RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10467
(304 letters)
>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 = 116 bits (292), Expect = 4e-33
Identities = 43/69 (62%), Positives = 55/69 (79%)
Query: 143 CCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALL 202
+RL+GLP+ C KE++ +F GLEIVPNGIT+P DY GR TG AY+QF +E+AE+AL
Sbjct: 1 GVVRLRGLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERALG 60
Query: 203 RHKEKIGHR 211
+HKEKIGHR
Sbjct: 61 KHKEKIGHR 69
Score = 74.0 bits (182), Expect = 4e-17
Identities = 29/57 (50%), Positives = 39/57 (68%), Gaps = 2/57 (3%)
Query: 21 SQFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
+QFF IVP I L D GRS+GEA V+F+S + A+RAL +HK +G RYIE++
Sbjct: 18 AQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERALGKHKEKIGHRYIEIF 74
>gnl|CDD|241176 cd12732, RRM2_hnRNPH3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H') and hnRNP F. This family
is involved in mRNA processing and exhibit extensive
sequence homology. Currently, little is known about the
functions of hnRNP H3 except for its role in the
splicing arrest induced by heat shock. In addition, the
typical hnRNP H proteins contain 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 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, like other hnRNP H protein family members,
hnRNP H3 has an extensive glycine-rich region near the
C-terminus, which may allow it to homo- or
heterodimerize. .
Length = 96
Score = 113 bits (283), Expect = 1e-31
Identities = 48/95 (50%), Positives = 61/95 (64%), Gaps = 1/95 (1%)
Query: 124 MDWALKRQGAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRC 183
MDW LK G +RL+GLP+ C KE++ +F GLEIVPNGIT+ DY GR
Sbjct: 1 MDWVLKHNGPT-DYDGSSGGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQGRS 59
Query: 184 TGVAYIQFVDKENAEKALLRHKEKIGHRLVTLVMS 218
TG A++QF KE AE AL +HKE+IGHR + + S
Sbjct: 60 TGEAFVQFASKEIAENALGKHKERIGHRYIEIFKS 94
Score = 56.1 bits (135), Expect = 3e-10
Identities = 28/56 (50%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 22 QFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
QFF IVP I L D GRS+GEA V+F+S + A+ AL +HK +G RYIE++
Sbjct: 37 QFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHRYIEIF 92
>gnl|CDD|241175 cd12731, RRM2_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM2 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 83
Score = 96.2 bits (239), Expect = 3e-25
Identities = 42/74 (56%), Positives = 57/74 (77%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+RL+GLP+ C KE++ +F GLEIVPNGIT+P D+ GR TG A++QF +E AEKAL +H
Sbjct: 4 VRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKH 63
Query: 205 KEKIGHRLVTLVMS 218
KE+IGHR + + S
Sbjct: 64 KERIGHRYIEIFKS 77
Score = 53.5 bits (128), Expect = 2e-09
Identities = 28/56 (50%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 22 QFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
QFF IVP I L D GRS+GEA V+F+S + A++AL++HK +G RYIE++
Sbjct: 20 QFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 75
>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 = 88.8 bits (221), Expect = 1e-22
Identities = 31/72 (43%), Positives = 47/72 (65%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
+RL+GLP+ +ED+ F GL+I P+GI I +D GR TG AY++F E+A +AL +
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60
Query: 204 HKEKIGHRLVTL 215
H K+G R + +
Sbjct: 61 HNNKMGGRYIEV 72
Score = 75.7 bits (187), Expect = 1e-17
Identities = 28/56 (50%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 22 QFFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
FF I P I ++ DD GR +GEA VEF+S +DA+RAL++H + MG RYIE++
Sbjct: 18 DFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNKMGGRYIEVF 73
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 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 = 75
Score = 85.6 bits (212), Expect = 3e-21
Identities = 34/66 (51%), Positives = 47/66 (71%)
Query: 146 RLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHK 205
RL+GLPY C ++D+ F GL+IV +G+ I + GR TG AY+QF E A KALL+H+
Sbjct: 5 RLRGLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKHR 64
Query: 206 EKIGHR 211
E+IG+R
Sbjct: 65 EEIGNR 70
Score = 55.5 bits (134), Expect = 2e-10
Identities = 20/56 (35%), Positives = 38/56 (67%), Gaps = 2/56 (3%)
Query: 22 QFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
FF+ IV ++++ + GR +GEA V+F++ + A +AL +H+ +G+RYIE++
Sbjct: 20 DFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKHREEIGNRYIEVF 75
>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1) and similar
proteins. This subfamily corresponds to the RRM3 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 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. For instance, 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. The family also includes a cytoplasmic
poly(A)+ mRNA binding protein, GRSF-1, 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 also 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 = 75
Score = 78.1 bits (193), Expect = 1e-18
Identities = 25/56 (44%), Positives = 41/56 (73%)
Query: 21 SQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYM 76
+FF P+ PVN+ + + GR++GEADVEF++ +DA A+ + + +MG RYIEL++
Sbjct: 18 FEFFSPLNPVNVRIEYNADGRATGEADVEFATHEDAVAAMSKDREHMGHRYIELFL 73
Score = 60.4 bits (147), Expect = 4e-12
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
+ ++GLPY + D+ +F L P + I ++ GR TG A ++F E+A A+ +
Sbjct: 2 TVHMRGLPYRATENDIFEFFSPL--NPVNVRIEYNADGRATGEADVEFATHEDAVAAMSK 59
Query: 204 HKEKIGHRLVTL 215
+E +GHR + L
Sbjct: 60 DREHMGHRYIEL 71
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM2 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli.Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. It shows high sequence
homology to ESRPs and contains three RRMs as well. It
also has an N-terminal domain with unknown function and
a C-terminal domain particularly rich in alanine,
glutamine, and serine. .
Length = 80
Score = 74.3 bits (183), Expect = 4e-17
Identities = 31/80 (38%), Positives = 45/80 (56%), Gaps = 3/80 (3%)
Query: 142 QCCMRLQGLPYECKKEDVEKFLEGLEIV---PNGITIPHDYAGRCTGVAYIQFVDKENAE 198
Q +R++GLPY D+ F GL V P+GI GR TG A++ F +E+A+
Sbjct: 1 QVIIRMRGLPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQ 60
Query: 199 KALLRHKEKIGHRLVTLVMS 218
+AL +HKE +G R + L S
Sbjct: 61 RALGKHKENLGSRYIELFRS 80
Score = 71.6 bits (176), Expect = 4e-16
Identities = 28/59 (47%), Positives = 37/59 (62%), Gaps = 5/59 (8%)
Query: 22 QFFKPIVPVN-----ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
FF + PV IL +T GR +G+A V F + +DAQRAL +HK N+G RYIEL+
Sbjct: 20 AFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRALGKHKENLGSRYIELF 78
>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 = 68.2 bits (167), Expect = 7e-15
Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 146 RLQGLPYECKKEDVEKFLEGLEIV--PNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
R++GLP+ EDV F I NGI + GR +G A+I+ +E+ EKAL +
Sbjct: 3 RIRGLPWSATAEDVLNFFSDCRIKGGENGIHFTYSREGRPSGEAFIELESEEDVEKALEK 62
Query: 204 HKEKIGHRLV 213
H E +GHR +
Sbjct: 63 HNEHMGHRYI 72
Score = 54.7 bits (132), Expect = 5e-10
Identities = 18/36 (50%), Positives = 27/36 (75%)
Query: 40 GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
GR SGEA +E S +D ++AL++H +MG RYIE++
Sbjct: 40 GRPSGEAFIELESEEDVEKALEKHNEHMGHRYIEVF 75
>gnl|CDD|241177 cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM3 of G-rich sequence factor 1
(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 = 75
Score = 66.0 bits (161), Expect = 4e-14
Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEE 78
FF P+ P IL+ GR++GEADV F S DDA A+ + +++M RYIEL++
Sbjct: 19 NFFAPLKPTRILIEYSSDGRATGEADVHFESHDDAVAAMAKDRAHMQHRYIELFLNS 75
Score = 40.6 bits (95), Expect = 5e-05
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKE 206
++GLP++ +D+ F L P I I + GR TG A + F ++A A+ + +
Sbjct: 5 MRGLPFQASGQDIVNFFAPL--KPTRILIEYSSDGRATGEADVHFESHDDAVAAMAKDRA 62
Query: 207 KIGHRLVTL 215
+ HR + L
Sbjct: 63 HMQHRYIEL 71
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 63.9 bits (156), Expect = 2e-13
Identities = 24/72 (33%), Positives = 44/72 (61%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
C++++ +P++ K +V F G+ I GI I +D G+ G AY++FV +E+A +A
Sbjct: 1 CIKIKNIPFDVTKGEVLAFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERL 60
Query: 204 HKEKIGHRLVTL 215
H++K+ R + L
Sbjct: 61 HRKKLKGREILL 72
Score = 46.2 bits (110), Expect = 4e-07
Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 22 QFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
FF I I +L D G++ GEA VEF S +DA RA + H+ + R I L
Sbjct: 18 AFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERLHRKKLKGREILL 72
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding
protein 19 (RBM19) and similar proteins. This
subfamily corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 72
Score = 63.5 bits (155), Expect = 3e-13
Identities = 25/55 (45%), Positives = 38/55 (69%)
Query: 21 SQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
+FF P+ PV I ++ +D GR +G A V+ S +D ++AL+R+K MG RYIEL+
Sbjct: 18 REFFSPLKPVAIRIVKNDHGRKTGFAFVDLKSEEDLKKALKRNKDYMGGRYIELF 72
Score = 54.3 bits (131), Expect = 6e-10
Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 146 RLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHK 205
+++G P+ K++ + +F L+ V I I + GR TG A++ +E+ +KAL R+K
Sbjct: 4 KMRGAPFNVKEKHIREFFSPLKPV--AIRIVKNDHGRKTGFAFVDLKSEEDLKKALKRNK 61
Query: 206 EKIGHRLVTLV 216
+ +G R + L
Sbjct: 62 DYMGGRYIELF 72
>gnl|CDD|240951 cd12507, RRM1_ESRPs_Fusilli, RNA recognition motif 1 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM1 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B). These are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of the fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli. Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous fibroblast growth factor
receptor 2 (FGFR2) splicing and functions as a splicing
factor. It shows high sequence homology to ESRPs and
contains three RRMs as well. It also has an N-terminal
domain with unknown function and a C-terminal domain
particularly rich in alanine, glutamine, and serine. .
