRAR 259
++ R R + + R R
Sbjct: 488 QNNQRQSQGPNQGPRGQGGYNLRPR 512
>gnl|CDD|241174 cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM1 of GRSF-1, 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. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 79
Score = 26.7 bits (59), Expect = 3.7
Identities = 8/22 (36%), Positives = 16/22 (72%)
Query: 148 RHRNEGVVEFESSSDMKKALDK 169
+ R + ++E ES D++KAL++
Sbjct: 43 KPRGDALIELESEEDVQKALEQ 64
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. The additional
cytoplasmic localization of SAFB2 implies that it could
play additional roles in the cytoplasmic compartment
which are distinct from the nuclear functions shared
with SAFB1.
Length = 76
Score = 26.6 bits (58), Expect = 3.9
Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 116 LIVENLSSRVSWQDLKDFMRQVGEVCYADAHKRHRNEGV-----VEFESSSDMKKALDKL 170
L V LSS DLK+ + G+V A R+ G V +S + K ++ L
Sbjct: 4 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63
Query: 171 DNAELNGRRI 180
EL+GR I
Sbjct: 64 HRTELHGRMI 73
>gnl|CDD|197205 cd09106, PLDc_vPLD3_4_5_like_1, Putative catalytic domain, repeat
1, of vertebrate phospholipases, PLD3, PLD4 and PLD5,
viral envelope proteins K4 and p37, and similar
proteins. Putative catalytic domain, repeat 1, of
vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC
3.1.4.4), viral envelope proteins (vaccinia virus
proteins K4 and p37), and similar proteins. Most family
members contain two copies of the HKD motifs
(H-x-K-x(4)-D, where x represents any amino acid
residue), and have been classified into the
phospholipase D (PLD) superfamily. Proteins in this
subfamily are associated with Golgi membranes, altering
their lipid content by the conversion of phospholipids
into phosphatidic acid, which is thought to be involved
in the regulation of lipid movement. ADP ribosylation
factor (ARF), a small guanosine triphosphate binding
protein, might be required activity. The vaccinia virus
p37 protein, encoded by the F13L gene, is also
associated with Golgi membranes and is required for the
envelopment and spread of the extracellular enveloped
virus (EEV). The vaccinia virus protein K4, encoded by
the HindIII K4L gene, remains to be characterized.
Sequence analysis indicates that the vaccinia virus
proteins K4 and p37 might have evolved from one or more
captured eukaryotic genes involved in cellular lipid
metabolism. Up to date, no catalytic activity of PLD3
has been shown. Furthermore, due to the lack of
functional important histidine and lysine residues in
the HKD motif, mammalian PLD5 has been characterized as
an inactive PLD. The poxvirus p37 proteins may also lack
PLD enzymatic activity, since they contain only one
partially conserved HKD motif (N-x-K-x(4)-D).
Length = 153
Score = 27.6 bits (62), Expect = 3.9
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 150 RNEGVVEFESSSDMKKALDKLDNAELNGRRIRLIEDKP 187
R S+ + + + L A G +IR+++DKP
Sbjct: 45 RGTDTNPDSSAQEGEDIFNALLEAAKRGVKIRILQDKP 82
>gnl|CDD|117908 pfam09366, DUF1997, Protein of unknown function (DUF1997). This
family of proteins are functionally uncharacterized.
Length = 170
Score = 27.9 bits (63), Expect = 4.1
Identities = 7/25 (28%), Positives = 14/25 (56%)
Query: 115 RLIVENLSSRVSWQDLKDFMRQVGE 139
+ I+ + R++ Q L+DF + E
Sbjct: 146 QGILRQIKRRLTRQLLEDFHAWIAE 170
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, and in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; it binds RNA through its RRM domains. .
Length = 79
Score = 26.5 bits (58), Expect = 4.5
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 13/75 (17%)
Query: 3 GTKVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAV 54
GT+V++G +P + E +L + G I D+ L G+ F+ F A +AV
Sbjct: 1 GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60
Query: 55 -----YELNGKSLLG 64
YE+ LG
Sbjct: 61 KLCDNYEIRPGKHLG 75
>gnl|CDD|225791 COG3252, COG3252, Methenyltetrahydromethanopterin cyclohydrolase
[Coenzyme metabolism].
