RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3068
(152 letters)
>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 = 129 bits (326), Expect = 3e-40
Identities = 52/75 (69%), Positives = 60/75 (80%), Gaps = 1/75 (1%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSKD 113
HTVHMRGLP+R E DI +FFSP+ PV V I Y +GR +GEADV FATHEDA+ AMSKD
Sbjct: 1 HTVHMRGLPYRATENDIFEFFSPLNPVNVRIEYNADGRATGEADVEFATHEDAVAAMSKD 60
Query: 114 RTNIRHRYIELFLNS 128
R ++ HRYIELFLNS
Sbjct: 61 REHMGHRYIELFLNS 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 = 114 bits (286), Expect = 4e-34
Identities = 44/75 (58%), Positives = 61/75 (81%), Gaps = 1/75 (1%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSKD 113
H VHMRGLPF+ + +DIV+FF+P+ P + I Y +GR +GEADV+F +H+DA+ AM+KD
Sbjct: 1 HFVHMRGLPFQASGQDIVNFFAPLKPTRILIEYSSDGRATGEADVHFESHDDAVAAMAKD 60
Query: 114 RTNIRHRYIELFLNS 128
R +++HRYIELFLNS
Sbjct: 61 RAHMQHRYIELFLNS 75
>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 = 105 bits (263), Expect = 1e-30
Identities = 48/75 (64%), Positives = 59/75 (78%), Gaps = 1/75 (1%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSKD 113
H VHMRGLPFR E DI +FFSP+ P+ V I+ +GR +GEADV F THEDA+ AMSKD
Sbjct: 1 HFVHMRGLPFRATESDIANFFSPLTPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKD 60
Query: 114 RTNIRHRYIELFLNS 128
+ +++HRYIELFLNS
Sbjct: 61 KNHMQHRYIELFLNS 75
>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 = 102 bits (254), Expect = 2e-29
Identities = 49/76 (64%), Positives = 60/76 (78%), Gaps = 1/76 (1%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSKD 113
H VHMRGLP+R E DI +FFSP+ PV V I +GR +GEADV FATHEDA+ AMSKD
Sbjct: 1 HCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKD 60
Query: 114 RTNIRHRYIELFLNSS 129
+ N++HRY+ELFLNS+
Sbjct: 61 KANMQHRYVELFLNST 76
>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 = 90.7 bits (226), Expect = 6e-25
Identities = 33/73 (45%), Positives = 43/73 (58%), Gaps = 3/73 (4%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDI---NYKNGRPSGEADVYFATHEDAMQAMSK 112
V +RGLPF E+DI DFFS + I +GRP+GEA V FA+ EDA +A+ K
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRK 60
Query: 113 DRTNIRHRYIELF 125
+ RYIE+F
Sbjct: 61 HNNKMGGRYIEVF 73
>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 = 82.7 bits (205), Expect = 1e-21
Identities = 31/78 (39%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 54 HHTVHMRGLPFRVNEKDIVDFFSPVVPVYVD------INYKNGRPSGEADVYFATHEDAM 107
+ MRGLP+ DI+ FF + PV + +GRP+G+A V F T EDA
Sbjct: 1 QVIIRMRGLPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQ 60
Query: 108 QAMSKDRTNIRHRYIELF 125
+A+ K + N+ RYIELF
Sbjct: 61 RALGKHKENLGSRYIELF 78
>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 = 77.4 bits (191), Expect = 1e-19
Identities = 33/78 (42%), Positives = 50/78 (64%), Gaps = 5/78 (6%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFS--PVVP--VYVDINYKNGRPSGEADVYFATHEDAMQAM 110
V +RGLPF ++++I FFS +VP + + ++Y GR +GEA V FA+ E A +A+
Sbjct: 1 GVVRLRGLPFGCSKEEIAQFFSGLEIVPNGITLPMDY-RGRSTGEAYVQFASQESAERAL 59
Query: 111 SKDRTNIRHRYIELFLNS 128
K + I HRYIE+F +S
Sbjct: 60 GKHKEKIGHRYIEIFRSS 77
>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 = 73.2 bits (180), Expect = 4e-18
Identities = 32/72 (44%), Positives = 44/72 (61%), Gaps = 1/72 (1%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDI-NYKNGRPSGEADVYFATHEDAMQAMSKD 113
TV MRG PF V EK I +FFSP+ PV + I +GR +G A V + ED +A+ ++
Sbjct: 1 FTVKMRGAPFNVKEKHIREFFSPLKPVAIRIVKNDHGRKTGFAFVDLKSEEDLKKALKRN 60
Query: 114 RTNIRHRYIELF 125
+ + RYIELF
Sbjct: 61 KDYMGGRYIELF 72
>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 = 69.8 bits (171), Expect = 1e-16
Identities = 34/72 (47%), Positives = 44/72 (61%), Gaps = 3/72 (4%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSKD 113
V +RGLP+ E DI+DFF +V V I + GR +GEA V FAT E A +A+ K
Sbjct: 4 VRLRGLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKH 63
Query: 114 RTNIRHRYIELF 125
R I +RYIE+F
Sbjct: 64 REEIGNRYIEVF 75
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 63.3 bits (155), Expect = 2e-14
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPSGEADVYFATHEDAMQAMSK-DR 114
+++R LP V E+D+ +FFSP V V + RP G A V FA+ EDA A+ K +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 115 TNIRHRYIE 123
+ R +
Sbjct: 61 LVLDGRTLR 69
>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 = 63.1 bits (153), Expect = 7e-14
Identities = 39/94 (41%), Positives = 59/94 (62%), Gaps = 11/94 (11%)
Query: 45 WVNESSGPGHH------TVHMRGLPFRVNEKDIVDFFS--PVVP--VYVDINYKNGRPSG 94
WV + +GP + TV +RGLPF ++++IV FFS +VP + + ++Y+ GR +G
Sbjct: 3 WVLKHNGPTDYDGSSGGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMDYQ-GRSTG 61
Query: 95 EADVYFATHEDAMQAMSKDRTNIRHRYIELFLNS 128
EA V FA+ E A A+ K + I HRYIE+F +S
Sbjct: 62 EAFVQFASKEIAENALGKHKERIGHRYIEIFKSS 95
>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 = 59.3 bits (144), Expect = 1e-12
Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 7/75 (9%)
Query: 57 VHMRGLPFRVNEKDIVDFFS------PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
V +RGLP+ +D+++FFS ++ + + GRPSGEA + + ED +A+
Sbjct: 2 VRIRGLPWSATAEDVLNFFSDCRIKGGENGIHFTYS-REGRPSGEAFIELESEEDVEKAL 60
Query: 111 SKDRTNIRHRYIELF 125
K ++ HRYIE+F
Sbjct: 61 EKHNEHMGHRYIEVF 75
>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 = 58.6 bits (142), Expect = 2e-12
Identities = 27/67 (40%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 59 MRGLPFRVNEKDIVDFFSP-VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
+RGLPF V E ++ DFFS V + + + G +G + V FAT EDA++ + +DR +
Sbjct: 4 LRGLPFSVTEDNVRDFFSGLKVDGVIFLKNRRGLNNGNSMVKFATKEDAIEGLKRDRQYM 63
Query: 118 RHRYIEL 124
RYIE+
Sbjct: 64 GSRYIEI 70
>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 = 59.2 bits (143), Expect = 3e-12
Identities = 30/80 (37%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPV------YVDINYKNGRPSGEADVYFATHEDAMQAM 110
+ MRGLPF D++ F P PV + + Y +GRP+G+A V FA E A A+
Sbjct: 19 IRMRGLPFTATPTDVLGFLGPECPVTGGTEGLLFVKYPDGRPTGDAFVLFACEEYAQNAL 78
Query: 111 SKDRTNIRHRYIELFLNSSS 130
K + + RYIELF ++++
Sbjct: 79 KKHKGILGKRYIELFRSTAA 98
>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 = 58.5 bits (141), Expect = 3e-12
Identities = 33/76 (43%), Positives = 52/76 (68%), Gaps = 5/76 (6%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVP--VYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
V +RGLPF ++++IV FFS +VP + + ++++ GR +GEA V FA+ E A +A+ K
Sbjct: 4 VRLRGLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQ-GRSTGEAFVQFASQEIAEKALKK 62
Query: 113 DRTNIRHRYIELFLNS 128
+ I HRYIE+F +S
Sbjct: 63 HKERIGHRYIEIFKSS 78
>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 = 58.5 bits (141), Expect = 5e-12
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPV------YVDINYKNGRPSGEADVYFATHEDAMQAM 110
V MRGLPF ++++ FF PV + + Y + RP+G+A V FA E A A+
Sbjct: 19 VRMRGLPFTATAEEVLAFFGQHCPVTGGKEGILFVTYPDSRPTGDAFVLFACEEYAQNAL 78
Query: 111 SKDRTNIRHRYIELFLNSSS 130
K + + RYIELF ++++
Sbjct: 79 KKHKDLLGKRYIELFRSTAA 98
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 56.4 bits (137), Expect = 1e-11