Length = 75
Score = 62.1 bits (151), Expect = 1e-12
Identities = 26/70 (37%), Positives = 41/70 (58%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
+R +GLP++ +D+ +F GL I G+ + GR G A I+FVD+E+ + AL R
Sbjct: 1 VVRARGLPWQSSDQDIAQFFRGLNIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQR 60
Query: 204 HKEKIGHRLV 213
HK +G R +
Sbjct: 61 HKHHMGTRYI 70
Score = 51.7 bits (124), Expect = 5e-09
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 21 SQFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
+QFF+ I + L GR +GEA + F + ALQRHK +MG RYIE+Y
Sbjct: 17 AQFFRGLNIAKGGVALCLSAQGRRNGEALIRFVDQEHRDLALQRHKHHMGTRYIEVY 73
>gnl|CDD|241179 cd12735, RRM3_hnRNPH3, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM3 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), and hnRNP F. This
family is involved in mRNA processing and exhibit
extensive sequence homology. Currently, little is known
about the functions of hnRNP H3 except for its role in
the splicing arrest induced by heat shock. In addition,
the typical hnRNP H proteins contain 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, like other hnRNP H
protein family members, hnRNP H3 has an extensive
glycine-rich region near the C-terminus, which may
allow it to homo- or heterodimerize. .
Length = 75
Score = 59.6 bits (144), Expect = 9e-12
Identities = 23/56 (41%), Positives = 38/56 (67%)
Query: 21 SQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYM 76
+ FF P+ P+ + + GR++GEADVEF + +DA A+ + K++M RYIEL++
Sbjct: 18 ANFFSPLTPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNHMQHRYIELFL 73
Score = 40.8 bits (95), Expect = 4e-05
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+ ++GLP+ + D+ F L + I I D GR TG A ++FV E+A A+ +
Sbjct: 3 VHMRGLPFRATESDIANFFSPLTPIRVHIDIGAD--GRATGEADVEFVTHEDAVAAMSKD 60
Query: 205 KEKIGHRLVTLVMS 218
K + HR + L ++
Sbjct: 61 KNHMQHRYIELFLN 74
>gnl|CDD|241182 cd12738, RRM1_Fusilli, RNA recognition motif 1 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM1 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 80
Score = 58.4 bits (141), Expect = 3e-11
Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+R +GLP++ +D+ KF GL I G+ + + GR G A ++F E+ + AL RH
Sbjct: 2 VRARGLPWQSSDQDIAKFFRGLNIAKGGVALCLNPQGRRNGEALVRFTCTEHRDLALKRH 61
Query: 205 KEKIGHRLV 213
K IG R +
Sbjct: 62 KHHIGQRYI 70
Score = 44.1 bits (104), Expect = 3e-06
Identities = 19/40 (47%), Positives = 26/40 (65%)
Query: 40 GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEG 79
GR +GEA V F+ + AL+RHK ++G RYIE+Y G
Sbjct: 38 GRRNGEALVRFTCTEHRDLALKRHKHHIGQRYIEVYKATG 77
>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 = 58.4 bits (141), Expect = 4e-11
Identities = 28/96 (29%), Positives = 55/96 (57%), Gaps = 10/96 (10%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
C+ L+GLPYE + + V F + L+IV + I I + G+ TG +++F ++ + + AL R
Sbjct: 11 CVYLKGLPYEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 70
Query: 204 HKEKIGHRLVTLVMSGAQWFLSPPLTNETPISRLDL 239
HK+ +G+R + + P+T + + ++D+
Sbjct: 71 HKQYMGNRFIQV----------HPITKKAMLEKIDM 96
Score = 40.7 bits (95), Expect = 9e-05
Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 22 QFFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
FFK IV +I + G+++GE VEF + D + AL RHK MG+R+I+++
Sbjct: 28 DFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVH 83
>gnl|CDD|241180 cd12736, RRM1_ESRP1, RNA recognition motif 1 in epithelial splicing
regulatory protein 1 (ESRP1) and similar proteins. This
subgroup corresponds to the RRM1 of ESRP1, also termed
RNA-binding motif protein 35A (RBM35A), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (p120-Catenin) and
ENAH (hMena) splicing. It enhances epithelial-specific
exons of CD44 and ENAH, silences mesenchymal exons of
CTNND1, or both within FGFR2. Additional research
indicated that ESRP1 functions as a tumor suppressor in
colon cancer cells. It may be involved in
posttranscriptional regulation of various genes by
exerting a differential effect on protein translation
via 5' untranslated regions (UTRs) of mRNAs. ESRP1
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 85
Score = 57.3 bits (138), Expect = 7e-11
Identities = 26/83 (31%), Positives = 47/83 (56%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
D +R +GLP++ +D+ +F +GL I G + + GR G A ++FV +E+ + A
Sbjct: 3 DNTVIRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVSEEHRDLA 62
Query: 201 LLRHKEKIGHRLVTLVMSGAQWF 223
L RHK +G+R + + + + F
Sbjct: 63 LQRHKHHMGNRYIEVYKATGEDF 85
Score = 46.6 bits (110), Expect = 5e-07
Identities = 27/61 (44%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 21 SQFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEE 78
++FFK I L + GR +GEA V F S + ALQRHK +MG+RYIE+Y
Sbjct: 22 ARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVSEEHRDLALQRHKHHMGNRYIEVYKAT 81
Query: 79 G 79
G
Sbjct: 82 G 82
>gnl|CDD|241185 cd12741, RRM2_Fusilli, RNA recognition motif 2 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM2 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 100
Score = 57.2 bits (138), Expect = 1e-10
Identities = 32/93 (34%), Positives = 47/93 (50%), Gaps = 9/93 (9%)
Query: 133 AVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVP-------NGITIPHDYAGRCTG 185
A LS Q +R++GLPY+C + V +F + P G+ GR TG
Sbjct: 10 AFLSRGG--QVIVRMRGLPYDCTAKQVLEFFTTGDTPPCHVLDGNEGVLFVKKPDGRATG 67
Query: 186 VAYIQFVDKENAEKALLRHKEKIGHRLVTLVMS 218
A++ F +E+A KAL +H+E IG R + L S
Sbjct: 68 DAFVLFATEEDAPKALGKHRESIGSRYIELFRS 100
Score = 44.9 bits (106), Expect = 2e-06
Identities = 18/44 (40%), Positives = 32/44 (72%)
Query: 32 ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
+L + GR++G+A V F++ +DA +AL +H+ ++G RYIEL+
Sbjct: 55 VLFVKKPDGRATGDAFVLFATEEDAPKALGKHRESIGSRYIELF 98
>gnl|CDD|241181 cd12737, RRM1_ESRP2, RNA recognition motif 1 in epithelial splicing
regulatory protein 2 (ESRP2) and similar proteins. This
subgroup corresponds to the RRM1 of ESRP2, also termed
RNA-binding motif protein 35B (RBM35B), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. ESRP2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 80
Score = 56.5 bits (136), Expect = 1e-10
Identities = 25/79 (31%), Positives = 45/79 (56%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+R +GLP++ +D+ +F +GL I G+ + + GR G A ++FV+ E + AL RH
Sbjct: 2 IRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNAQGRRNGEALVRFVNSEQRDLALQRH 61
Query: 205 KEKIGHRLVTLVMSGAQWF 223
K +G R + + + + F
Sbjct: 62 KHHMGSRYIEVYKATGEEF 80
Score = 45.0 bits (106), Expect = 1e-06
Identities = 29/63 (46%), Positives = 37/63 (58%), Gaps = 6/63 (9%)
Query: 21 SQFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQR--ALQRHKSNMGDRYIELYM 76
++FFK I + L + GR +GEA V F V+ QR ALQRHK +MG RYIE+Y
Sbjct: 17 ARFFKGLNIAKGGVALCLNAQGRRNGEALVRF--VNSEQRDLALQRHKHHMGSRYIEVYK 74
Query: 77 EEG 79
G
Sbjct: 75 ATG 77
>gnl|CDD|241178 cd12734, RRM3_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM3 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F, which represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth
factor receptor 2 (FGFR2) transcripts. The presence of
Fox 2 can allows hnRNP H and hnRNP F to better compete
with the SR protein ASF/SF2 for binding to FGFR2 exon
IIIc. Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; bothe have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently
silencing the exon. In addition, the family members
have an extensive glycine-rich region near the
C-terminus, which may allow them to homo- or
heterodimerize. .
Length = 76
Score = 55.9 bits (134), Expect = 2e-10
Identities = 24/54 (44%), Positives = 37/54 (68%)
Query: 23 FFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYM 76
FF P+ PV + + GR +GEADVEF++ +DA A+ + K+NM RY+EL++
Sbjct: 20 FFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKANMQHRYVELFL 73
Score = 46.6 bits (110), Expect = 4e-07
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
C+ ++GLPY + D+ F L V I I D GR TG A ++F E+A A+ +
Sbjct: 2 CVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPD--GRVTGEADVEFATHEDAVAAMSK 59
Query: 204 HKEKIGHRLVTLVMS 218
K + HR V L ++
Sbjct: 60 DKANMQHRYVELFLN 74
>gnl|CDD|240953 cd12509, RRM3_ESRPs_Fusilli, RNA recognition motif 3 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM3 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli. Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. Fusilli shows high
sequence homology to ESRPs and contains three RRMs as
well. It also has an N-terminal domain with unknown
function and a C-terminal domain particularly rich in
alanine, glutamine, and serine. .