Length = 314
Score = 28.2 bits (63), Expect = 4.5
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 23 FVKGYGRIRDVILKNGFGF--VEFEDYRDADDAVYELNGKSLLGERVTVEIAKGIDRSQE 80
F G G R + LK + + +ED DAD AV L L E+V +AK E
Sbjct: 104 FAMGSGPARALALKPKETYEEIGYED--DADVAVLTLESDKLPDEKVAEYVAKECGVEPE 161
>gnl|CDD|115579 pfam06933, SSP160, Special lobe-specific silk protein SSP160. This
family consists of several special lobe-specific silk
protein SSP160 sequences which appear to be specific to
Chironomus (Midge) species.
Length = 758
Score = 28.2 bits (62), Expect = 4.7
Identities = 14/65 (21%), Positives = 28/65 (43%), Gaps = 1/65 (1%)
Query: 186 KPRGGGRGRSRSSSSRSRSKSR-SRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPS 244
K G ++S + + K+R + R+ R+ +R K ++ +S+AK +
Sbjct: 369 KAAKTASGCAKSGEKKVKRKARLEKMRAKCRRAVGNRMKGSMKKRVRSRAKKFGEAAKSG 428
Query: 245 KTRKR 249
R R
Sbjct: 429 VRRYR 433
>gnl|CDD|215182 PLN02321, PLN02321, 2-isopropylmalate synthase.
Length = 632
Score = 28.4 bits (63), Expect = 4.7
Identities = 13/46 (28%), Positives = 21/46 (45%)
Query: 198 SSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSP 243
SS+ S +R + +RSP S++ S + V+R P P
Sbjct: 29 SSASSARFPAFLARPAAARSPSLASRASSALAASPSRPQVARRPRP 74
>gnl|CDD|222259 pfam13608, Potyvirid-P3, Protein P3 of Potyviral polyprotein. This
is the P3 protein section of the Potyviridae
polyproteins. The function is not known except that the
protein is essential to viral survival.
Length = 445
Score = 28.3 bits (64), Expect = 5.0
Identities = 13/58 (22%), Positives = 23/58 (39%)
Query: 205 KSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRARKVS 262
K + RS K R + + S+S + K ++R ++ S +KVS
Sbjct: 163 KLSAIWRSRKFRKRSEKCLKPKAAEDLKGKYSISVTACFGKAKQRLKAAVSSVVQKVS 220
>gnl|CDD|200219 TIGR02927, SucB_Actino, 2-oxoglutarate dehydrogenase, E2 component,
dihydrolipoamide succinyltransferase. This model
represents an Actinobacterial clade of E2 enzyme, a
component of the 2-oxoglutarate dehydrogenase complex
involved in the TCA cycle. These proteins have multiple
domains including the catalytic domain (pfam00198), one
or two biotin domains (pfam00364) and an E3-component
binding domain (pfam02817).
Length = 579
Score = 28.4 bits (63), Expect = 5.0
Identities = 5/51 (9%), Positives = 23/51 (45%)
Query: 212 SSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRARKVS 262
+ + R+ + + + + + + ++ P + R ++ +R R+++
Sbjct: 304 AKAAEEARAAAAAPAAAAAPAAPAAAAKPAEPDTAKLRGTTQKMNRIRQIT 354
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 77
Score = 26.5 bits (58), Expect = 5.0
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 8 IGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYELNG 59
I LP ++ E+ V+ +G + L G+GFVE+ A A +L G
Sbjct: 4 IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63
Query: 60 KSL 62
K L
Sbjct: 64 KQL 66
>gnl|CDD|240947 cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, G-rich sequence factor 1 (GRSF-1) and
similar proteins. This subfamily corresponds to the
RRM1 of hnRNP H proteins and GRSF-1. 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. These proteins have similar RNA
binding affinities and specifically recognize the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. hnRNP H and
hnRNP H2 are almost identical; both have been found to
bind nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements downstream
of the 5' splice site in the transcripts of c-src, human
immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and
myelin. It silences exons when bound to exonic elements
in the transcripts of beta-tropomyosin, HIV-1, and
alpha-tropomyosin. hnRNP H2 has been implicated in
pre-mRNA 3' end formation. hnRNP H3 may be involved in
splicing arrest induced by heat shock. Most family
members contain three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and play an
important role in efficiently silencing the exon.
Members in this family can regulate the alternative
splicing of fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced silencing
activity within hnRNP H3. Members in this family have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. They also
include a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. They may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 contains three
potential RRMs responsible for the RNA binding, and two
auxiliary domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 77
Score = 26.2 bits (58), Expect = 5.0
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 148 RHRNEGVVEFESSSDMKKALDK 169
R E +E ES D++KAL+K
Sbjct: 41 RPSGEAFIELESEEDVEKALEK 62
>gnl|CDD|235370 PRK05244, PRK05244, Der GTPase activator; Provisional.
