RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16454
(304 letters)
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM1 in hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 78
Score = 141 bits (357), Expect = 1e-42
Identities = 49/78 (62%), Positives = 62/78 (79%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLFIGGL Y T+ ++LK++F WG++ D VVMKDP TK+SRGFGF+T++SA VD A A
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 70 RPHTIDSKVVEPKRAVPR 87
RPH +D + VEPKRAVPR
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
Score = 73.9 bits (182), Expect = 5e-17
Identities = 30/78 (38%), Positives = 47/78 (60%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLF+G L + T++ LK YF Q+GE+T ++ + T + RGFGFV + VD A
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 161 GTHLVKGKKVDVKKALSK 178
H V G++V+ K+A+ +
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 120 bits (303), Expect = 1e-34
Identities = 46/73 (63%), Positives = 59/73 (80%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLFVG L++D+TEEDL+EYF Q+G V SV +VT+KETGKKRGF FV ++DYDPVDK L+
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 161 GTHLVKGKKVDVK 173
H + G +V+VK
Sbjct: 61 KYHTINGHRVEVK 73
Score = 64.2 bits (157), Expect = 1e-13
Identities = 28/73 (38%), Positives = 41/73 (56%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+GGL + E L+ +F +G+V V ++ D +T K RGF F+T+ VD
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 70 RPHTIDSKVVEPK 82
+ HTI+ VE K
Sbjct: 61 KYHTINGHRVEVK 73
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE) independently of hnRNP A2
and participates in the trafficking of A2RE-containing
RNA. hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 117 bits (295), Expect = 1e-33
Identities = 51/81 (62%), Positives = 63/81 (77%)
Query: 7 HLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
LRKLFIGGL + T+ ++L+ HFE WG + D VVM+DPQTK+SRGFGF+TYS VD A
Sbjct: 1 QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60
Query: 67 QAARPHTIDSKVVEPKRAVPR 87
+ARPH +D +VVEPKRAV R
Sbjct: 61 MSARPHKVDGRVVEPKRAVSR 81
Score = 62.4 bits (151), Expect = 8e-13
Identities = 29/80 (36%), Positives = 52/80 (65%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
++KLF+G L + T++ L+E+F ++G +T ++ + +T + RGFGFV Y+ + VD A
Sbjct: 2 LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61
Query: 159 LKGTHLVKGKKVDVKKALSK 178
H V G+ V+ K+A+S+
Sbjct: 62 SARPHKVDGRVVEPKRAVSR 81
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, and is an abundant eukaryotic nuclear
RNA-binding protein that may modulate splice site
selection in pre-mRNA splicing. hnRNP A1 has been
characterized as a splicing silencer, often acting in
opposition to an activating hnRNP H. It silences exons
when bound to exonic elements in the alternatively
spliced transcripts of c-src, HIV, GRIN1, and
beta-tropomyosin. hnRNP A1 can shuttle between the
nucleus and the cytoplasm. Thus, it may be involved in
transport of cellular RNAs, including the packaging of
pre-mRNA into hnRNP particles and transport of poly A+
mRNA from the nucleus to the cytoplasm. The cytoplasmic
hnRNP A1 has high affinity with AU-rich elements,
whereas the nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 81
Score = 117 bits (293), Expect = 3e-33
Identities = 53/81 (65%), Positives = 63/81 (77%)
Query: 7 HLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
LRKLFIGGL + T+ E+L+SHFE WG + D VVM+DP TK+SRGFGF+TYSS VD A
Sbjct: 1 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60
Query: 67 QAARPHTIDSKVVEPKRAVPR 87
ARPH +D +VVEPKRAV R
Sbjct: 61 MNARPHKVDGRVVEPKRAVSR 81
Score = 63.2 bits (153), Expect = 5e-13
Identities = 30/80 (37%), Positives = 50/80 (62%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
++KLF+G L + T+E L+ +F Q+G +T ++ + T + RGFGFV Y+ + VD A
Sbjct: 2 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61
Query: 159 LKGTHLVKGKKVDVKKALSK 178
H V G+ V+ K+A+S+
Sbjct: 62 NARPHKVDGRVVEPKRAVSR 81
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM1 of hnRNP A2/B1 which is an RNA trafficking
response element-binding protein that interacts with
the hnRNP A2 response element (A2RE). Many mRNAs, such
as myelin basic protein (MBP), myelin-associated
oligodendrocytic basic protein (MOBP), carboxyanhydrase
II (CAII), microtubule-associated protein tau, and
amyloid precursor protein (APP) are trafficked by hnRNP
A2/B1. hnRNP A2/B1 also functions as a splicing factor
that regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Moreover, the overexpression of hnRNP A2/B1 has been
described in many cancers. It functions as a nuclear
matrix protein involving in RNA synthesis and the
regulation of cellular migration through alternatively
splicing pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 81
Score = 113 bits (283), Expect = 8e-32
Identities = 49/81 (60%), Positives = 64/81 (79%)
Query: 7 HLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
RKLFIGGL + T+ E+L++++E WG + D VVM+DP +K+SRGFGF+T+S + VD A
Sbjct: 1 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA 60
Query: 67 QAARPHTIDSKVVEPKRAVPR 87
AARPHTID +VVEPKRAV R
Sbjct: 61 MAARPHTIDGRVVEPKRAVAR 81
Score = 60.1 bits (145), Expect = 7e-12
Identities = 27/79 (34%), Positives = 50/79 (63%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
+KLF+G L + TEE L+ Y+ Q+G++T ++ + + + RGFGFV ++ + VD A
Sbjct: 3 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62
Query: 160 KGTHLVKGKKVDVKKALSK 178
H + G+ V+ K+A+++
Sbjct: 63 ARPHTIDGRVVEPKRAVAR 81