Length = 81
Score = 54.4 bits (131), Expect = 7e-10
Identities = 29/73 (39%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGL--EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEK-A 200
C+RL+GLPYE ED+ FL L I P G+ + + GR +G A+IQ + E A + A
Sbjct: 3 CIRLRGLPYEATVEDILNFLGELARSIAPQGVHMVLNAQGRPSGDAFIQMLSAEFATRAA 62
Query: 201 LLRHKEKIGHRLV 213
HK +G R +
Sbjct: 63 NELHKHHMGERYI 75
Score = 48.6 bits (116), Expect = 8e-08
Identities = 19/55 (34%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQR-ALQRHKSNMGDRYIELY 75
+ + I P + ++ + GR SG+A ++ S + A R A + HK +MG+RYIE++
Sbjct: 24 ELARSIAPQGVHMVLNAQGRPSGDAFIQMLSAEFATRAANELHKHHMGERYIEVF 78
>gnl|CDD|241193 cd12749, RRM4_RBM12, RNA recognition motif 4 in RNA-binding protein
12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM4 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 = 88
Score = 52.9 bits (127), Expect = 3e-09
Identities = 23/72 (31%), Positives = 41/72 (56%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
C + +PY K+D+ +FLEG+ + N + + D G+ G A +QF +++A K+
Sbjct: 1 CAHISNIPYSITKKDILQFLEGIGVDENSVQVLVDNNGQGLGQALVQFKSEDDARKSERL 60
Query: 204 HKEKIGHRLVTL 215
H++K+ R V L
Sbjct: 61 HRKKLNGRDVFL 72
Score = 35.2 bits (81), Expect = 0.005
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 21 SQFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRA--LQRHKSNMGDRYIELYM 76
QF + + ++ +L D+ G+ G+A V+F S DDA+++ L R K N D ++ L
Sbjct: 17 LQFLEGIGVDENSVQVLVDNNGQGLGQALVQFKSEDDARKSERLHRKKLNGRDVFLHLVT 76
Query: 77 EEGTSSKEAN 86
E E N
Sbjct: 77 AEEMRDIERN 86
>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 = 50.9 bits (122), Expect = 1e-08
Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKE 206
L GLPY + DV++F GL++ + + GR G A ++F ++A++AL RH+E
Sbjct: 4 LHGLPYTADEHDVKEFFHGLDV--EDVIFLKRHNGRNNGNAIVKFATFQDAKEALKRHRE 61
Query: 207 KIGHRLVTLVMS 218
+G R + L++S
Sbjct: 62 LMGSRYIELMLS 73
Score = 47.1 bits (112), Expect = 2e-07
Identities = 22/52 (42%), Positives = 34/52 (65%)
Query: 23 FFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
FF + +++ L GR++G A V+F++ DA+ AL+RH+ MG RYIEL
Sbjct: 19 FFHGLDVEDVIFLKRHNGRNNGNAIVKFATFQDAKEALKRHRELMGSRYIEL 70
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 50.7 bits (122), Expect = 1e-08
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR-HKEK 207
LP + +ED++ + I I D GR G A+++F D+E+AEKAL + ++
Sbjct: 5 NLPPDTTEEDLKDLFSKFGPI-ESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKE 63
Query: 208 IGHRLVT 214
+G R +
Sbjct: 64 LGGRELR 70
Score = 39.5 bits (93), Expect = 1e-04
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIE 73
F P+ +I ++ D+ GRS G A VEF +DA++AL+ + +G R +
Sbjct: 17 DLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70
>gnl|CDD|241173 cd12729, RRM1_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM1 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical. Both of them
have been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 79
Score = 49.5 bits (118), Expect = 3e-08
Identities = 22/76 (28%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYA--GRCTGVAYIQFVDKENAEKALL 202
++++GLP+ C ++V++F +I I Y GR +G A+++ +E+ + AL
Sbjct: 4 VKVRGLPWSCSVDEVQRFFSDCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALK 63
Query: 203 RHKEKIGHRLVTLVMS 218
+ +E +GHR V + S
Sbjct: 64 KDRETMGHRYVEVFKS 79
Score = 43.7 bits (103), Expect = 5e-06
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 40 GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
GR SGEA VE S +D + AL++ + MG RY+E++
Sbjct: 42 GRPSGEAFVELESEEDVKLALKKDRETMGHRYVEVF 77
>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 = 48.6 bits (116), Expect = 8e-08
Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIV--PNGITIPHDYAGRCTGVAYIQFVDKENAEKALL 202
+R +GLP+ C EDV F + I NG+ + G+ G A I+ +E+ +KAL
Sbjct: 4 VRAKGLPWSCTAEDVMNFFDDCRIRNGENGVHFLLNRDGKPRGDALIELESEEDVQKALE 63
Query: 203 RHKEKIGHRLV 213
+H+ +G R V
Sbjct: 64 QHRHYMGQRYV 74
Score = 46.3 bits (110), Expect = 6e-07
Identities = 19/46 (41%), Positives = 30/46 (65%), Gaps = 2/46 (4%)
Query: 30 VNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
V+ LL D G+ G+A +E S +D Q+AL++H+ MG RY+E+
Sbjct: 34 VHFLLNRD--GKPRGDALIELESEEDVQKALEQHRHYMGQRYVEVR 77
>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 = 48.5 bits (116), Expect = 8e-08
Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 22 QFFK---PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
+FFK +V V I DD GRS G VEF++ + AQ+AL++ + R I
Sbjct: 18 EFFKECGEVVDVRIA--QDDDGRSKGFGHVEFATEEGAQKALEKSGEELLGREI 69
Score = 43.8 bits (104), Expect = 4e-06
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 150 LPYECKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEKI 208
L + +++D+E+F + E+V + I D GR G +++F +E A+KAL + E++
Sbjct: 7 LSWSAEQDDLEEFFKECGEVV--DVRIAQDDDGRSKGFGHVEFATEEGAQKALEKSGEEL 64
Query: 209 GHR 211
R
Sbjct: 65 LGR 67
>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 = 48.1 bits (115), Expect = 1e-07
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 147 LQGLPYECKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LR 203
+ LP + +ED+ + EI + I D G+ G A+++F E+AEKAL L
Sbjct: 3 VGNLPPDTTEEDLRELFSKFGEIE--SVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 204 HKEKIGHRL 212
KE G +L
Sbjct: 61 GKELDGRKL 69
Score = 40.4 bits (95), Expect = 5e-05
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 22 QFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL 74
+ F + ++ ++ D G+S G A VEF S +DA++AL+ + + R +++
Sbjct: 17 ELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKV 71
>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM2 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 78
Score = 46.7 bits (111), Expect = 3e-07
Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 23 FFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
FF + ++ L + G ++G + V+F++ +DA L+R + MG RYIE+
Sbjct: 19 FFSGLKVDGVIFLKNRRGLNNGNSMVKFATKEDAIEGLKRDRQYMGSRYIEI 70
Score = 44.8 bits (106), Expect = 2e-06
Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+ L+GLP+ +++V F GL++ +G+ + G G + ++F KE+A + L R
Sbjct: 2 LFLRGLPFSVTEDNVRDFFSGLKV--DGVIFLKNRRGLNNGNSMVKFATKEDAIEGLKRD 59
Query: 205 KEKIGHRLV 213
++ +G R +
Sbjct: 60 RQYMGSRYI 68
>gnl|CDD|241184 cd12740, RRM2_ESRP2, RNA recognition motif 2 in epithelial splicing
regulatory protein 2 (ESRP2) and similar proteins. This
subgroup corresponds to the RRM2 of ESRP2, also termed
RNA-binding motif protein 35B (RBM35B), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. ESRP2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 107
Score = 47.3 bits (112), Expect = 4e-07
Identities = 32/95 (33%), Positives = 45/95 (47%), Gaps = 21/95 (22%)
Query: 138 SAVDQCCMRLQGLPYECKKEDVEKFL----------EGLEIV--PNGITIPHDYAGRCTG 185
S +Q +R++GLP+ DV FL EGL V P+G R TG
Sbjct: 12 SKENQVIIRMRGLPFTATPTDVLGFLGPECPVTGGTEGLLFVKYPDG---------RPTG 62
Query: 186 VAYIQFVDKENAEKALLRHKEKIGHRLVTLVMSGA 220
A++ F +E A+ AL +HK +G R + L S A
Sbjct: 63 DAFVLFACEEYAQNALKKHKGILGKRYIELFRSTA 97
Score = 43.1 bits (101), Expect = 1e-05
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 23 FFKPIVPVN-----ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
F P PV +L + GR +G+A V F+ + AQ AL++HK +G RYIEL+
Sbjct: 36 FLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNALKKHKGILGKRYIELF 93
>gnl|CDD|241186 cd12742, RRM3_ESRP1_ESRP2, RNA recognition motif in epithelial
splicing regulatory protein ESRP1, ESRP2 and similar
proteins. This subgroup corresponds to the RRM3 of
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B). These are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of the fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 46.3 bits (110), Expect = 5e-07
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 144 CMRLQGLPYECKKEDVEKFL--EGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
C+RL+GLPY ED+ +FL +I P+G+ + + GR +G A+IQ E A A
Sbjct: 3 CIRLRGLPYTATIEDILEFLGEFAADIRPHGVHMVLNQQGRPSGDAFIQMKSAERAFLAA 62
Query: 202 LR-HKEKIGHRLV 213
+ HK+ + R V
Sbjct: 63 QKCHKKMMKDRYV 75
Score = 40.9 bits (96), Expect = 4e-05
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 27 IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELY 75
I P + ++ + GR SG+A ++ S + A A Q+ HK M DRY+E++
Sbjct: 29 IRPHGVHMVLNQQGRPSGDAFIQMKSAERAFLAAQKCHKKMMKDRYVEVF 78
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 45.2 bits (108), Expect = 1e-06
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 146 RLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHK 205
++ LP +ED+ +F V G+ + + R G A+++F E+AE AL +
Sbjct: 2 YVRNLPPSVTEEDLREFFSPYGKV-EGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59
Query: 206 EKI--GHRL 212
+ G L
Sbjct: 60 GLVLDGRTL 68
Score = 44.1 bits (105), Expect = 2e-06
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 23 FFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKS-NMGDRYIE 73
FF P V + L + R G A VEF+S +DA+ AL++ + R +
Sbjct: 18 FFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 44.5 bits (106), Expect = 2e-06
Identities = 16/69 (23%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKAL-LRHKE 206
LP + +E++ + V + + + D G+ G A+++F +E+AEKAL + +