Length = 177
Score = 27.6 bits (62), Expect = 5.2
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 231 KSKAKSVSRSPSPSKTRKRSRSRSDSRARK 260
K K S RS +K++K++R D+ AR+
Sbjct: 1 KKKKSSPKRSKGMAKSKKKTREELDAEARE 30
>gnl|CDD|240956 cd12512, RRM3_RBM12, RNA recognition motif 3 in RNA-binding
protein 12 (RBM12) and similar proteins. This
subfamily corresponds to the RRM3 of RBM12. 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. The biological role of
RBM12 remains unclear. .
Length = 101
Score = 26.8 bits (59), Expect = 5.6
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 11/56 (19%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEF---EDYRDA 50
VY+ GLPY + + F K + D I G GFVEF DY+ A
Sbjct: 12 VYLKGLPYEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 67
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 26.2 bits (57), Expect = 5.8
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 29 RIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVEIAK 73
++RD + FV F + DA A+ +NGK + G + V +AK
Sbjct: 35 KLRD------YAFVHFFNREDAVAAMSVMNGKCIDGASIEVTLAK 73
>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 = 26.9 bits (59), Expect = 5.9
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRI 30
KV++GGLP+ + E D+ + +G +
Sbjct: 2 KVFVGGLPWDITEADILNSFRRFGSL 27
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 26.5 bits (58), Expect = 6.0
Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILKN-------GFGFVEFEDYRDADDAVYELN 58
++IG L + V E +L + YG I +V++K + F++F++ A A ++
Sbjct: 11 LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAMS 70
Query: 59 GKSLLGERVTVEIAK 73
G+ + + + K
Sbjct: 71 GRVIGRNPIKIGYGK 85
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 27.7 bits (62), Expect = 6.4
Identities = 12/38 (31%), Positives = 13/38 (34%)
Query: 188 RGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSG 225
GGR S + SRS S RS S G
Sbjct: 3 ASGGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGG 40
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 28.0 bits (63), Expect = 6.7
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 13 YGVRERDLEKFVK------GYGRIRDVILKNGFGFVEFEDYRDADDAVYE 56
Y + E+ L FVK GY R+R+++ K GF ++ ++ D Y
Sbjct: 231 YLLEEKGLNTFVKLNPTLLGYERVREILDKMGFDYIGLKEEHFDHDLQYT 280
>gnl|CDD|201147 pfam00313, CSD, 'Cold-shock' DNA-binding domain.
Length = 66
Score = 25.6 bits (57), Expect = 7.0
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 7/45 (15%)
Query: 36 KNGFGFVEFEDYRDADDAVY--ELNG---KSL-LGERVTVEIAKG 74
K GFGF+ ED D D V+ + G +SL G+RV +I +G
Sbjct: 11 KKGFGFITPED-GDKDVFVHFSAIQGDGFRSLQEGQRVEFDIVEG 54
>gnl|CDD|177439 PHA02620, PHA02620, VP3; Provisional.
Length = 353
Score = 27.7 bits (61), Expect = 7.1
Identities = 16/39 (41%), Positives = 19/39 (48%)
Query: 184 EDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRS 222
ED P R SR SS +++ S S K RS SRS
Sbjct: 315 EDGPNKKKRRMSRGSSQKAKGPRASSKTSYKRRSRSSRS 353
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 27.7 bits (61), Expect = 7.4
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 6/61 (9%)
Query: 187 PRGGGRGRSRSSSSRSRSKSRSRSRSSK------SRSPRSRSKSGSPRKSKSKAKSVSRS 240
G R + + ++ SR+ + S S + + PR KS SP +++ K + + S
Sbjct: 134 AAGTERVKEDTPATPSRALNHYISTSGRQRVKSYTPKPRGEVKSSSPTQTREKVRKYTPS 193
Query: 241 P 241
P
Sbjct: 194 P 194
>gnl|CDD|205936 pfam13763, DUF4167, Domain of unknown function (DUF4167).