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
T+ + LP E+++ + FS V V + + + G+ G A V F + EDA +A+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 113 -DRTNIRHRYIEL 124
+ + R +++
Sbjct: 61 LNGKELDGRPLKV 73
>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 = 56.0 bits (135), Expect = 4e-11
Identities = 34/86 (39%), Positives = 47/86 (54%), Gaps = 10/86 (11%)
Query: 50 SGPGHHTVHMRGLPFRVNEKDIVDFFSP--VVPVYVD--------INYKNGRPSGEADVY 99
S G V MRGLP+ K +++FF+ P +V + +GR +G+A V
Sbjct: 13 SRGGQVIVRMRGLPYDCTAKQVLEFFTTGDTPPCHVLDGNEGVLFVKKPDGRATGDAFVL 72
Query: 100 FATHEDAMQAMSKDRTNIRHRYIELF 125
FAT EDA +A+ K R +I RYIELF
Sbjct: 73 FATEEDAPKALGKHRESIGSRYIELF 98
>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 = 53.7 bits (129), Expect = 2e-10
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 5/74 (6%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVPVYVDINY---KNGRPSGEADVYFATHEDAMQAMS 111
V +RGLP+ + ++ FFS + I++ + GRPSGEA V + ED A+
Sbjct: 4 VKVRGLPWSCSVDEVQRFFSDCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALK 63
Query: 112 KDRTNIRHRYIELF 125
KDR + HRY+E+F
Sbjct: 64 KDRETMGHRYVEVF 77
>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 = 52.5 bits (126), Expect = 4e-10
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPV-VPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRT 115
V + GLP+ +E D+ +FF + V + + NGR +G A V FAT +DA +A+ + R
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGLDVEDVIFLKRHNGRNNGNAIVKFATFQDAKEALKRHRE 61
Query: 116 NIRHRYIELFL 126
+ RYIEL L
Sbjct: 62 LMGSRYIELML 72
>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 = 51.9 bits (125), Expect = 6e-10
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPV-YVDINY-KNGRPSGEADVYFATHEDAMQAMSK-D 113
+ + LP E+D+ + FS + V I K+G+ G A V F + EDA +A+ +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 114 RTNIRHRYIEL 124
+ R +++
Sbjct: 61 GKELDGRKLKV 71
>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 = 51.3 bits (123), Expect = 1e-09
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 8/76 (10%)
Query: 57 VHMRGLPFRVNEKDIVDFFSP----VVP--VYVDINYKNGRPSGEADVYFATHEDA-MQA 109
+ +RGLP+ +DI++F + P V++ +N + GRPSG+A + + E A A
Sbjct: 4 IRLRGLPYEATVEDILNFLGELARSIAPQGVHMVLNAQ-GRPSGDAFIQMLSAEFATRAA 62
Query: 110 MSKDRTNIRHRYIELF 125
+ ++ RYIE+F
Sbjct: 63 NELHKHHMGERYIEVF 78
>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 = 49.6 bits (119), Expect = 6e-09
Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 9/76 (11%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPV-VP---VYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ ++ LP+ DI FFS + +P V++ G GEA + FAT EDA AMS+
Sbjct: 4 IRLQNLPWEAGSLDIRRFFSGLTIPDGGVHI-----IGGEMGEAFIAFATDEDARLAMSR 58
Query: 113 DRTNIRHRYIELFLNS 128
D I+ ++LFL+S
Sbjct: 59 DGQTIKGSKVKLFLSS 74
>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 = 47.6 bits (114), Expect = 3e-08
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINY-KNGRPSGEADVYFATHEDAMQAMSK 112
+ + L + V E+D+ + F V V V INY ++GR G ADV F EDA +A+ +
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60
>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 = 46.5 bits (111), Expect = 1e-07
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
T+ + L + + D+ +FF VV V + + +GR G V FAT E A +A+ K
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEK 59
Query: 113 DRTNIRHRYIELFLNSSSPR 132
+ R E+ ++ ++ R
Sbjct: 60 SGEELLGR--EIRVDLATER 77
>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 = 46.3 bits (110), Expect = 1e-07
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSKD 113
V ++ LPF ++I+DFF V+P V + Y NG P+GEA V F TH +AM A+ ++
Sbjct: 3 VKVQNLPFTATIEEILDFFYGYRVIPGSVSLLYNDNGAPTGEATVAFDTHREAMAAV-RE 61
Query: 114 RTN--IRHRYIELF 125
I R ++L
Sbjct: 62 LNGRPIGTRKVKLT 75
>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 = 46.0 bits (109), Expect = 2e-07
Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPV---YVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
T+ +R L F V ++D+ DFFS V P+ V + + G G V FA EDA +A++K
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60
Query: 113 DRTNIRHRYIELFLNSSSPR 132
+ H I L L+ + R
Sbjct: 61 LKNKKLHGRI-LRLDIAERR 79
>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 = 45.4 bits (108), Expect = 2e-07
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 57 VHMRGLPFRVNEKDIVDFF--SPVVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSKD 113
+ ++ +PF V + +++ FF + + I Y K G+ GEA V F + EDAM+A
Sbjct: 2 IKIKNIPFDVTKGEVLAFFAGIAIAEQGIHILYDKTGKTLGEAYVEFVSEEDAMRAERLH 61
Query: 114 RTNIRHRYIEL 124
R ++ R I L
Sbjct: 62 RKKLKGREILL 72
>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 = 45.2 bits (107), Expect = 3e-07
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 57 VHMRGLPFRVNEKDIVDFFSP------VVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
V +GLP+ +D+++FF V+ +N ++G+P G+A + + ED +A+
Sbjct: 4 VRAKGLPWSCTAEDVMNFFDDCRIRNGENGVHFLLN-RDGKPRGDALIELESEEDVQKAL 62
Query: 111 SKDRTNIRHRYIELF 125
+ R + RY+E+
Sbjct: 63 EQHRHYMGQRYVEVR 77
>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 = 43.8 bits (104), Expect = 9e-07
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINY-KNGRPSGEADVYFATHEDAMQAMSK 112
+ + L F V++ DI + F+ + ++Y ++GR G ADV F DA++AM +
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60
>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 = 43.6 bits (103), Expect = 1e-06
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPV-VPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRT 115
V + GLPF V E DI DFF + + + GR +G A V F + D +A+ ++R
Sbjct: 4 VSLHGLPFSVLEHDIRDFFHGLRIDAIHLLKDHVGRNNGNALVKFYSPHDTFEALKRNRM 63
Query: 116 NIRHRYIEL 124
+ RYIE+
Sbjct: 64 LMGQRYIEV 72
>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 = 43.6 bits (103), Expect = 1e-06
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVP------VYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+ +RGLP+ +DI++F V++ +N + GRPSG+A + + E A A
Sbjct: 4 IRLRGLPYTATIEDILEFLGEFAADIRPHGVHMVLNQQ-GRPSGDAFIQMKSAERAFLAA 62
Query: 111 SK-DRTNIRHRYIELF 125
K + ++ RY+E+F
Sbjct: 63 QKCHKKMMKDRYVEVF 78
>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 = 42.9 bits (101), Expect = 2e-06
Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 9/78 (11%)
Query: 57 VHMRGLPFRVNEKDIVDFFS----PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ ++GLP +DI FF+ P V++ G GEA + FAT EDA +AMS+
Sbjct: 4 IRLQGLPVVAGSEDIRHFFTGLRIPDGGVHI-----IGGELGEAFIIFATDEDARRAMSR 58
Query: 113 DRTNIRHRYIELFLNSSS 130
I+ +ELFL+S +
Sbjct: 59 SGGFIKDSTVELFLSSKA 76
>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 = 42.2 bits (100), Expect = 3e-06
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 59 MRGLPFRVNEKDIVDFFSPVVPV-YVDINYKN-GRPSGEADVYFATHEDAMQAMSK-DRT 115
+ LP E+D+ D FS P+ + I GR G A V F EDA +A+ +
Sbjct: 3 VGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGK 62
Query: 116 NIRHRYIE 123
+ R +
Sbjct: 63 ELGGRELR 70
>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 = 41.3 bits (97), Expect = 7e-06
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVP--VYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