Sbjct: 6 NLPPDTTEEELRELFSKFGKVES-VRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGK 64
Query: 207 KIGHRLVTL 215
++ R + +
Sbjct: 65 ELDGRPLKV 73
Score = 38.3 bits (90), Expect = 3e-04
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 22 QFFKPIVPV-NILLLTD-DAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL 74
+ F V ++ L+ D + G+S G A VEF S +DA++AL+ + + R +++
Sbjct: 18 ELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
>gnl|CDD|240954 cd12510, RRM1_RBM12_like, RNA recognition motif 1 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM1 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 = 74
Score = 44.2 bits (105), Expect = 2e-06
Identities = 26/73 (35%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 146 RLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHK 205
RLQ LP+E D+ +F GL I G+ I G G A+I F E+A A+ R
Sbjct: 5 RLQNLPWEAGSLDIRRFFSGLTIPDGGVHI----IGGEMGEAFIAFATDEDARLAMSRDG 60
Query: 206 EKIGHRLVTLVMS 218
+ I V L +S
Sbjct: 61 QTIKGSKVKLFLS 73
Score = 27.6 bits (62), Expect = 1.9
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 10/46 (21%)
Query: 21 SQFFKPI-VP---VNILLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
+FF + +P V+I+ G GEA + F++ +DA+ A+ R
Sbjct: 19 RRFFSGLTIPDGGVHII------GGEMGEAFIAFATDEDARLAMSR 58
>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 = 43.8 bits (104), Expect = 3e-06
Identities = 15/62 (24%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEKIG 209
L Y ++++ K + + + + +Y G+ G AY++F ++E+ ++AL +E I
Sbjct: 7 LDYSVPEDELRKLFSKCGEITD-VRLVKNYKGKSKGYAYVEFENEESVQEALKLDRELIK 65
Query: 210 HR 211
R
Sbjct: 66 GR 67
Score = 29.9 bits (68), Expect = 0.24
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 30 VNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDR 70
++ L+ + G+S G A VEF + + Q AL+ + + R
Sbjct: 27 TDVRLVKNYKGKSKGYAYVEFENEESVQEALKLDRELIKGR 67
>gnl|CDD|241183 cd12739, RRM2_ESRP1, RNA recognition motif 2 in epithelial splicing
regulatory protein 1 (ESRP1) and similar proteins. This
subgroup corresponds to the RRM2 of ESRP1, also termed
RNA-binding motif protein 35A (RBM35A), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. Additional research indicated that ESRP1
functions as a tumor suppressor in colon cancer cells.
It may be involved in posttranscriptional regulation of
various genes by exerting a differential effect on
protein translation via 5' untranslated regions (UTRs)
of mRNAs. ESRP1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 109
Score = 44.3 bits (104), Expect = 6e-06
Identities = 29/89 (32%), Positives = 44/89 (49%), Gaps = 9/89 (10%)
Query: 138 SAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNG------ITIPHDYAGRCTGVAYIQF 191
S +Q +R++GLP+ E+V F V G +T P R TG A++ F
Sbjct: 12 SKENQVIVRMRGLPFTATAEEVLAFFGQHCPVTGGKEGILFVTYPD---SRPTGDAFVLF 68
Query: 192 VDKENAEKALLRHKEKIGHRLVTLVMSGA 220
+E A+ AL +HK+ +G R + L S A
Sbjct: 69 ACEEYAQNALKKHKDLLGKRYIELFRSTA 97
Score = 43.1 bits (101), Expect = 2e-05
Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 23 FFKPIVPVN-----ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
FF PV IL +T R +G+A V F+ + AQ AL++HK +G RYIEL+
Sbjct: 36 FFGQHCPVTGGKEGILFVTYPDSRPTGDAFVLFACEEYAQNALKKHKDLLGKRYIELF 93
>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 = 42.8 bits (101), Expect = 1e-05
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYA-GRCTGVAYIQFVDKENAEKALL 202
++ LPY CK++D+EK + + + D G+ G AY+ F+D E+A KA
Sbjct: 7 VRNLPYSCKEDDLEKLFSKFGELSE-VHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62
>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 = 42.5 bits (100), Expect = 1e-05
Identities = 23/53 (43%), Positives = 31/53 (58%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
FF + I LL D GR++G A V+F S D AL+R++ MG RYIE+
Sbjct: 20 DFFHGLRIDAIHLLKDHVGRNNGNALVKFYSPHDTFEALKRNRMLMGQRYIEV 72
Score = 40.2 bits (94), Expect = 6e-05
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKE 206
L GLP+ + D+ F GL I + I + D+ GR G A ++F + +AL R++
Sbjct: 6 LHGLPFSVLEHDIRDFFHGLRI--DAIHLLKDHVGRNNGNALVKFYSPHDTFEALKRNRM 63
Query: 207 KIGHRLV 213
+G R +
Sbjct: 64 LMGQRYI 70
>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 = 41.6 bits (98), Expect = 2e-05
Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHD--YAGRCTGVAYIQFVDKENAEKALLRH 204
L LPY+ +ED+++F GL + + + +P + GR G Y +F D+++ +AL +
Sbjct: 6 LGNLPYDVTEEDIKEFFRGLNV--SSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLN 63
Query: 205 KEKIGHR 211
E + +R
Sbjct: 64 DESLKNR 70
Score = 28.5 bits (64), Expect = 1.1
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 21 SQFFKPIVPVNILLLTD--DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
+FF+ + ++ L + D GR G EF D +AL + ++ +R I
Sbjct: 19 KEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLNDESLKNRRI 72
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 44.9 bits (105), Expect = 2e-05
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 138 SAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKEN 196
S + + + LPY+ +ED+ + + V + + D G+ G A+++F +E+
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPV-KRVRLVRDRETGKSRGFAFVEFESEES 169
Query: 197 AEKALLRHKEKI 208
AEKA+ K
Sbjct: 170 AEKAIEELNGKE 181
Score = 31.5 bits (70), Expect = 0.52
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 23 FFKPIVPVN-ILLLTD-DAGRSSGEADVEFSSVDDAQRALQRH 63
FK PV + L+ D + G+S G A VEF S + A++A++
Sbjct: 135 LFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEEL 177
>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 = 41.1 bits (97), Expect = 3e-05
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 152 YECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKALL 202
Y E++++ + + N ITI D + G+ G AYI+F+DK + E ALL
Sbjct: 9 YGTTPEELQEHFKSCGTI-NRITILCDKFTGQPKGFAYIEFLDKSSVENALL 59
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 40.8 bits (96), Expect = 5e-05
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 22 QFFKPIV-PVNILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
FK P ++ LLTD G+S G A VEF + + +AL+ H + + R I
Sbjct: 19 AHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLKGRKI 71
Score = 27.7 bits (62), Expect = 2.0
Identities = 16/62 (25%), Positives = 26/62 (41%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEKIG 209
LPY+ ED+ + P+ + G+ G A+++F E KAL H +
Sbjct: 8 LPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLLK 67
Query: 210 HR 211
R
Sbjct: 68 GR 69
>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 = 39.5 bits (93), Expect = 1e-04
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
LP++C + D++K V +TIP G+ G A++QF K +AEKA+
Sbjct: 7 LPFKCTEADLKKLFSPFGFVWE-VTIPRKPDGKKKGFAFVQFTSKADAEKAI 57
>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 = 38.9 bits (91), Expect = 2e-04
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 150 LPYECKKEDV-EKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
L ++ ++ + E F E EI + + +P D +GR G Y++F +E A+ AL
Sbjct: 6 LSFDADEDSIYEAFGEYGEI--SSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57
Score = 29.3 bits (66), Expect = 0.44
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 29 PVNILLLTD-DAGRSSGEADVEFSSVDDAQRAL 60
++ L TD D+GR G VEFSS + AQ AL
Sbjct: 25 ISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57
>gnl|CDD|241189 cd12745, RRM1_RBM12, RNA recognition motif 1 in RNA-binding protein
12 (RBM12) and similar proteins. This subgrup
corresponds to the RRM1 of 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 = 92
Score = 39.2 bits (91), Expect = 2e-04
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+RLQGLP D+ F GL I G+ I G G A+I F E+A ++R
Sbjct: 5 IRLQGLPIVAGTMDIRHFFSGLTIPDGGVHI----VGGELGEAFIVFATDEDARLGMMRT 60
Query: 205 KEKIGHRLVTLVMS 218
I V+L++S
Sbjct: 61 GGTIKGSKVSLLLS 74
>gnl|CDD|241188 cd12744, RRM1_RBM12B, RNA recognition motif 1 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM1 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 79
Score = 38.3 bits (89), Expect = 4e-04
Identities = 27/74 (36%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+RLQGLP ED+ F GL I G+ I G G A+I F E+A +A+ R
Sbjct: 4 IRLQGLPVVAGSEDIRHFFTGLRIPDGGVHI----IGGELGEAFIIFATDEDARRAMSRS 59
Query: 205 KEKIGHRLVTLVMS 218
I V L +S
Sbjct: 60 GGFIKDSTVELFLS 73
Score = 26.7 bits (59), Expect = 4.2
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 4/44 (9%)
Query: 40 GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGTSSK 83
G GEA + F++ +DA+RA+ R + D +EL++ SSK
Sbjct: 36 GGELGEAFIIFATDEDARRAMSRSGGFIKDSTVELFL----SSK 75
>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 = 38.2 bits (89), Expect = 4e-04
Identities = 17/71 (23%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR-HKEK 207
GLP+ KE++EK + +V + + + +G+ G+AY+++ ++ +A +A+L+ +
Sbjct: 9 GLPFSVTKEELEKLFKKHGVV-KSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTE 67
Query: 208 IGHRLVTLVMS 218
I + +++ +S
Sbjct: 68 IKEKTISVAIS 78
>gnl|CDD|241187 cd12743, RRM3_Fusilli, RNA recognition motif 3 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM3 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 85
Score = 37.9 bits (88), Expect = 6e-04
Identities = 20/59 (33%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 144 CMRLQGLPYECKKEDVEKFLE--GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