Length = 80
Score = 25.7 bits (57), Expect = 7.6
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 192 RGRSRSSSSRSRSKSRSRSRSSKSRSPRSR 221
RGR+ ++ + +RS R+R S P +
Sbjct: 1 RGRNNNNRNNNRSGGNPRNRVFDSNGPDVK 30
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.0 bits (62), Expect = 7.8
Identities = 11/48 (22%), Positives = 19/48 (39%)
Query: 215 SRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKRSRSRSDSRARKVS 262
S SP + P + + P+P + + R+R RA + S
Sbjct: 2630 SPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQAS 2677
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 27.7 bits (62), Expect = 7.8
Identities = 16/62 (25%), Positives = 22/62 (35%), Gaps = 3/62 (4%)
Query: 192 RGRSRSSSSRSRSKSRSRSRSSK---SRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRK 248
SSSS S S+S S +S R P + S +P S PS +
Sbjct: 10 SQSHASSSSSSSSQSSPPSSTSPRPRRRKPSASSLLHTPSILPLPKLSSPSPPSVTLPPA 69
Query: 249 RS 250
+
Sbjct: 70 AT 71
>gnl|CDD|220728 pfam10390, ELL, RNA polymerase II elongation factor ELL. ELL is a
family of RNA polymerase II elongation factors. It is
bound stably to elongation-associated factors 1 and 2,
EAFs, and together these act as a strong regulator of
transcription activity. by direct interaction with Pol
II. ELL binds to pol II on its own but the affinity is
greatly increased by the cooperation of EAF. Some
members carry an Occludin domain pfam07303 just
downstream. There is no S. cerevisiae member.
Length = 285
Score = 27.4 bits (61), Expect = 7.8
Identities = 18/89 (20%), Positives = 29/89 (32%), Gaps = 7/89 (7%)
Query: 164 KKALDKLDNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSK 223
+ +++ AE R + KP GG + + S S S S K
Sbjct: 122 QATRERMAQAEEEERSRGTKQIKP--GGPEGGKKVQIKKPL-----SEISVSSPLASNRK 174
Query: 224 SGSPRKSKSKAKSVSRSPSPSKTRKRSRS 252
P S ++ + S + K R R
Sbjct: 175 QSLPGNGSSSSRKANGSSAVMKRPLRERV 203
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a highly acidic carboxyl-terminal half. The family
also includes CUS2, a yeast homolog of human Tat-SF1.
CUS2 interacts with U2 RNA in splicing extracts and
functions as a splicing factor that aids assembly of
the splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the
conserved splicing factor SF3a. Like Tat-SF1, CUS2
contains two RRMs as well. .
Length = 91
Score = 26.0 bits (58), Expect = 8.0
Identities = 14/57 (24%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 18 RDLEKFVKGYGRIRDVIL----KNGFGFVEFEDYRDADDAVYELNGKSLLGERVTVE 70
DL + + +G+++ V++ +G V+F++ +AD + LNG+ G ++ E
Sbjct: 27 DDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEAE 83
>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 = 14/67 (20%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 5 KVYIGGLPYGVRERDLEKFVKGYGRIRDVIL--------KNGFGFVEFEDYRDADDAVYE 56
K+++G +P + E+++ + +G + +V + + G FV++ +AD A+
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60
Query: 57 LNGKSLL 63
L+ + L
Sbjct: 61 LHNQRTL 67
>gnl|CDD|241191 cd12747, RRM2_RBM12, RNA recognition motif 2 in RNA-binding
protein 12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM2 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which 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. The biological role of RBM12
remains unclear. .
Length = 75
Score = 25.5 bits (56), Expect = 8.1
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 6 VYIGGLPYGVRERDLEKFVKGYGRIRDVILK------NGFGFVEFEDYRDADDAVYELNG 59
V + GLP+ V E D+ F G +LK NG V+F D +A+
Sbjct: 4 VSLHGLPFSVLEHDIRDFFHGLRIDAIHLLKDHVGRNNGNALVKFYSPHDTFEALKR--N 61
Query: 60 KSLLGER 66
+ L+G+R
Sbjct: 62 RMLMGQR 68
>gnl|CDD|165391 PHA03118, PHA03118, multifunctional expression regulator;
Provisional.