V RGLP++ +++DI FF + V + ++ GR +GEA + F E A+ +
Sbjct: 2 VRARGLPWQSSDQDIAQFFRGLNIAKGGVALCLS-AQGRRNGEALIRFVDQEHRDLALQR 60
Query: 113 DRTNIRHRYIELF 125
+ ++ RYIE++
Sbjct: 61 HKHHMGTRYIEVY 73
>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 = 40.9 bits (96), Expect = 1e-05
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQA-M 110
H + + GLPF V ++++ F V V + + ++G+P G A V + A QA +
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRL-VTNRSGKPKGLAYVEYENESSASQAVL 61
Query: 111 SKDRTNIRHRYIELFLNSSSP 131
D T I+ + I + + S+ P
Sbjct: 62 KMDGTEIKEKTISVAI-SNPP 81
>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 = 40.7 bits (95), Expect = 1e-05
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVPVYVDINYKN-GRPSGEADVYFATHEDAMQAM 110
+ ++ +PF V +I+DFF V+P V + + + G P+GEA V F + ++AM A+
Sbjct: 4 IKVQNMPFTVTVDEILDFFYGYQVIPGSVCLKFSDKGMPTGEAMVAFESRDEAMAAV 60
>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 = 41.1 bits (96), Expect = 1e-05
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 57 VHMRGLPFRVNEKDIVDFFSP--VVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSKD 113
V+++GLP+ K ++DFF +V + I Y NG+ +GE V F D A+ +
Sbjct: 12 VYLKGLPYEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 71
Query: 114 RTNIRHRYIEL 124
+ + +R+I++
Sbjct: 72 KQYMGNRFIQV 82
>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 = 40.7 bits (95), Expect = 2e-05
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVPVYVDINY-KNGRPSGEADVYFATHEDAMQAMSK 112
+ + LPF+ +I+DFF V+P V + Y + G P+G A V + +AM A+++
Sbjct: 3 IRLENLPFKATINEILDFFHGYRVIPDSVSMQYNEQGLPTGTAIVAMENYYEAMAAINE 61
>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 = 39.5 bits (92), Expect = 5e-05
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVV----PVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
V RGLP++ +++DI FF + V + +N GR +GEA V F E A+ +
Sbjct: 2 VRARGLPWQSSDQDIAKFFRGLNIAKGGVALCLN-PQGRRNGEALVRFTCTEHRDLALKR 60
Query: 113 DRTNIRHRYIELF 125
+ +I RYIE++
Sbjct: 61 HKHHIGQRYIEVY 73
>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 = 39.2 bits (92), Expect = 5e-05
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 4/68 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
TV + L + V E ++ FS + V + NYK G+ G A V F E +A+
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKL 59
Query: 113 DRTNIRHR 120
DR I+ R
Sbjct: 60 DRELIKGR 67
>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 = 37.6 bits (88), Expect = 2e-04
Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYK--NGRPSGEADVYFATHEDA 106
TV +R LPF E+++ + FS V Y I G G A V F T E A
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESA 55
>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 = 37.3 bits (87), Expect = 2e-04
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 60 RGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
R LPF E+++ + F + V++ ++ + R G A V F E A++A S
Sbjct: 5 RNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYS 59
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 39.2 bits (90), Expect = 3e-04
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 55 HTVHMRGLPFRVNEKDIVDFF---SPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+T+ + LP+ V E+D+ + F PV V + + + G+ G A V F + E A +A+
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAI 174
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 37.1 bits (86), Expect = 3e-04
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPV-VPVYVDINYKNGRPSGEADVYFATHEDAMQAM-SKD 113
+H+ LP V E+D+++ + V V V + NG+ +A V FAT E A +A+ K
Sbjct: 9 MIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKK--QALVEFATEEQATEALACKH 66
Query: 114 RTNIRHRYIEL 124
+++ I L
Sbjct: 67 ASSLNGSTIRL 77
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 77
Score = 37.0 bits (86), Expect = 3e-04
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 4/67 (5%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GLP++ E+D+ D+FS ++ V V + K G+ G V FA +ED ++ +S+ R I
Sbjct: 6 GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ-RHMI 64
Query: 118 RHRYIEL 124
R+ ++
Sbjct: 65 DGRWCDV 71
>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 = 36.8 bits (86), Expect = 4e-04
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRT 115
TV ++ LP E I FF + ++ A + F T ++A+ A++KD
Sbjct: 2 TVKVKNLPKDTTENKIRQFFKDCGEI-REVKIVESEGGLVAVIEFETEDEALAALTKDHK 60
Query: 116 NIRHRYIE 123
+ I
Sbjct: 61 RLGGNEIS 68
>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 = 36.5 bits (85), Expect = 4e-04
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKN-GRPSGEADVYFATHEDAMQAMSK 112
+ +R LPF V +D+ D F V D+ N GR G V F + EDA +A+
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEM 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 = 36.0 bits (84), Expect = 7e-04
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 69 KDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNIRHRYIELFLN 127
+++ F P+ VY+ + + G+ G A V F T EDA +A+ K N Y L L+
Sbjct: 17 RELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK--LN-GFGYDNLILS 72
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 36.1 bits (84), Expect = 7e-04
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPV---YVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
T+ +R LP+ ++ + +FFS V P+ +V + + + G V FA EDA +A+ +
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60
>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 = 36.1 bits (84), Expect = 8e-04
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 12/78 (15%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSP-------VVPVYVD--INYKNGRPSGEADVYFATHED 105
+++R L F+++E D+ FS +P D N G A V F
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNN---GFAFVTFKDASS 57
Query: 106 AMQAMSKDRTNIRHRYIE 123
A A+ + T + R I
Sbjct: 58 AENALQLNGTELGGRKIS 75
>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 = 35.6 bits (82), Expect = 0.001
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 62 LPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM-SKDRTNIRHR 120
L + +E + + F + + N NGRP G A V F + EDA +A+ S + T I R
Sbjct: 9 LSYSASEDSLQEVFEKATSIRIPQN--NGRPKGYAFVEFESAEDAKEALNSCNNTEIEGR 66
Query: 121 YIEL 124
I L
Sbjct: 67 SIRL 70
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 34.9 bits (81), Expect = 0.002
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+++ GL V+EK + F P + + + ++Y+ + G A V F EDA A+
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57
>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 = 35.3 bits (81), Expect = 0.002
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 10/79 (12%)
Query: 57 VHMRGLPFRVNEKDIV----DFFSPVVPVYVDINYKN-GRPSGEADVYFATHEDAMQAMS 111
+ +RGLP+ + I+ DF +V V + Y G+PSGEA + + + A
Sbjct: 4 IRLRGLPYEAQVEHILEFLGDFAKMIVFQGVHMVYNAQGQPSGEAFIQMDSEQSASACAQ 63
Query: 112 KDRTNI-----RHRYIELF 125
+ + RYIE+F
Sbjct: 64 QRHNRYMVFGKKQRYIEVF 82
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. SKAR is
widely expressed and localizes to the nucleus. It may be
a critical player in the function of S6K1 in cell and
organism growth control by binding the activated,
hyperphosphorylated form of S6K1 but not S6K2.