C+RL+GLPYE + E + +FL IV G+ + ++ G+ +G A+IQ +++A
Sbjct: 3 CIRLRGLPYEAQVEHILEFLGDFAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASAC 61
>gnl|CDD|241194 cd12750, RRM5_RBM12B, RNA recognition motif 5 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM5 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 77
Score = 37.2 bits (86), Expect = 7e-04
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+RL+ LP++ ++ F G ++P+ +++ ++ G TG A + + A A+
Sbjct: 3 IRLENLPFKATINEILDFFHGYRVIPDSVSMQYNEQGLPTGTAIVAMENYYEAMAAINEL 62
Query: 205 KEK-IGHRLVTLVM 217
++ IG R V L +
Sbjct: 63 NDRPIGPRKVKLSL 76
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 36.8 bits (86), Expect = 0.001
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 12/58 (20%)
Query: 150 LPYECKKEDVEKFLEG------LEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
LP++ +E++++ IV + +T G G A+++F KE+A+K L
Sbjct: 8 LPFDATEEELKELFSQFGEVKYARIVKDKLT------GHSKGTAFVKFKTKESAQKCL 59
Score = 27.2 bits (61), Expect = 2.7
Identities = 10/59 (16%), Positives = 18/59 (30%), Gaps = 14/59 (23%)
Query: 14 ITYCLLCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
+ Y + G S G A V+F + + AQ+ L+ +
Sbjct: 27 VKYARIV--------------KDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLS 71
>gnl|CDD|240957 cd12513, RRM3_RBM12B, RNA recognition motif 3 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM3 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 81
Score = 36.9 bits (86), Expect = 0.001
Identities = 20/70 (28%), Positives = 34/70 (48%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
+ L+ LP+ +K D+ F L++ + IT D G+ T A++ F + AL
Sbjct: 2 YIHLENLPFSVEKRDIRAFFGDLDLPDSQITFLSDKKGKRTRSAFVMFKSLRDYCAALAH 61
Query: 204 HKEKIGHRLV 213
HK + +R V
Sbjct: 62 HKRVLYNREV 71
Score = 29.2 bits (66), Expect = 0.51
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 32 ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
I L+D G+ + A V F S+ D AL HK + +R + ++
Sbjct: 31 ITFLSDKKGKRTRSAFVMFKSLRDYCAALAHHKRVLYNREVYVF 74
>gnl|CDD|241192 cd12748, RRM4_RBM12B, RNA recognition motif 4 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM4 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role remains
unclear. .
Length = 76
Score = 36.3 bits (84), Expect = 0.002
Identities = 17/57 (29%), Positives = 29/57 (50%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
C+ + P++ K +V+KF I + I + +D G G A ++F +E A KA
Sbjct: 2 CIYARNFPFDVTKVEVQKFFAPFNIDEDDIYLLYDDKGVGLGEALVKFKSEEQAMKA 58
Score = 28.6 bits (64), Expect = 0.95
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 23 FFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR--HKSNMG 68
FF P I +I LL DD G GEA V+F S + A +A +R + +G
Sbjct: 20 FFAPFNIDEDDIYLLYDDKGVGLGEALVKFKSEEQAMKA-ERLNGQRFLG 68
>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 = 36.0 bits (84), Expect = 0.002
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
+R+ L Y+ +ED+E+ + V + I +D +GR G A + F +E+AE+A
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKK-VKINYDRSGRSEGTADVVFEKREDAERA 57
Score = 32.2 bits (74), Expect = 0.046
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 37 DDAGRSSGEADVEFSSVDDAQRA 59
D +GRS G ADV F +DA+RA
Sbjct: 35 DRSGRSEGTADVVFEKREDAERA 57
>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 = 35.6 bits (83), Expect = 0.004
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 161 KFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
F + GI +P D G+ G A+++F E A++A+
Sbjct: 27 IFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAV 67
Score = 34.1 bits (79), Expect = 0.013
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 24 FKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
F V I + D+ G++ G A VEF++ ++A+ A++
Sbjct: 31 FGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVK 68
>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 = 34.9 bits (81), Expect = 0.005
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 149 GLPYECKKEDVEKFLEGLEIVP--NGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
LPY+ E +E+F E+ P + + +C G Y+ F +E+A++AL
Sbjct: 6 NLPYDTTDEQLEEFFS--EVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRAL 58
Score = 29.5 bits (67), Expect = 0.48
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 22 QFFKPIVPV-NILLLTD-DAGRSSGEADVEFSSVDDAQRAL-QRHKSNMGDRYIEL 74
+FF + P+ ++ D + + G V F+ +DA+RAL ++ K+ G R I +
Sbjct: 18 EFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHV 73
>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 = 34.2 bits (79), Expect = 0.008
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
++ LP+ +E++ + E + + +P D R G A++ F+ E+A KA
Sbjct: 4 VRNLPFTTTEEELRELFEAFGEISE-VHLPLDKETKRSKGFAFVSFMFPEHAVKAY 58
>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 = 34.1 bits (79), Expect = 0.009
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 173 ITIPHDY-AGRCTGVAYIQFVDKENAEKALLRHKEKIGHRLVTLVMSGAQW 222
+ + D G+ G A++ F +E+AE+A+ + G L++S +W
Sbjct: 29 VYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN---GFGYDNLILS-VEW 75
Score = 29.8 bits (68), Expect = 0.31
Identities = 15/41 (36%), Positives = 27/41 (65%), Gaps = 2/41 (4%)
Query: 24 FKPIVPVN-ILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
F+P P++ + L D + G+S G A V F + +DA+RA+++
Sbjct: 20 FRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic
RNA-binding protein RBM24, RBM38 and similar proteins.
This subfamily corresponds to the RRM of RBM24 and RBM38
from vertebrate, SUPpressor family member SUP-12 from
Caenorhabditis elegans and similar proteins. Both, RBM24
and RBM38, are preferentially expressed in cardiac and
skeletal muscle tissues. They regulate myogenic
differentiation by controlling the cell cycle in a
p21-dependent or -independent manner. RBM24, also termed
RNA-binding region-containing protein 6, interacts with
the 3'-untranslated region (UTR) of myogenin mRNA and
regulates its stability in C2C12 cells. RBM38, also
termed CLL-associated antigen KW-5, or HSRNASEB, or
RNA-binding region-containing protein 1(RNPC1), or
ssDNA-binding protein SEB4, is a direct target of the
p53 family. It is required for maintaining the stability
of the basal and stress-induced p21 mRNA by binding to
their 3'-UTRs. It also binds the AU-/U-rich elements in
p63 3'-UTR and regulates p63 mRNA stability and
activity. SUP-12 is a novel tissue-specific splicing
factor that controls muscle-specific splicing of the
ADF/cofilin pre-mRNA in C. elegans. All family members
contain a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 34.1 bits (79), Expect = 0.009
Identities = 15/53 (28%), Positives = 25/53 (47%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
GLPY + + K+ + + I G+ G ++ F DKE+AE+A
Sbjct: 7 GLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59
Score = 27.2 bits (61), Expect = 2.7
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 40 GRSSGEADVEFSSVDDAQRALQ 61
G+S G V F + A+RA +
Sbjct: 39 GKSRGYGFVTFKDKESAERACK 60
>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 = 34.0 bits (78), Expect = 0.010
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 147 LQGLPYECKKEDV-EKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
++ LPY +++ E F + ++I +P G G+AYI+F + AEKAL
Sbjct: 8 VKNLPYNITVDELKEVFEDAVDI-----RLPSGKDGSSKGIAYIEFKTEAEAEKAL 58
Score = 30.2 bits (68), Expect = 0.22
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 30 VNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
V+I L + G S G A +EF + +A++AL+
Sbjct: 28 VDIRLPSGKDGSSKGIAYIEFKTEAEAEKALE 59
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. The family also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 33.8 bits (78), Expect = 0.015
Identities = 15/27 (55%), Positives = 18/27 (66%)
Query: 36 TDDAGRSSGEADVEFSSVDDAQRALQR 62
DD GRS+GE VEFS AQ A++R
Sbjct: 33 VDDRGRSTGEGIVEFSRKPGAQAAIKR 59
>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 = 33.4 bits (77), Expect = 0.017
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 37 DDAGRSSGEADVEFSSVDDAQRALQRH 63
D +GRS G ADV F DA +A++++
Sbjct: 35 DRSGRSLGTADVVFERRADALKAMKQY 61
>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 = 33.4 bits (77), Expect = 0.017
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 173 ITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+ + D GR G +IQF D E+A+KAL
Sbjct: 28 VQLQRDPETGRSKGYGFIQFADAEDAKKAL 57
Score = 31.1 bits (71), Expect = 0.12
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 6 YVIDILIHITYCLLCSQFFKPIVPV-NILLLTDD-AGRSSGEADVEFSSVDDAQRALQ 61
YV ++ +IT L F+P + + L D GRS G ++F+ +DA++AL+
Sbjct: 2 YVGNLHFNITEDDL-RGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALE 58
>gnl|CDD|241195 cd12751, RRM5_RBM12, RNA recognition motif 5 in RNA-binding protein
12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM5 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which is
ubiquitously expressed. It contains five distinct RNA
binding motifs (RBMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), two
proline-rich regions, and several putative transmembrane
domains. The biological role of RBM12 remains unclear. .