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to
the RRM1 of hnRNP A0 which is a low abundance hnRNP
protein that has been implicated in mRNA stability in
mammalian cells. It has been identified as the
substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 79
Score = 108 bits (272), Expect = 4e-30
Identities = 42/78 (53%), Positives = 55/78 (70%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQ 67
L KLF+GGL+ +TS L+ HF +G + + VVM DP TK+SRGFGFIT+SSA D+A
Sbjct: 2 LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
Query: 68 AARPHTIDSKVVEPKRAV 85
A+PH+ID +E KRA
Sbjct: 62 EAQPHSIDGNQIELKRAK 79
Score = 58.6 bits (142), Expect = 2e-11
Identities = 23/75 (30%), Positives = 45/75 (60%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLFVG L ++ L+ +F ++G++T ++ + T + RGFGF+ ++ D D+A
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63
Query: 161 GTHLVKGKKVDVKKA 175
H + G ++++K+A
Sbjct: 64 QPHSIDGNQIELKRA 78
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in
mRNA stability in mammalian cells. hnRNP A1 is an
abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The hnRNP D subfamily includes hnRNP D0,
hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a
UUAG-specific nuclear RNA binding protein that may be
involved in pre-mRNA splicing and telomere elongation.
hnRNP A/B is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus, plays an
important role in apoB mRNA editing. hnRNP DL (or hnRNP
D-like) is a dual functional protein that possesses
DNA- and RNA-binding properties. It has been implicated
in mRNA biogenesis at the transcriptional and
post-transcriptional levels. All members in this
subfamily contain two putative RRMs and a glycine- and
tyrosine-rich C-terminus. The family also contains
DAZAP1 (Deleted in azoospermia-associated protein 1),
RNA-binding protein Musashi homolog Musashi-1,
Musashi-2 and similar proteins. They all harbor two
RRMs. .
Length = 72
Score = 108 bits (271), Expect = 6e-30
Identities = 36/72 (50%), Positives = 53/72 (73%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
LFIGGL + T+ E+L+ +F +G+VVD V+MKDP T +SRGFGF+T++ VD AA+
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 71 PHTIDSKVVEPK 82
PH +D + ++PK
Sbjct: 61 PHVLDGREIDPK 72
Score = 87.3 bits (217), Expect = 5e-22
Identities = 31/72 (43%), Positives = 45/72 (62%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
LF+G L D TEE L+EYF ++GEV ++ + TG+ RGFGFV + D VDK
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 162 THLVKGKKVDVK 173
H++ G+++D K
Sbjct: 61 PHVLDGREIDPK 72
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 96.3 bits (240), Expect = 2e-25
Identities = 34/75 (45%), Positives = 51/75 (68%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+FVG L + TEE ++EYFG+FG + + L +K+T K+RGF F+ ++ +PV K
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 161 GTHLVKGKKVDVKKA 175
H++ GKKV+VKKA
Sbjct: 61 QFHVIGGKKVEVKKA 75
Score = 66.6 bits (163), Expect = 2e-14
Identities = 28/75 (37%), Positives = 44/75 (58%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GGL T+ E ++ +F +G++V++ + D +T K RGF FIT+ S V
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 70 RPHTIDSKVVEPKRA 84
+ H I K VE K+A
Sbjct: 61 QFHVIGGKKVEVKKA 75
>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 = 95.0 bits (236), Expect = 7e-25
Identities = 41/80 (51%), Positives = 56/80 (70%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLFVG L+ D+ E DL E+F QFG V ++ +K+TGKKRGFGFV + ++D DKA +
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 161 GTHLVKGKKVDVKKALSKEE 180
H + G +V+VKKA+ KEE
Sbjct: 61 KFHPINGHRVEVKKAVPKEE 80
Score = 56.8 bits (137), Expect = 1e-10
Identities = 32/80 (40%), Positives = 42/80 (52%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+GGL L HF +G V V+ D QT K RGFGF+ + + D A
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 70 RPHTIDSKVVEPKRAVPRTE 89
+ H I+ VE K+AVP+ E
Sbjct: 61 KFHPINGHRVEVKKAVPKEE 80
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM2
of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Overexpression of hnRNP
A2/B1 has been described in many cancers. It functions
as a nuclear matrix protein involving in RNA synthesis
and the regulation of cellular migration through
alternatively splicing pre-mRNA. It may play a role in
tumor cell differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 80
Score = 93.6 bits (232), Expect = 3e-24
Identities = 36/80 (45%), Positives = 62/80 (77%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
KKLFVG +++D E L++YF ++G++ ++ ++T++++GKKRGFGFV ++D+DPVDK L
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60
Query: 160 KGTHLVKGKKVDVKKALSKE 179
+ H + G +V+KALS++
Sbjct: 61 QKYHTINGHNAEVRKALSRQ 80
Score = 55.5 bits (133), Expect = 3e-10
Identities = 27/79 (34%), Positives = 45/79 (56%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+KLF+GG+ T L+ +FE +G + + ++ D Q+ K RGFGF+T+ VD
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60
Query: 69 ARPHTIDSKVVEPKRAVPR 87
+ HTI+ E ++A+ R
Sbjct: 61 QKYHTINGHNAEVRKALSR 79
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions
as a translational regulator that activates translation
in an mRNA-specific manner. DAZAP1 was initially
identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might
associate and cooperate with hnRNP particles to
regulate adenylate-uridylate-rich elements (AU-rich
element or ARE)-containing mRNAs. DAZAP1 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal proline-rich domain. .