Furthermore, SKAR functions as a protein partner of the
p50 subunit of DNA polymerase delta. In addition, SKAR
may have particular importance in pancreatic beta cell
size determination and insulin secretion. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 34.6 bits (80), Expect = 0.002
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ + L V E DIV+ FS + + + RP G A+V + +DA+ A+ K
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLV----RP-GVAEVVYVRKDDALTAIDK 54
>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 = 34.7 bits (80), Expect = 0.003
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 75 FSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM-SKDRTNIRHRYIEL 124
+ P+V VY+ +++ RP G A V F DA A+ DRT R IE+
Sbjct: 24 YGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEI 74
>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 = 34.4 bits (80), Expect = 0.003
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 7/54 (12%)
Query: 62 LPFRVNEKDIVDFFSPVVP-----VYVDINYKNGRPSGEADVYFATHEDAMQAM 110
L V E + + FSP P V D+ R G A V F DA +A+
Sbjct: 7 LHPDVTEAMLYEIFSPAGPVLSIRVCRDLI--TRRSLGYAYVNFQNPADAERAL 58
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 34.5 bits (80), Expect = 0.003
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ + GL R EK++ FS V V + + + G G V F + EDA A+
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62
Query: 113 -DRTNIRHRYI 122
+ + R I
Sbjct: 63 LNGKELEGRVI 73
>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 = 34.2 bits (79), Expect = 0.004
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINY---KNGRPSGEADVYFATHEDAMQAMS 111
+ +H+ LPF V ++DI FF + I + K G+ + A V F + D A++
Sbjct: 1 YYIHLENLPFSVEKRDIRAFFGDLDLPDSQITFLSDKKGKRTRSAFVMFKSLRDYCAALA 60
Query: 112 KDRTNIRHRYIELF 125
+ + +R + +F
Sbjct: 61 HHKRVLYNREVYVF 74
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 34.4 bits (79), Expect = 0.004
Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 57 VHMRGLPFRVNEKDIVDFFSP--VVPV-------YVDINYKNGRPSGEADVYFATHEDAM 107
+++ LP + ++ +F+ V PV + Y + + S F +HE+AM
Sbjct: 3 LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62
Query: 108 QAMS 111
+A++
Sbjct: 63 EALA 66
>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 = 34.2 bits (78), Expect = 0.004
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVV----PVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ RGLP++ +++DI FF + V + +N + GR +GEA V F E A+ +
Sbjct: 2 IRARGLPWQSSDQDIARFFKGLNIAKGGVALCLNAQ-GRRNGEALVRFVNSEQRDLALQR 60
Query: 113 DRTNIRHRYIELF 125
+ ++ RYIE++
Sbjct: 61 HKHHMGSRYIEVY 73
>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 = 33.9 bits (78), Expect = 0.004
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 56 TVHMRGLPFRVNEKDIVDFF--SPVVPVYVDI-NYKNGRPSGEADVYFATHEDAMQAMSK 112
T ++ LP+ V E+DI +FF V V + GR G F + +QA+S
Sbjct: 3 TAYLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSL 62
Query: 113 DRTNIRHRYI 122
+ ++++R I
Sbjct: 63 NDESLKNRRI 72
>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 = 33.8 bits (77), Expect = 0.006
Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 5/73 (6%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVV----PVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ RGLP++ +++DI FF + + +N + GR +GEA V F + E A+ +
Sbjct: 7 IRARGLPWQSSDQDIARFFKGLNIAKGGAALCLNAQ-GRRNGEALVRFVSEEHRDLALQR 65
Query: 113 DRTNIRHRYIELF 125
+ ++ +RYIE++
Sbjct: 66 HKHHMGNRYIEVY 78
>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 = 33.3 bits (77), Expect = 0.006
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDI----NYKNGRPSGEADVYFATHEDAMQAM 110
TV + L +V E+D+ +FFS V D+ + + R G A V F E A+
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKV-RDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58
>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 = 33.4 bits (77), Expect = 0.007
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+++ LP+ V E+D+ D F V V + + GR G V T E+A A+ K
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 33.3 bits (77), Expect = 0.009
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 62 LPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
LP E+D+ F + V + + G+ G A V F++ E+A +A+
Sbjct: 7 LPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAI 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 = 33.0 bits (76), Expect = 0.010
Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
GL E+D+ + FS P+ V V + K GR G VYF + EDA +A K+R N
Sbjct: 6 GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEA--KERLN 62
>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 = 33.1 bits (75), Expect = 0.012
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
+ ++GLP DI FFS + ++ G GEA + FAT EDA M +
Sbjct: 5 IRLQGLPIVAGTMDIRHFFSGLTIPDGGVHIVGGE-LGEAFIVFATDEDARLGMMRTGGT 63
Query: 117 IRHRYIELFLNSSS 130
I+ + L L+S +
Sbjct: 64 IKGSKVSLLLSSKT 77
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 32.9 bits (76), Expect = 0.013
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVD----INYKNGRPS-GEADVYFATHEDAMQA 109
+T+ +RGL E+DI+ S + V + I K S G A V F + EDA Q
Sbjct: 3 NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQW 62
Query: 110 MS 111
M
Sbjct: 63 MD 64
>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 = 32.9 bits (75), Expect = 0.014
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 58 HMRGLPFRVNEKDIVDFFSPV------VPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
H+ +P+ + +KDI+ F + V V VD NG+ G+A V F + +DA ++
Sbjct: 3 HISNIPYSITKKDILQFLEGIGVDENSVQVLVD---NNGQGLGQALVQFKSEDDARKSER 59
Query: 112 KDRTNIRHR 120
R + R
Sbjct: 60 LHRKKLNGR 68
>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 = 32.6 bits (74), Expect = 0.014
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 75 FSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRTNIRHRYIEL 124
+ P+V VYV +++ RP G A V F DA A+ DR I R IE+
Sbjct: 24 YGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEI 74
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 31.8 bits (73), Expect = 0.026
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 13/59 (22%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPV-----VPVYVDINYKNGRPSGEADVYFATHEDAMQA 109
TV++ LP + E+++ FSP V V+ D Y A V F THE A A
Sbjct: 2 TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGY--------AFVRFDTHEAAATA 52
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 31.9 bits (72), Expect = 0.027
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
GL E+D+ + FS P+ V V + + GR G A VYF +D+ +AM
Sbjct: 6 GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60
>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 = 31.8 bits (73), Expect = 0.027
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYK-NGRPSGEADVYFATHEDAMQAMSK 112
+ +R +PF +K++ + FSP V V + K +G G A V F T ++A AM
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 31.2 bits (71), Expect = 0.049
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPSGEADVYFATHEDAMQAMSKD 113
T+H+ G+ ++E D+ +FFS V V + + A V FA E A+ A++
Sbjct: 2 TIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALNLS 60
>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 = 30.8 bits (70), Expect = 0.060
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINYK----NGRPSGEADVYFATHEDAMQAMSK 112
V++ G+P+ E +I +FS + +++ GR G A + F T E A +A++
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEI-EELDLMTFPDTGRFRGIAFITFKTEEAAKRALAL 59
Query: 113 DRTNIRHRYI 122
D ++ R++
Sbjct: 60 DGEDMGGRFL 69
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 31.0 bits (71), Expect = 0.065
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 24/75 (32%)
Query: 61 GLPFRVNEKDIVDFFS--------------PVVPVYV--DINYKNGRPSGEADVYFATHE 104
LP + E+++VDFF+ PV+ V + + N+ A V F T E
Sbjct: 8 NLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNF--------AFVEFRTVE 59
Query: 105 DAMQAMSKDRTNIRH 119
+A A++ D +
Sbjct: 60 EATAALALDGIIFKG 74
>gnl|CDD|240889 cd12443, RRM_MCM3A_like, RNA recognition motif in 80 kDa
MCM3-associated protein (Map80) and similar proteins.