Length = 76
Score = 32.6 bits (74), Expect = 0.035
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+++Q +P+ +++ F G +++P + + G TG A + F ++ A A++
Sbjct: 4 IKVQNMPFTVTVDEILDFFYGYQVIPGSVCLKFSDKGMPTGEAMVAFESRDEAMAAVVDL 63
Query: 205 KEK-IGHRLVTL 215
++ IG R V L
Sbjct: 64 NDRPIGSRKVKL 75
>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 = 32.4 bits (74), Expect = 0.036
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
C+++Q LP+ E++ F G ++P +++ ++ G TG A + F A A+
Sbjct: 2 CVKVQNLPFTATIEEILDFFYGYRVIPGSVSLLYNDNGAPTGEATVAFDTHREAMAAVRE 61
Query: 204 HKEK-IGHRLVTL 215
+ IG R V L
Sbjct: 62 LNGRPIGTRKVKL 74
>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 = 32.7 bits (74), Expect = 0.039
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 33 LLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
+++ DD GR +G+ VEF+ A++AL R
Sbjct: 30 VVIVDDRGRPTGKGIVEFAGKPSARKALDR 59
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline-
and glutamine-rich splicing factor, or 100 kDa
DNA-pairing protein (POMp100), or 100 kDa subunit of
DNA-binding p52/p100 complex, a multifunctional protein
that mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response
element (IGFRE). Moreover, PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. PSF is an essential pre-mRNA
splicing factor and is dissociated from PTB and binds
to U1-70K and serine-arginine (SR) proteins during
apoptosis. PSF forms a heterodimer with the nuclear
protein p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO). The PSF/p54nrb complex
displays a variety of functions, such as DNA
recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), which are
responsible for interactions with RNA and for the
localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. .
Length = 80
Score = 32.4 bits (73), Expect = 0.046
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 19 LCSQFFKPIVPVN-ILLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
L + F PV +++ DD GRS+G+ VEF+S A++A +R
Sbjct: 15 LLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFER 59
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily
corresponds to the RRM2 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 31.6 bits (72), Expect = 0.072
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 30 VNILLLTD-DAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIE 73
+ + TD + G S G A +EF SVD ++AL+ S++G +
Sbjct: 31 TRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLV 75
>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 = 34.0 bits (78), Expect = 0.090
Identities = 27/89 (30%), Positives = 40/89 (44%), Gaps = 4/89 (4%)
Query: 4 SFYVIDILIHITYCLLCSQFFKPIVPVNILLLTDDA--GRSSGEADVEFSSVDDAQRAL- 60
S YV D+ +T L FKP PV + + D+ RS G V F + DA+RAL
Sbjct: 2 SLYVGDLDPDVTEAKL-YDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE 60
Query: 61 QRHKSNMGDRYIELYMEEGTSSKEANGRG 89
+ +G + I + + S +G G
Sbjct: 61 TMNFKRLGGKPIRIMWSQRDPSLRRSGVG 89
>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 = 31.8 bits (72), Expect = 0.092
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 147 LQGLPYECKK-EDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
++ LP+ KK ++K V TIP G+ G A++ ++NAE AL
Sbjct: 5 IRNLPWSIKKPVKLKKIFGRYGKVRE-ATIPRKRGGKLCGFAFVTMKKRKNAEIAL 59
>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 = 31.6 bits (72), Expect = 0.100
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+ + +D+ + + + + IP D Y R G AY+QF D +AE AL
Sbjct: 8 VADATRPDDLRRLFGKYGPIVD-VYIPLDFYTRRPRGFAYVQFEDVRDAEDAL 59
Score = 28.5 bits (64), Expect = 1.3
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 24 FKPIVPVNILLLTDD--AGRSSGEADVEFSSVDDAQRAL-QRHKSNMGDRYIELYMEEG 79
+ PIV V I L D R G A V+F V DA+ AL ++ R IE+ +G
Sbjct: 24 YGPIVDVYIPL---DFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFAQG 79
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 31.2 bits (70), Expect = 0.11
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 19 LCSQFFKPIVPVN-ILLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
L Q F PV +++ DD GR +G+ VEF++ A++AL+R
Sbjct: 15 LLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALER 59
>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 = 31.0 bits (71), Expect = 0.13
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 181 GRCTGVAYIQFVDKENAEKAL 201
R GVAY++F D+E+ AL
Sbjct: 38 RRSKGVAYVEFYDEESVPLAL 58
>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 = 31.0 bits (71), Expect = 0.13
Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 150 LPYECKKEDVEK-FLEGLEIVPNGITI---PHDYAGRCTGVAYIQFVDKENAEKALLRHK 205
LP++ ++E++ K F + ++ + I G+ G Y+ F K++ AL +
Sbjct: 7 LPFDIEEEELRKHFEDCGDV--EAVRIVRDRKTGIGK--GFGYVLFKTKDSVALALKLNG 62
Query: 206 EKIGHR 211
K+ R
Sbjct: 63 IKLKGR 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 = 30.7 bits (70), Expect = 0.15
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 8/55 (14%)
Query: 22 QFFK---PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIE 73
QFFK I V I+ A +EF + D+A AL + +G I
Sbjct: 19 QFFKDCGEIREVKIVESEGGL-----VAVIEFETEDEALAALTKDHKRLGGNEIS 68
Score = 29.1 bits (66), Expect = 0.45
Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 148 QGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEK 207
+ LP + + + +F + + + I G VA I+F ++ A AL + ++
Sbjct: 6 KNLPKDTTENKIRQFFKDCGEIRE-VKIVESEGGL---VAVIEFETEDEALAALTKDHKR 61
Query: 208 IG 209
+G
Sbjct: 62 LG 63
>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 = 30.7 bits (70), Expect = 0.16
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 35 LTDDAGRSSGEADVEFSSVDDAQRALQ 61
TD+ GRS G V F S +DAQRA++
Sbjct: 31 KTDNDGRSKGFGTVLFESPEDAQRAIE 57
>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 = 30.5 bits (69), Expect = 0.16
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 152 YECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
Y E++E G V N +TI D ++G G AYI+F DKE+ AL
Sbjct: 9 YGATAEELEAHFHGCGSV-NRVTILCDKFSGHPKGFAYIEFSDKESVRTAL 58
>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 = 30.4 bits (69), Expect = 0.18
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 149 GLPYECKKEDVEKFLE--GLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKE 206
G+PY ++++ + G + +T P GR G+A+I F +E A++AL E
Sbjct: 5 GIPYYSTEDEIRSYFSYCGEIEELDLMTFPDT--GRFRGIAFITFKTEEAAKRALALDGE 62
Query: 207 KIGHRLVT 214
+G R +
Sbjct: 63 DMGGRFLK 70
Score = 26.9 bits (60), Expect = 3.1
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 37 DDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYI 72
D GR G A + F + + A+RAL +MG R++
Sbjct: 34 PDTGRFRGIAFITFKTEEAAKRALALDGEDMGGRFL 69
>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 = 30.7 bits (70), Expect = 0.19
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 21 SQFFKPIVPVNIL-LLTD-DAGRSSGEADVEFSSVDDAQRALQ 61
F V ++TD + GRS G VE + ++A A++
Sbjct: 17 KDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE 59
>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 = 32.9 bits (75), Expect = 0.20
Identities = 21/94 (22%), Positives = 40/94 (42%)
Query: 141 DQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
D + + L + ++ D+ +F + V + I + R GVAY++F D E+ KA
Sbjct: 88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKA 147
Query: 201 LLRHKEKIGHRLVTLVMSGAQWFLSPPLTNETPI 234
L + + R + + S A+ + P
Sbjct: 148 LALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPG 181
Score = 32.2 bits (73), Expect = 0.36
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 178 DYAGRCTGVAYIQFVDKENAEKAL 201
GR G +IQF D E A++AL
Sbjct: 222 PETGRSKGFGFIQFHDAEEAKEAL 245
>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 = 29.9 bits (67), Expect = 0.28
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 40 GRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIEL 74
GR G A VEF S +DA+ AL + + + R I L
Sbjct: 35 GRPKGYAFVEFESAEDAKEALNSCNNTEIEGRSIRL 70
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type
and RNA-binding motif-containing protein 1 (ZCRB1) and
similar proteins. This subfamily corresponds to the RRM
of ZCRB1, also termed MADP-1, or U11/U12 small nuclear
ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or
U11/U12-31K), a novel multi-functional nuclear factor,
which may be involved in morphine dependence, cold/heat
stress, and hepatocarcinoma. It is located in the
nucleoplasm, but outside the nucleolus. ZCRB1 is one of
the components of U11/U12 snRNPs that bind to U12-type
pre-mRNAs and form a di-snRNP complex, simultaneously
recognizing the 5' splice site and branchpoint sequence.
ZCRB1 is characterized by an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 30.0 bits (68), Expect = 0.30
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYAGR-CTGVAYIQFVDKENAEKAL--LRHKE 206
LP+ D+ K V +TI D R GVA+I F+D+E+A K + L +KE
Sbjct: 9 LPFSLTNNDLHKIFSKYGKVVK-VTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKE 67
Query: 207 KIGHRL 212
G L
Sbjct: 68 LFGRTL 73
>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 = 29.6 bits (67), Expect = 0.33
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 10/67 (14%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRHKE 206
LPY ++ DVE+F +G + I + + G +++F D +A+ A+ L KE
Sbjct: 6 RLPYRARERDVERFFKGYGRI-REINLKN-------GFGFVEFEDPRDADDAVYELNGKE 57
Query: 207 KIGHRLV 213
G R++
Sbjct: 58 LCGERVI 64
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor; it specifically binds poly(G)
RNA. RBM10, a paralog of RBM5, may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. Both, RBM5
and RBM10, contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc
fingers, and a G-patch/D111 domain. .