Length = 474
Score = 27.3 bits (60), Expect = 8.3
Identities = 19/85 (22%), Positives = 26/85 (30%), Gaps = 5/85 (5%)
Query: 171 DNAELNGRRIRLIEDKPRGGGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKS 230
D GR G R +S + +SR K R S +K P SG P S
Sbjct: 111 DINHHGGRDTEPGHAHIENGERKSPKSYNQQSRKKHRDESLRNKHGRP-----SGPPAMS 165
Query: 231 KSKAKSVSRSPSPSKTRKRSRSRSD 255
+ + +R D
Sbjct: 166 PGEHFDQTHDAEYRLRFNERDARRD 190
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 27.6 bits (62), Expect = 8.5
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 16 RERDLEKFVKGYGRIRDVILKNGFGFVEFEDYRDADDAVYELNGKSLL-GERVTVEIAKG 74
E G + ++GFGF+ ED + D + + G+RV V I
Sbjct: 59 LYALPESLKLVKGTVI--AHRDGFGFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGK 116
Query: 75 IDR 77
D
Sbjct: 117 PDG 119
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal
region, followed by a G-patch motif and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors a RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain)
and an Arg-Xaa-Phe sequence motif. SPF45 regulates
alternative splicing of the apoptosis regulatory gene
FAS (also known as CD95). It induces exon 6 skipping in
FAS pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 26.1 bits (58), Expect = 8.6
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 41 FVEFEDYRDADDAVYELNGK 60
FVEFE A AV +LNG+
Sbjct: 55 FVEFERVESAIKAVVDLNGR 74
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 25.6 bits (57), Expect = 8.7
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 7/62 (11%)
Query: 17 ERDLEKFVKGYGRIRDVIL-------KNGFGFVEFEDYRDADDAVYELNGKSLLGERVTV 69
+ D+ + YG I + F +V+F A AV LNGK G ++ V
Sbjct: 14 QSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLNGKLGEGYKLVV 73
Query: 70 EI 71
+I
Sbjct: 74 KI 75
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 27.5 bits (61), Expect = 8.9
Identities = 19/63 (30%), Positives = 25/63 (39%)
Query: 190 GGRGRSRSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPRKSKSKAKSVSRSPSPSKTRKR 249
S SSS S SRS S +RSPR+ S S S S + + S + +
Sbjct: 10 AAASTSLSSSRPQLSSFSSRSPQSATRSPRASSIKCSASASASSSATSSSASLVANGAVA 69
Query: 250 SRS 252
S
Sbjct: 70 LLS 72
>gnl|CDD|227651 COG5347, COG5347, GTPase-activating protein that regulates ARFs
(ADP-ribosylation factors), involved in ARF-mediated
vesicular transport [Intracellular trafficking and
secretion].
Length = 319
Score = 27.4 bits (61), Expect = 9.0
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 197 SSSSRSRSKSRSRSRSSKSRS-PRSRSKSGSPRKSKSKAKSVSRSPSPSKTRK 248
S R S S+SRSS + +R +S S RS + +K+ K
Sbjct: 143 VDSVDDRLDSESQSRSSSASLGNSNRPDDELNVESFQSTGSKPRSLTSTKSNK 195
>gnl|CDD|215175 PLN02309, PLN02309, 5'-adenylylsulfate reductase.
Length = 457
Score = 27.4 bits (61), Expect = 9.0
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 195 SRSSSSRSRSKSRSRSRSSKSRSPRSRSKSG-SPRKSKSKAKSVSRSPSPSKTRKRSRSR 253
+ SSS SRS + S S++ + S R + G S R K S + + ++
Sbjct: 6 AISSSGSSRSGASSESKAKQIGSLRLLDRGGLSARAYSLSGKRSSAAKPLNAQPAARQAM 65
Query: 254 SDSRA 258
S A
Sbjct: 66 IPSAA 70
>gnl|CDD|218187 pfam04637, Herpes_pp85, Herpesvirus phosphoprotein 85 (HHV6-7
U14/HCMV UL25). This family includes UL25 proteins from
HCMV, as well as U14 proteins from HHV 6 and HHV7. These
85 kD phosphoproteins appear to act as structural
antigens, but their precise function is otherwise
unknown.
Length = 502
Score = 27.4 bits (61), Expect = 9.4
Identities = 11/33 (33%), Positives = 12/33 (36%)
Query: 196 RSSSSRSRSKSRSRSRSSKSRSPRSRSKSGSPR 228
SS S SRS+ R S G PR
Sbjct: 467 SPSSDSRAGHSTPSSRSASIPGSRPYSIYGRPR 499
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
0.314 0.132 0.374
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: 13,293,240
Number of extensions: 1286309
Number of successful extensions: 3901
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2997
Number of HSP's successfully gapped: 869
Length of query: 262
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 167
Effective length of database: 6,723,972
Effective search space: 1122903324
Effective search space used: 1122903324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.0 bits)