This subfamily corresponds to the RRM of Map80, also
termed germinal center-associated nuclear protein
(GANP), involved in the nuclear localization pathway of
MCM3, a protein necessary for the initiation of DNA
replication and also involves in controls that ensure
DNA replication is initiated once per cell cycle. Map80
contains one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 73
Score = 30.4 bits (69), Expect = 0.070
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 11/74 (14%)
Query: 56 TVHMRGLPFRVNEKDIVD-FFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
T+ + +P +N+KD ++ F V VY + K+ A V+F H A A
Sbjct: 2 TIQCKNIPDELNDKDWLERHFGKFGKVARVYCNPRKKS------AVVHFFDHASAALAKK 55
Query: 112 KDRTNIRHRYIELF 125
K + ++H+ I++F
Sbjct: 56 KGK-LLQHKPIQIF 68
>gnl|CDD|240960 cd12516, RRM1_RBM26, RNA recognition motif 1 of vertebrate
RNA-binding protein 26 (RBM26). This subgroup
corresponds to the RRM1 of RBM26, also known as
cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2,
which 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. .
Length = 76
Score = 30.8 bits (69), Expect = 0.072
Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 89 NGRPSGEADVYFATHEDAMQAMSKDRTNIRHRYIELF 125
G P G A + FATHE+A +A+S + +R+I+++
Sbjct: 37 KGDPEG-ALIQFATHEEAKKAISSTEAVLNNRFIKVY 72
>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 = 32.1 bits (73), Expect = 0.092
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 57 VHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
++++ L VNE + + F+ + V + +GR G A V F HEDA +A+ +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEE 238
Score = 30.9 bits (70), Expect = 0.21
Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 11/80 (13%)
Query: 66 VNEKDIVDFFSPVVPVY-----VDINYKNGRPSGEADVYFATHEDAMQAM-SKDRTNIRH 119
V E + D F P PV D R G V F DA +A+ + + +
Sbjct: 12 VTEAKLYDLFKPFGPVLSVRVCRDSV--TRRSLGYGYVNFQNPADAERALETMNFKRLGG 69
Query: 120 RYIELFLNSSSP---RGGVG 136
+ I + + P R GVG
Sbjct: 70 KPIRIMWSQRDPSLRRSGVG 89
>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein
Vip1 and similar proteins. This subfamily corresponds
to Vip1, an RNA-binding protein encoded by gene vip1
from fission yeast Schizosaccharomyces pombe. Its
biological role remains unclear. Vip1 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 68
Score = 30.2 bits (68), Expect = 0.098
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
V++ + + EK I DFFS + +++ N S A + F A A+ D
Sbjct: 1 VYVSNISPKTTEKQISDFFSFCGKI-SNLDLTNDGESQTATITFEKPSAAKTALLLDNAL 59
Query: 117 IRHRYIEL 124
+ + I++
Sbjct: 60 LGGKVIQV 67
>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 = 30.1 bits (68), Expect = 0.11
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 59 MRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+R L + E+D+ FS P+ V++ I+ +P G A V + E A++A +
Sbjct: 7 IRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFA 62
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 30.1 bits (68), Expect = 0.11
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNG-RPSGEADVYFATHEDAMQAM 110
TV++ LP + E+++ D F P+ VDI+ K RP G A + F DA A+
Sbjct: 1 TVYVGNLPGDIREREVEDLFYKYGPI-VDIDLKLPPRPPGYAFIEFEDARDAEDAI 55
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 30.0 bits (67), Expect = 0.14
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
GL E+D+ + FS P+ V + + ++ R G A VYF +DA +A K+R N
Sbjct: 16 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA--KERAN 72
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM1 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 87
Score = 30.0 bits (67), Expect = 0.17
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 4/81 (4%)
Query: 56 TVHMRGLPFRVNEKDI---VDFFSPVVPVYVDI-NYKNGRPSGEADVYFATHEDAMQAMS 111
T+ +RGLP + E DI ++ F P V + K G G A V F +DA M
Sbjct: 7 TIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDATSWME 66
Query: 112 KDRTNIRHRYIELFLNSSSPR 132
++ + + + ++ S+PR
Sbjct: 67 ANQKKLVIQGKTIAMHYSNPR 87
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed in
all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. The family also
includes yeast ortholog mRNA 3'-end-processing protein
RNA15 and similar proteins. RNA15 is a core subunit of
cleavage factor IA (CFIA), an essential transcriptional
3'-end processing factor from Saccharomyces cerevisiae.
RNA recognition by CFIA is mediated by an N-terminal
RRM, which is contained in the RNA15 subunit of the
complex. The RRM of RNA15 has a strong preference for
GU-rich RNAs, mediated by a binding pocket that is
entirely conserved in both yeast and vertebrate RNA15
orthologs.
Length = 75
Score = 29.5 bits (67), Expect = 0.19
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 9/55 (16%)
Query: 62 LPFRVNEKDIVDFFSPVVPVYVDINYK------NGRPSGEADVYFATHEDAMQAM 110
+P+ E+ +++ FS V PV ++++ G+P G F E A A+
Sbjct: 6 IPYDATEEQLIEIFSEVGPV---VSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 29.5 bits (66), Expect = 0.20
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQA 109
GL V E D+ + FS PV V + + G+ G VYF H+ A +A
Sbjct: 6 GLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 29.3 bits (66), Expect = 0.20
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHEDAMQAMSK- 112
+ + + L RV+ +D+ DF V Y D + + E V FAT+ D +A+ K
Sbjct: 1 YRLIVENLSSRVSWQDLKDFMRKAGEVTYAD---AHKQRPNEGVVEFATYSDMKRAIEKL 57
Query: 113 DRTNIRHRYIEL 124
D T + R I+L
Sbjct: 58 DGTELNGRKIKL 69
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 29.4 bits (66), Expect = 0.21
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRTN 116
G+ F+ NE D+ FFS V V + +N + G G V F T EDA + + + +R
Sbjct: 9 GIDFKTNENDLRKFFSQYGTVKEVKI-VNDRAGVSKGYGFVTFETQEDAQKILQEANRLC 67
Query: 117 IRHR 120
R +
Sbjct: 68 FRDK 71
>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 = 29.5 bits (67), Expect = 0.21
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 4/72 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ + G+P E+++ DFFS V V + I + G G V F T EDA + ++
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKI-ITDRAGVSKGYGFVTFETQEDAEKILAM 62
Query: 113 DRTNIRHRYIEL 124
N R + + +
Sbjct: 63 GNLNFRGKKLNI 74
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 29.4 bits (67), Expect = 0.22
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 16/61 (26%)
Query: 57 VHMRGLPFRVNEKDIVDFFS-------------PVVPVYVDINYKNGRPSGEADVYFATH 103
V++ GLP + ++ V+ FS P + +Y D +NG G+A +
Sbjct: 4 VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRD---ENGNLKGDALCCYLKE 60
Query: 104 E 104
E
Sbjct: 61 E 61
>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional.