Length = 81
Score = 30.0 bits (68), Expect = 0.34
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 27 IVPVNILLLTD-DAGRSSGEADVEFSSVDDAQR--ALQRHKSNMGDRYIEL 74
+ P ++ L+ G S G A VEF S+++A R L + K + D I L
Sbjct: 28 VEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMELNQGKLQLQDYKITL 78
>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 = 29.4 bits (67), Expect = 0.36
Identities = 10/20 (50%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 185 GVAYIQFVDKENAEKALLRH 204
G AY++F E+AEKA ++H
Sbjct: 41 GYAYVEFESPEDAEKA-IKH 59
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 29.8 bits (67), Expect = 0.36
Identities = 15/65 (23%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRHKEK 207
L + +ED+ F + + + + + G G ++ F E+A++AL L++K+
Sbjct: 7 LAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKL 66
Query: 208 IGHRL 212
G L
Sbjct: 67 HGRIL 71
Score = 28.6 bits (64), Expect = 1.0
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 21 SQFFKPIVPVN--ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHK 64
+ FF + P+ +++ + G S G V F+ ++DAQ AL + K
Sbjct: 17 TDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLK 62
>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 = 29.2 bits (66), Expect = 0.48
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+++ L Y +D+ + E V + + IP D Y G A+++F DK +AE A+
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGD-VYIPRDRYTRESRGFAFVRFYDKRDAEDAM 57
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 29.3 bits (66), Expect = 0.48
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
++ L Y C +ED+EK + + +P D + G A++ ++ E+A KA
Sbjct: 7 IRNLAYTCTEEDLEKLFSKYGPLSE-VHLPIDKLTKKPKGFAFVTYMIPEHAVKAF 61
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 29.1 bits (66), Expect = 0.57
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 44 GEADVEFSSVDDAQRALQRHKSNMGDRYIELYM 76
G A V F A+ ALQ + + +G R I + +
Sbjct: 46 GFAFVTFKDASSAENALQLNGTELGGRKISVSL 78
Score = 28.8 bits (65), Expect = 0.74
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 146 RLQGLPYECKKEDVEKFLEGL-EIVPNGITIP---HDYAGRC-TGVAYIQFVDKENAEKA 200
++ L ++ ++D+ E+ I IP + GR G A++ F D +AE A
Sbjct: 4 YVRNLDFKLDEDDLRGIFSKFGEV--ESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 201 LLRHKEKIGHR 211
L + ++G R
Sbjct: 62 LQLNGTELGGR 72
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 29.3 bits (66), Expect = 0.57
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 34 LLTDDAGRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYI 72
L D+ G+S G VEF + Q+AL+ ++ + R +
Sbjct: 32 LFKDEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKL 71
>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 = 28.9 bits (65), Expect = 0.61
Identities = 15/57 (26%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 23 FFKPIVPVNILLLT-DDAGRSSGEADVEFSSVDDAQRALQRHKSNM--GDRYIELYM 76
F I P+ +LL+ ++ G+S+G A++ F DA +A + + G+R +++ +
Sbjct: 20 FVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRIDDGNRKMKVEV 76
>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 = 28.8 bits (64), Expect = 0.68
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKALLR 203
M + GL ++ K+D++ + V + TI D GR G +I F D + EK +L
Sbjct: 2 MFVGGLSWDTSKKDLKDYFTKFGEVTD-CTIKMDPNTGRSRGFGFILFKDASSVEK-VLE 59
Query: 204 HKEKIGHRL 212
KE HRL
Sbjct: 60 QKE---HRL 65
>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 = 29.1 bits (65), Expect = 0.69
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 145 MRLQGLPYECKKEDVEKFLEGL-EIVPNGITIPHD-YAGRCTGVAYIQFVDKENAEKALL 202
M + GL ++ K+D++++ E+V TI D GR G ++ F D + EK L
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVV--DCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD 58
Query: 203 RHKEKIGHRLV 213
+ + K+ R++
Sbjct: 59 QKEHKLDGRVI 69
>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 = 28.8 bits (65), Expect = 0.81
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
G+P + +E++ F V + + I D AG G ++ F +E+AEK L
Sbjct: 9 GIPPDTTEEELRDFFSRFGSVKD-VKIITDRAGVSKGYGFVTFETQEDAEKIL 60
Score = 26.9 bits (60), Expect = 3.6
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 34 LLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
++TD AG S G V F + +DA++ L N + + +
Sbjct: 34 IITDRAGVSKGYGFVTFETQEDAEKILAMGNLNFRGKKLNI 74
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La
or LARP3) and similar proteins. This subfamily
corresponds to the RRM1 of La autoantigen, also termed
Lupus La protein, or La ribonucleoprotein, or Sjoegren
syndrome type B antigen (SS-B), a highly abundant
nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. La contains an N-terminal La motif
(LAM), followed by two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also possesses a short
basic motif (SBM) and a nuclear localization signal
(NLS) at the C-terminus. .
Length = 72
Score = 28.7 bits (65), Expect = 0.82
Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 23 FFKPIVPVNILLLTDDAGRS-SGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
FF+ VN + + D + G VEF + +DA++ L++ K ++ + +
Sbjct: 19 FFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEKEKLKYKEKELTV 71
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and
the RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 28.7 bits (65), Expect = 0.83
Identities = 8/30 (26%), Positives = 22/30 (73%)
Query: 46 ADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
A V+FS+ ++A++A + ++ +R+I+++
Sbjct: 41 ALVQFSTSEEAKKAYRSPEAVFNNRFIKVF 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 = 28.8 bits (64), Expect = 0.90
Identities = 16/55 (29%), Positives = 26/55 (47%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ GLP ++DVE + N + G GVA+I+F + AE+A+
Sbjct: 5 ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAI 59
>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 = 28.8 bits (64), Expect = 0.90
Identities = 16/69 (23%), Positives = 32/69 (46%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
M + GL ++ K+D+ ++L V + GR G ++ F D + +K L
Sbjct: 2 MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61
Query: 205 KEKIGHRLV 213
+ K+ +L+
Sbjct: 62 EHKLDGKLI 70
>gnl|CDD|223432 COG0355, AtpC, F0F1-type ATP synthase, epsilon subunit
(mitochondrial delta subunit) [Energy production and
conversion].
Length = 135
Score = 29.5 bits (67), Expect = 0.96
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 166 LEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEKIGHR 211
LE+ PN +TI D A R +D+ AE+A R ++++
Sbjct: 70 LEVQPNEVTILADSAERADD------IDEARAEEAKERAEKELESA 109
>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 = 28.5 bits (64), Expect = 1.0
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 173 ITIP-HDYAGRCTGVAYIQFVDKENAEKAL 201
+++P + + G G A+I+F E A+KA
Sbjct: 29 VSLPRYKHTGDIKGFAFIEFETPEEAQKAC 58
>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 = 28.0 bits (63), Expect = 1.3
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 40 GRSSGEADVEFSSVDDAQRALQR 62
GRS G V F SV+DA+ A +R
Sbjct: 38 GRSRGFGFVYFESVEDAKEAKER 60
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM1 of the majority of family
members that include polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. Rod1 is
a mammalian polypyrimidine tract binding protein (PTB)
homolog of a regulator of differentiation in the
fission yeast Schizosaccharomyces pombe, where the nrd1
gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It might play a role controlling
differentiation in mammals. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. In addition, this family also includes
RNA-binding motif protein 20 (RBM20) that is an
alternative splicing regulator associated with dilated
cardiomyopathy (DCM) and contains only one RRM. .
Length = 74
Score = 27.9 bits (63), Expect = 1.6
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 19 LCSQFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
L S F K N+LLL R +A VE SV+ A+ +
Sbjct: 19 LVSPFGKV---TNVLLL-----RGKNQALVEMDSVESAKSMVD 53
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 27.6 bits (62), Expect = 1.7
Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 150 LPYECKKEDVEKFLEGL-EIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRHKE 206
+P+E K+++ + ++ + +P + G G A+++FV K+ A+ A+ L+
Sbjct: 8 VPFEATKKELRELFSPFGQVK--SVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTH 65
Query: 207 KIGHRLV 213
G LV
Sbjct: 66 LYGRHLV 72
>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 = 28.0 bits (62), Expect = 1.7
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 173 ITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+ +P D Y R G AY+QF D +AE AL
Sbjct: 30 VYVPLDFYTRRPRGFAYVQFEDVRDAEDAL 59
>gnl|CDD|221165 pfam11680, DUF3276, Protein of unknown function (DUF3276). This
bacterial family of proteins has no known function.