Length = 243
Score = 30.6 bits (69), Expect = 0.23
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFS 76
PG +T + L + EKD+ DFFS
Sbjct: 3 PGGYTAEVTNLSPKATEKDVYDFFS 27
>gnl|CDD|181053 PRK07590, PRK07590, L,L-diaminopimelate aminotransferase;
Validated.
Length = 409
Score = 30.6 bits (70), Expect = 0.24
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 10/36 (27%)
Query: 71 IVDFFS---------PVVPVYVDINYKNGRPSGEAD 97
I+D F PV PVYVD N GR +GEA+
Sbjct: 115 ILDIFGPDNTIAVTDPVYPVYVDTNVMAGR-TGEAN 149
>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 = 29.1 bits (66), Expect = 0.27
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQA 109
+ + GLP+ + + +FS + V + + G+ G V F E A +A
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA 58
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 28.7 bits (65), Expect = 0.34
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 62 LPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK-DRTNI 117
L F E+ I + FS + + + ++ P G V + T EDA A+ + T +
Sbjct: 6 LSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKL 65
Query: 118 RHRYI 122
R I
Sbjct: 66 DDRII 70
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 28.8 bits (65), Expect = 0.35
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 78 VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
V V + N + G+ +G V FATHE A QA+
Sbjct: 26 VTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 28.8 bits (65), Expect = 0.38
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 6/54 (11%)
Query: 65 RVNEKDIVDFFSPVVPV------YVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
R+ E ++ FS + + G+P G V F T E+A +A+
Sbjct: 10 RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKS 63
>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 = 28.6 bits (64), Expect = 0.41
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDIN--YKN-GRPSGEADVYFATHEDAMQA 109
++ R PF V + ++ FF+P DI Y + G GEA V F + E AM+A
Sbjct: 3 IYARNFPFDVTKVEVQKFFAPFNIDEDDIYLLYDDKGVGLGEALVKFKSEEQAMKA 58
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 28.4 bits (64), Expect = 0.41
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 19/68 (27%)
Query: 57 VHMRGLPFRVNEKDIVDFFS-------------PVVPVYVDINYKNGRPSGEADVYFATH 103
+++ GLP V E + + F P++ +Y D K P GEA V T+
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTD---KETEPKGEATV---TY 54
Query: 104 EDAMQAMS 111
+D A +
Sbjct: 55 DDPSAAQA 62
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, may play an important role in
mRNA generation, processing and degradation in several
cell types. The rat homolog of human RBM10 is protein
S1-1, a hypothetical RNA binding protein with poly(G)
and poly(U) binding capabilities. Both, RBM5 and RBM10,
contain two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two C2H2-type zinc fingers, and a G-patch/D111
domain. .
Length = 81
Score = 28.5 bits (64), Expect = 0.47
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGE----ADVYFATHEDAMQAM 110
T+ +RGLP V E+DI + D+ + +G A V F + E+A + M
Sbjct: 4 TIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWM 62
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma
Protein (EWS). This subgroup corresponds to the RRM of
EWS, also termed Ewing sarcoma breakpoint region 1
protein, a member of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the FET
family, EWS contains an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U RNA.
It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor gene.
.
Length = 84
Score = 28.3 bits (63), Expect = 0.49
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 15/58 (25%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS-------------PVVPVYVDINYKNGRPSGEADVYF 100
T++++GL V +++ DFF P+V +Y D + G+P G+A V +
Sbjct: 2 TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTD--KETGKPKGDATVSY 57
>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 = 0.56
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
+H+R LP V E D++ SP V N R +A V + E A + T
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKV---TNVLLLRGKNQALVEMDSVESAKSMVDYYLTV 58
Query: 117 ---IRHRYIELFLNSSS 130
IR R +++ S+
Sbjct: 59 PALIRGR--RVYIQYSN 73
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 27.4 bits (61), Expect = 0.87
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGR-PSGEADVYFATHEDAMQAM 110
+++ LP + E+DI D F P+ I+ KN R A V F DA A+
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPI-KAIDLKNRRRGPPFAFVEFEDPRDAEDAV 55
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 27.8 bits (62), Expect = 0.92
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFF-SPVVPV-YVDINY-KNGRPSGEADVYFATHEDAMQAMSK 112
V + LP V E I ++F S + P+ V ++Y + G+ +G A++ F DA +A K
Sbjct: 2 VIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 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 = 0.95
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 75 FSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM-SKDRTNIRHRYIEL 124
+ P+V VYV +++ RP G A + F DA A+ + +R + R IE+
Sbjct: 24 YGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEI 74
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 27.3 bits (61), Expect = 1.0
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GLP V E D+ +FS V V V +++ RP G + F + + Q +++ +I
Sbjct: 9 GLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEHFHDI 68
Query: 118 RHRYIE 123
+ +E
Sbjct: 69 NGKKVE 74
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 27.6 bits (61), Expect = 1.1
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+H+R LP+ E+++++ P + V+ G +A V FA A+ +S
Sbjct: 5 LHLRNLPWECTEEELIELCKPFGKI-VNTKCNVGANRNQAFVEFADLNQAIAMVS 58
>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 = 27.2 bits (61), Expect = 1.2
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 60 RGLPFRVNEKDIVDFFSPVVPVYVDINY---KNGRPSGEADVYFATHEDAMQA 109
R LPF+ E D+ FSP V ++ +G+ G A V F + DA +A
Sbjct: 5 RNLPFKCTEADLKKLFSPFGFV-WEVTIPRKPDGKKKGFAFVQFTSKADAEKA 56
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 80
Score = 27.3 bits (61), Expect = 1.3
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPV-YV 83
VH+RGLP V E D+V+ S P+ YV
Sbjct: 5 VHVRGLPDGVTEADLVEALSEFGPISYV 32
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 27.2 bits (61), Expect = 1.3
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 56 TVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAM 107
V++ LP E ++ +FS V + + + K G+ G A V F + E A
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAK 55
>gnl|CDD|178207 PLN02597, PLN02597, phosphoenolpyruvate carboxykinase [ATP].
Length = 555
Score = 28.6 bits (64), Expect = 1.4
Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 12/89 (13%)
Query: 34 GGFAGPRPGDRWV--NESS------GPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDI 85
G G P D+ V +E++ G G + M F VN + VD+ + + V+V+
Sbjct: 68 GAKTGRSPKDKRVVRDETTEDELWWGKGSPNIEMDEETFLVNRERAVDYLNSLDKVFVND 127
Query: 86 NYKNGRPSGEADVYF----ATHEDAMQAM 110
+ N P V A H M M
Sbjct: 128 QFLNWDPENRIKVRIVSARAYHSLFMHNM 156
>gnl|CDD|240392 PTZ00381, PTZ00381, aldehyde dehydrogenase family protein;
Provisional.
Length = 493
Score = 28.5 bits (64), Expect = 1.4
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 11/75 (14%)
Query: 75 FSPVVPV--YVDI----NYKNGRPSGEADVYFATHEDAMQAMSKDRTNIRHRYIE----L 124
F P++P+ Y +I + N RP A YF + + + + T+ I
Sbjct: 343 FGPILPILTYENIDEVLEFINSRPKPLALYYFGEDK-RHKELVLENTSSGAVVINDCVFH 401
Query: 125 FLNSSSPRGGVGGSG 139
LN + P GGVG SG
Sbjct: 402 LLNPNLPFGGVGNSG 416
>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 = 26.7 bits (60), Expect = 1.5
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 62 LPFRVNEKDIVDFFSPVVPV-YVDI--NYKNGRPSGEADVYFATHEDAMQAMSKDRTNIR 118
LPF + E+++ F V V I + K G G V F T + A+ + ++
Sbjct: 7 LPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNGIKLK 66
Query: 119 HRYIELF 125
R I +
Sbjct: 67 GRKIRVK 73
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM4 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 26.9 bits (60), Expect = 1.7
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSP 77
T+H+ +P V E+D+ + F+
Sbjct: 1 TLHLSNIPPSVTEEDLKELFTQ 22
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 26.8 bits (59), Expect = 1.8
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHEDAMQA 109
+ +R LPF K + D F+ V Y DI +NG+ G V F + E A +A
Sbjct: 2 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVRFESPEVAERA 55
>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 = 26.7 bits (60), Expect = 1.8
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 66 VNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
VN+ + + FS V V + I+ + P G A V F + EDA +A+
Sbjct: 10 VNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58
>gnl|CDD|143406 cd07087, ALDH_F3-13-14_CALDH-like, ALDH subfamily: Coniferyl
aldehyde dehydrogenase, ALDH families 3, 13, and 14, and
other related proteins. ALDH subfamily which includes
NAD(P)+-dependent, aldehyde dehydrogenase, family 3
member A1 and B1 (ALDH3A1, ALDH3B1, EC=1.2.1.5) and
fatty aldehyde dehydrogenase, family 3 member A2
(ALDH3A2, EC=1.2.1.3), and also plant ALDH family
members ALDH3F1, ALDH3H1, and ALDH3I1, fungal ALDH14
(YMR110C) and the protozoan family 13 member (ALDH13),
as well as coniferyl aldehyde dehydrogenases (CALDH,
EC=1.2.1.68), and other similar sequences, such as the
Pseudomonas putida benzaldehyde dehydrogenase I that is
involved in the metabolism of mandelate.
Length = 426
Score = 27.9 bits (63), Expect = 2.4
Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 21/83 (25%)
Query: 75 FSPVVPVYVDINYKNGRPSGEADVYFATHED--AMQAMSKDRTNIRHRYIEL-------- 124
F P++P+ + Y + EA + + A+ S+D+ E
Sbjct: 332 FGPILPI---LTYDD---LDEAIEFINSRPKPLALYLFSEDKAVQERVLAETSSGGVCVN 385
Query: 125 -----FLNSSSPRGGVGGSGFSR 142
+ P GGVG SG
Sbjct: 386 DVLLHAAIPNLPFGGVGNSGMGA 408
>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 = 26.6 bits (59), Expect = 2.4
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 56 TVHMRGLPFRVNEKDIVDF---FSPV---VPVYVDINYKNG--RPSGEADVYFATHEDAM 107
V++ L + +E+D+ +F F PV +P +++ RP G A F++ E A
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60
Query: 108 QA 109
+
Sbjct: 61 KV 62
>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 = 26.1 bits (58), Expect = 2.6
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 61 GLPFRVNEKDIVDFFSPVVPV-YVDINY--KNGRPSGEADVYFATHEDAMQAMSK 112
L F + E D+ F P + +V + + GR G + FA EDA +A+ +
Sbjct: 5 NLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 26.0 bits (58), Expect = 2.8
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFF---SPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
V++ L +V E+ + + F PVV V++ + G V F + EDA A+
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIK 58
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other EJC
components (such as Magoh, Aly/REF, RNPS1, Srm160, and
Upf3), plays critical roles in postsplicing processing,
including nuclear export and cytoplasmic localization of
the mRNA, and the nonsense-mediated mRNA decay (NMD)
surveillance process. RBM8 binds to mRNA 20-24
nucleotides upstream of a spliced exon-exon junction. It
is also involved in spliced mRNA nuclear export, and the
process of nonsense-mediated decay of mRNAs with
premature stop codons. RBM8 forms a specific heterodimer
complex with the EJC protein Magoh which then associates
with Aly/REF, RNPS1, DEK, and SRm160 on the spliced
mRNA, and inhibits ATP turnover by eIF4AIII, thereby
trapping the EJC core onto RNA. RBM8 contains an
N-terminal putative bipartite nuclear localization
signal, one RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
in the central region, and a C-terminal serine-arginine
rich region (SR domain) and glycine-arginine rich region
(RG domain). .
Length = 88
Score = 26.4 bits (59), Expect = 3.0
Identities = 10/48 (20%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 68 EKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
E+D+ D F+ + ++++++ + G G A + + T ++A A+
Sbjct: 20 EEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67
>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 = 26.1 bits (58), Expect = 3.4
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 90 GRPSGEADVYFATHEDAMQAMSKDRTNIRHRYIELFLNSSSPR 132
GR +GE V F+ A A+ + FL ++SPR
Sbjct: 37 GRSTGEGIVEFSRKPGAQAAIKRCSEG-------CFLLTASPR 72
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 77
Score = 26.1 bits (58), Expect = 3.6
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 60 RGLPFRVNEKDIVDFFSPVVPVYVDINY---KNGRPSGEADVYFATHEDAMQA 109
+ LP + E ++ + FS D+ ++G+ A + + T E+A +A
Sbjct: 6 KNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKA 58
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation factor
64 kDa subunit (CstF64), is the vertebrate conterpart of
yeast mRNA 3'-end-processing protein RNA15. It is
expressed in all somatic tissues and is one of three
cleavage stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. .
Length = 75
Score = 25.9 bits (57), Expect = 3.8
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 62 LPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+P+ E+ + D FS PVV + + + G+P G + E A+ AM
Sbjct: 6 IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAM 57
>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM1 of the CPEB family of proteins
that bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins have been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bind to a protein such as maskin or
neuroguidin, which blocks translation initiation through
interfering with the assembly of eIF-4E and eIF-4G.
Although CPEB-1 is mainly located in cytoplasm, it can
shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to high sequence similarity, members in
this subfamily may share similar expression patterns and
functions. CPEB-2 is an RNA-binding protein that is
abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
CPEB-2 impedes target RNA translation at elongation; it
directly interacts with the elongation factor, eEF2, to
reduce eEF2/ribosome-activated GTP hydrolysis in vitro
and inhibit peptide elongation of CPEB2-bound RNA in
vivo. CPEB-3 is a sequence-specific translational
regulatory protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 112
Score = 26.5 bits (58), Expect = 4.0
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
V + GLP+ + E DI++ F + VD K+ ++D +E + +++ D+
Sbjct: 3 VFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDSD-PSLCNEKSDGSINGDKGQ 61
Query: 117 IRHRYIEL 124
Y+ L
Sbjct: 62 HPKGYVFL 69
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 26.1 bits (58), Expect = 4.0
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINY----KNGRPSGEADVYFATHED 105
+++ GLP+ + E DI+ FS + VDIN K G+ G A F +ED
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEI-VDINLVRDKKTGKSKGFA---FLAYED 60
>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 = 25.7 bits (56), Expect = 4.6
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+++ GLP + +KD+ D FS ++ V ++ G G A + F +A +A++
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT 60
>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 = 25.4 bits (56), Expect = 4.6
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNG 90
V++ LP+R E+D+ FF + +IN KNG
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIR-EINLKNG 34
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 25.4 bits (56), Expect = 4.9
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPVY-VDINYKNGRPS-GEADVYFATHEDAMQAMSK-D 113
+H+ +PFR + D+ F P+ V+I + N R S G V FA DA +A K
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIF-NERGSKGFGFVTFANSADADRAREKLH 61
Query: 114 RTNIRHRYIEL 124
T + R IE+
Sbjct: 62 GTVVEGRKIEV 72
>gnl|CDD|204371 pfam09996, DUF2237, Uncharacterized protein conserved in bacteria
(DUF2237). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 117
Score = 25.9 bits (58), Expect = 5.3
Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 5/27 (18%)
Query: 24 FNNDRWND----RPG-GFAGPRPGDRW 45
F+ R ND RP GF G +PGDRW
Sbjct: 49 FSKSRGNDLSTPRPEFGFPGLKPGDRW 75
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia 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 = 25.6 bits (57), Expect = 5.4
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 4/38 (10%)
Query: 75 FSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
F PV + VD N P G V F T E A + +
Sbjct: 35 FGPVEHIKVDKN----SPEGVVYVKFKTVEAAQKCIQA 68
>gnl|CDD|163316 TIGR03542, DAPAT_plant, LL-diaminopimelate aminotransferase. This
clade of the pfam00155 superfamily of aminotransferases
includes several which are adjacent to elements of the
lysine biosynthesis via diaminopimelate pathway
(GenProp0125). This clade includes characterized species
in plants and Chlamydia. Every member of this clade is
from a genome which possesses most of the lysine
biosynthesis pathway but lacks any of the known
succinylases, desuccinylases, acetylases or deacetylases
typical of the acylated versions of this pathway nor do
they have the direct, NADPH-dependent enzyme (ddh).