Length = 123
Score = 28.8 bits (65), Expect = 1.8
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 19/52 (36%)
Query: 156 KEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEK 207
KED EKF+EGL I ++ KE E+ + +
Sbjct: 64 KEDFEKFMEGLLEA-------------------IDYIKKEKGEEVISERHQD 96
>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 = 27.7 bits (62), Expect = 2.0
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 24 FKPIVPVNILLLTDD--AGRSSGEADVEFSSVDDAQRALQ 61
F + PV + D G S G V++ S +DAQRA++
Sbjct: 21 FLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 27.5 bits (62), Expect = 2.1
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 187 AYIQFVDKENAEKALLRHKEKI--GHRLV 213
Y+QF E+A A+ K+ G++LV
Sbjct: 44 CYVQFTSPESAAAAVALLNGKLGEGYKLV 72
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 27.7 bits (61), Expect = 2.1
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
CM+L + D+E+F + V + I + R G+AY++FVD + A+
Sbjct: 6 CMQLAA---RIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60
>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 = 27.7 bits (61), Expect = 2.5
Identities = 15/30 (50%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 173 ITIPHD-YAGRCTGVAYIQFVDKENAEKAL 201
+ +P D Y R G AYIQF D +AE AL
Sbjct: 30 VYVPLDFYTRRPRGFAYIQFEDVRDAEDAL 59
>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 = 27.3 bits (61), Expect = 2.5
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGI---TIPHDYAG--RCTGVAYIQFVDKENAEKAL 201
L Y +ED+E+FL+ E V I T+ + R G+AY +F E AEK +
Sbjct: 7 LSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKVV 63
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 27.5 bits (61), Expect = 2.6
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 185 GVAYIQFVDKENAEKALLRHKEK 207
G AY+QF D+ EKALL +++K
Sbjct: 42 GFAYVQFKDENAVEKALLLNEKK 64
>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 = 27.3 bits (60), Expect = 3.0
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL--LRHKEK 207
L Y+ ++ DVE+F +G G + D G +++F D +A+ A+ L K+
Sbjct: 7 LSYQARERDVERFFKGY-----GKILEVDLK---NGYGFVEFDDLRDADDAVYELNGKDL 58
Query: 208 IGHRLV 213
G R++
Sbjct: 59 CGERVI 64
>gnl|CDD|240701 cd12255, RRM1_LKAP, RNA recognition motif 1 in Limkain-b1 (LKAP)
and similar proteins. This subfamily corresponds to
the RRM1 of LKAP, a novel peroxisomal autoantigen that
co-localizes with a subset of cytoplasmic microbodies
marked by ABCD3 (ATP-binding cassette subfamily D
member 3, known previously as PMP-70) and/or PXF
(peroxisomal farnesylated protein, known previously as
PEX19). It associates with LIM kinase 2 (LIMK2) and may
serve as a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. LKAP contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). However, whether
those RRMs are bona fide RNA binding sites remains
unclear. Moreover, there is no evidence of LAKP
localization in the nucleus. Therefore, if the RRMs are
functional, their interaction with RNA species would be
restricted to the cytoplasm and peroxisomes. .
Length = 73
Score = 26.9 bits (60), Expect = 3.0
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 42 SSGEADVEFSSVDDAQRALQR 62
S G A + F + D A+RAL+R
Sbjct: 38 SGGTAIIRFPNQDSARRALKR 58
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 26.7 bits (60), Expect = 3.1
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 185 GVAYIQFVDKENAEKAL 201
G A+++F +E AEKA+
Sbjct: 22 GFAFVEFSTEEAAEKAV 38
>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 = 27.2 bits (61), Expect = 3.1
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 185 GVAYIQFVDKENAEKAL--LRHKEKIGHRLV 213
G +++F KE A+KAL L+ GH L
Sbjct: 48 GYGFVEFKSKEAAQKALKRLQGTVLDGHALE 78
Score = 27.2 bits (61), Expect = 3.1
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 42 SSGEADVEFSSVDDAQRALQR 62
S G VEF S + AQ+AL+R
Sbjct: 46 SMGYGFVEFKSKEAAQKALKR 66
>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 = 28.8 bits (64), Expect = 3.7
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 23 FFKPIVPVNILLLTDD--AGRSSGEADVEFSSVDDAQRALQ 61
F+ I P+N + D G S G A V+F S D+QRA++
Sbjct: 127 LFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIK 167
>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 = 26.7 bits (60), Expect = 3.8
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 23 FFKPIVPVNILLLTDDA--GRSSGEADVEFSSVDDAQRAL 60
F P PV + + D RS G A V F + DA+RAL
Sbjct: 19 IFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERAL 58
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 26.8 bits (60), Expect = 3.8
Identities = 11/51 (21%), Positives = 20/51 (39%)
Query: 150 LPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
LP E E + + V + + G G ++++ K +A KA
Sbjct: 7 LPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57
>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 = 26.8 bits (60), Expect = 4.0
Identities = 13/38 (34%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 178 DYAGRCTGVAYIQFVDKENAEKALLR-HKEKI--GHRL 212
D++G G A++ + +KE A++A+ + H +I G RL
Sbjct: 36 DFSGLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRL 73
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM2 of RBM40 and the RRM
of RBM41. RBM40, also known as RNA-binding
region-containing protein 3 (RNPC3) or U11/U12 small
nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K
protein). It serves as a bridging factor between the
U11 and U12 snRNPs. It contains two RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), connected by a
linker that includes a proline-rich region. It binds to
the U11-associated 59K protein via its RRM1 and employs
the RRM2 to bind hairpin III of the U12 small nuclear
RNA (snRNA). The proline-rich region might be involved
in protein-protein interactions. RBM41 contains only
one RRM. Its biological function remains unclear. .
Length = 82
Score = 26.8 bits (60), Expect = 4.1
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 29 PVNILLLTDDAGRSSGEADVEFSSVDDAQRALQ 61
+I L+T+ GR G+A V F S + A +AL
Sbjct: 35 MFDIRLMTE--GRMKGQAFVTFPSEEIATKALN 65
>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 = 27.2 bits (61), Expect = 4.1
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 177 HDYAGRCTGVAYIQFVDKENAEKAL-LRHKEKIGHRL 212
HD AY+ F ++E+AEKAL L E GH +
Sbjct: 54 HDKKDNVN--AYVVFKEEESAEKALKLNGTEFEGHHI 88
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM2 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 = 86
Score = 26.9 bits (60), Expect = 4.6
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 41 RSSGEADVEFSSVDDAQRALQ 61
++ +A VEF SVD AQRA
Sbjct: 38 KNGVQAMVEFDSVDSAQRAKA 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 = 26.5 bits (58), Expect = 4.8
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 24 FKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
+ P+ VN++ GRS G A V F +DD++ A++
Sbjct: 23 YGPLAGVNVVY-DQRTGRSRGFAFVYFERIDDSKEAMEH 60
>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 = 26.5 bits (59), Expect = 4.9
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 40 GRSSGEADVEFSSVDDAQRALQ 61
G+S+G VEF++ + A++ALQ
Sbjct: 38 GKSAGYGFVEFATHEAAEQALQ 59
>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 = 26.5 bits (59), Expect = 5.8
Identities = 10/26 (38%), Positives = 12/26 (46%)
Query: 36 TDDAGRSSGEADVEFSSVDDAQRALQ 61
D G S G V FS + +RAL
Sbjct: 36 LDQNGNSRGYGFVRFSDESEQKRALT 61
>gnl|CDD|163520 TIGR03808, RR_plus_rpt_1, twin-arg-translocated uncharacterized
repeat protein. Members of this protein family have a
Sec-independent twin-arginine tranlocation (TAT) signal
sequence, which enables tranfer of proteins folded
around prosthetic groups to cross the plasma membrane.
These proteins have four copies of a repeat of about 23
amino acids that resembles the beta-helix repeat.
Beta-helix refers to a structural motif in which
successive beta strands wind around to stack parallel
in a right-handed helix, as in AlgG and related enzymes
of carbohydrate metabolism. The twin-arginine motif
suggests that members of this protein family bind some
unknown cofactor.
Length = 455
Score = 27.9 bits (62), Expect = 7.1
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 35 LTDDAGRSSGEADVEFSSVDDAQRALQR 62
LT GR + + V +S DD RALQR
Sbjct: 32 LTSTLGRDATQYGVRPNSPDDQTRALQR 59
>gnl|CDD|221623 pfam12531, DUF3731, DNA-K related protein. This domain family is
found in bacteria, and is approximately 250 amino acids
in length. There are two conserved sequence motifs: RPG
and WRR. The proteins in this family are frequently
annotated as DNA-K related proteins however there is
little accompanying literature to confirm this.
Length = 249
Score = 27.6 bits (62), Expect = 8.4
Identities = 11/35 (31%), Positives = 12/35 (34%), Gaps = 16/35 (45%)
Query: 270 HEWWALARLGSFLISRTHQIIIPRSYHRRPGYGEL 304
WWAL RLG+ R P YG
Sbjct: 135 QLWWALGRLGA----------------RTPFYGSA 153
>gnl|CDD|239828 cd04336, YeaK, YeaK is an uncharacterized Echerichia coli protein
with a YbaK-like domain of unknown function. The
YbaK-like domain family includes the INS amino
acid-editing domain of the bacterial class II prolyl
tRNA synthetase (ProRS), and it's trans-acting homologs,
YbaK, and ProX. The primary function of INS is to
hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping
ensure the fidelity of translation. Organisms whose
ProRS lacks the INS domain express a single-domain INS
homolog such as YbaK, ProX, or PrdX which supplies the
function of INS in trans.
Length = 153
Score = 26.9 bits (60), Expect = 9.0
Identities = 12/48 (25%), Positives = 18/48 (37%)
Query: 174 TIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEKIGHRLVTLVMSGAQ 221
+ H G VA I+ + KALL + R V V+ +
Sbjct: 17 VLDHPPEGTSEEVAAIRGTELGQGAKALLCKVKDGSRRFVLAVLPADK 64
>gnl|CDD|185081 PRK15127, PRK15127, multidrug efflux system protein AcrB;
Provisional.
Length = 1049
Score = 27.9 bits (62), Expect = 9.3
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 145 MRLQGLP-YECKKEDVEKF---LEGLEIVPNGITIPHDYAGRCTGVAYIQF 191
M +GLP E ++ + + L G+ +V + + +P + G TG Y QF
Sbjct: 420 MAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQF 470
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
0.323 0.138 0.430
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: 15,759,793
Number of extensions: 1497740
Number of successful extensions: 1742
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1708
Number of HSP's successfully gapped: 193
Length of query: 304
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 208
Effective length of database: 6,679,618
Effective search space: 1389360544
Effective search space used: 1389360544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.4 bits)