Length = 402
Score = 26.6 bits (59), Expect = 5.9
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 77 PVVPVYVDINYKNGRPSGEAD 97
PV P Y+D N GR +G D
Sbjct: 126 PVYPAYLDSNVMAGR-AGVLD 145
>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 = 26.4 bits (58), Expect = 6.6
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPV 81
TV + L + E+D+ +FFS V V
Sbjct: 91 TVFVLQLALKARERDLYEFFSKVGKV 116
>gnl|CDD|233494 TIGR01616, nitro_assoc, nitrogenase-associated protein. This model
describes a small family of uncharacterized proteins
found so far in alpha and gamma proteobacteria and in
Nostoc sp. PCC 7120, a cyanobacterium. The gene for this
protein is associated with nitrogenase genes. This
family shows sequence similarity to TIGR00014, a
glutaredoxin-dependent arsenate reductase that converts
arsentate to arsenite for disposal. This family is one
of several included in pfam03960 [Unknown function,
General].
Length = 126
Score = 25.7 bits (56), Expect = 6.9
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 8/52 (15%)
Query: 93 SGEADVYFATHEDAMQAMSKDRTNIRHRYIELFLNSSSPRGGVGGSGFSRSE 144
SGE + A+ M D IR ++L GG+ +GF R
Sbjct: 65 SGEVNPDSIDEASALALMVSDPLLIRRPLMDL--------GGIRCAGFDREP 108
>gnl|CDD|173858 cd08493, PBP2_DppA_like, The substrate-binding component of an
ABC-type dipeptide import system contains the type 2
periplasmic binding fold. This family represents the
substrate-binding domain of an ATP-binding cassette
(ABC)-type dipeptide import system. The DppA binds
dipeptides and some tripeptides and is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 amino acid
residues) and plays a role in recycling of cell wall
peptides, which precludes any involvement in chemotaxis.
Most of other periplasmic binding proteins are
comprised of only two globular subdomains corresponding
to domains I and III of the dipeptide/oligopeptide
binding proteins. The structural topology of these
domains is most similar to that of the type 2
periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 26.4 bits (59), Expect = 6.9
Identities = 19/88 (21%), Positives = 26/88 (29%), Gaps = 22/88 (25%)
Query: 23 CFNNDRWNDRPGGFAGPRPGDRWVNESSGPGH----------HTVHMRGLPFRVNEKDIV 72
F+ +RW D + G S G G +TV F + D
Sbjct: 83 VFSFNRWLDPNHPYHKVGGGGYPYFYSMGLGSLIKSVEAVDDYTVK-----FTLTRPDAP 137
Query: 73 -------DFFSPVVPVYVDINYKNGRPS 93
F S + P Y D G+P
Sbjct: 138 FLANLAMPFASILSPEYADQLLAAGKPE 165
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 25.3 bits (56), Expect = 7.5
Identities = 16/69 (23%), Positives = 23/69 (33%), Gaps = 18/69 (26%)
Query: 60 RGLPFRVNEKDIVDFFSPVVPVYVDINY------------------KNGRPSGEADVYFA 101
R LP V+EK + + F V G+ G V F
Sbjct: 6 RNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFT 65
Query: 102 THEDAMQAM 110
HE A++A+
Sbjct: 66 NHEHALKAL 74
>gnl|CDD|143419 cd07101, ALDH_SSADH2_GabD2, Mycobacterium tuberculosis
succinate-semialdehyde dehydrogenase 2-like.
Succinate-semialdehyde dehydrogenase 2 (SSADH2) and
similar proteins are in this CD. SSADH1 (GabD1,
EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation
of succinate semialdehyde to succinate. SSADH activity
in Mycobacterium tuberculosis is encoded by both gabD1
(Rv0234c) and gabD2 (Rv1731), however ,the Vmax of GabD1
was shown to be much higher than that of GabD2, and
GabD2 (SSADH2) is likely to serve physiologically as a
dehydrogenase for a different aldehyde(s).
Length = 454
Score = 26.5 bits (59), Expect = 7.6
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 10/78 (12%)
Query: 75 FSPVVPVY----VD--INYKNGRPSG-EADVYFATHEDAMQAMSKDRT---NIRHRYIEL 124
F PVV +Y D I N G A V+ + ++ R N+ Y
Sbjct: 359 FGPVVSIYRVADDDEAIELANDTDYGLNASVWTRDGARGRRIAARLRAGTVNVNEGYAAA 418
Query: 125 FLNSSSPRGGVGGSGFSR 142
+ + +P GG+ SG R
Sbjct: 419 WASIDAPMGGMKDSGLGR 436
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 25.0 bits (55), Expect = 8.2
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
P H + + LP + E ++ +FF V+ V ++ GR V F E +
Sbjct: 1 PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60
Query: 109 AMSKDRTNIRH 119
++ R
Sbjct: 61 ILANKPIYFRG 71
>gnl|CDD|240707 cd12261, RRM1_3_MRN1, RNA recognition motif 1 and 3 in RNA-binding
protein MRN1 and similar proteins. This subfamily
corresponds to the RRM1 and RRM3 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
which is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 73
Score = 24.9 bits (55), Expect = 8.5
Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 10/64 (15%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVV---PVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
TV++ LP +DI+ + P+ I + S V F A +
Sbjct: 2 TVYLGNLPEDTTIRDILS----AIRGGPLE-SIKLLPTKNSAT--VSFLDEAAAEAFYAY 54
Query: 113 DRTN 116
R N
Sbjct: 55 ARNN 58
>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 = 24.8 bits (54), Expect = 8.9
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GL + +KD+ ++FS VV + I+ GR G V F + + + +
Sbjct: 5 GLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQKEHKL 64
Query: 118 RHRYIE 123
R I+
Sbjct: 65 DGRVID 70
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 24.5 bits (54), Expect = 9.1
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGE-ADVYFATHEDAMQAMSK 112
T+++ GL RV EKD+ D F + +I P + A V F T E A +A +
Sbjct: 3 TLYVGGLGERVTEKDLRDHFYQ----FGEIRSITVVPRQQCAFVTFTTREAAEKAAER 56
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.136 0.435
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: 7,948,262
Number of extensions: 702314
Number of successful extensions: 873
Number of sequences better than 10.0: 1
Number of HSP's gapped: 801
Number of HSP's successfully gapped: 156
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.9 bits)