Length = 82
Score = 93.0 bits (231), Expect = 5e-24
Identities = 36/80 (45%), Positives = 52/80 (65%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+GGL + T+ ETL+ +F +G+VVD V+MKD T +SRGFGF+ + + V A
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 70 RPHTIDSKVVEPKRAVPRTE 89
PHT+D + ++PK PR
Sbjct: 61 GPHTLDGRTIDPKPCTPRGM 80
Score = 61.4 bits (149), Expect = 2e-12
Identities = 30/73 (41%), Positives = 44/73 (60%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLFVG L + T+E L+ YF Q+GEV ++ +K T + RGFGFV++ D + V
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 161 GTHLVKGKKVDVK 173
G H + G+ +D K
Sbjct: 61 GPHTLDGRTIDPK 73
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1)
is a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation,
and tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator
of the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 75
Score = 91.0 bits (226), Expect = 2e-23
Identities = 34/75 (45%), Positives = 53/75 (70%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+FIGGL ++T++E L+ +F +G++ + +VM+DP TK+SRGFGF+T+S VD A
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 71 PHTIDSKVVEPKRAV 85
PH +D K ++PK A
Sbjct: 61 PHELDGKKIDPKVAF 75
Score = 66.3 bits (162), Expect = 4e-14
Identities = 31/74 (41%), Positives = 45/74 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+F+G L T E L+EYF +FGE+ ++ + T + RGFGFV ++D VDK +G
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 162 THLVKGKKVDVKKA 175
H + GKK+D K A
Sbjct: 61 PHELDGKKIDPKVA 74
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 87.3 bits (217), Expect = 5e-22
Identities = 33/73 (45%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
LFVG+L D TEE+L+E F +FG+V SV LV +KETGK +GF FVE+ + +KA
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 161 -GTHLVKGKKVDV 172
+ G+ + V
Sbjct: 61 LNGKELDGRPLKV 73
Score = 76.9 bits (190), Expect = 3e-18
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+G L T+ E L+ F +G V V +++D +T KS+GF F+ + S +DA+ A
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFES---EEDAEKA 57
Query: 70 ----RPHTIDSKVVE 80
+D + ++
Sbjct: 58 LEALNGKELDGRPLK 72
>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 = 86.3 bits (214), Expect = 2e-21
Identities = 35/77 (45%), Positives = 51/77 (66%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
KK+FVG L ++TE DL++YF QFG VT V ++ + E + RGFGF+ + D VD+
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61
Query: 159 LKGTHLVKGKKVDVKKA 175
+ H + GKKV+VK+A
Sbjct: 62 NEHFHDINGKKVEVKRA 78
Score = 84.3 bits (209), Expect = 8e-21
Identities = 34/78 (43%), Positives = 46/78 (58%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+K+F+GGL + L+ +F +G V +VVVM D + K+ RGFGFIT+ S VD
Sbjct: 3 KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62
Query: 69 ARPHTIDSKVVEPKRAVP 86
H I+ K VE KRA P
Sbjct: 63 EHFHDINGKKVEVKRAEP 80
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 83.5 bits (206), Expect = 1e-20
Identities = 33/80 (41%), Positives = 59/80 (73%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
KK+FVG +++D E L++YF ++G++ ++ ++ ++++GKKRGF FV ++D+D VDK +
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 160 KGTHLVKGKKVDVKKALSKE 179
+ H + G +VKKALSK+
Sbjct: 61 QKYHTINGHNCEVKKALSKQ 80
Score = 63.5 bits (154), Expect = 4e-13
Identities = 27/79 (34%), Positives = 45/79 (56%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+K+F+GG+ T L+ +FE +G + + VM+D Q+ K RGF F+T+ VD
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 69 ARPHTIDSKVVEPKRAVPR 87
+ HTI+ E K+A+ +
Sbjct: 61 QKYHTINGHNCEVKKALSK 79
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, an abundant eukaryotic nuclear RNA-binding protein
that may modulate splice site selection in pre-mRNA
splicing. hnRNP A1 has been characterized as a splicing
silencer, often acting in opposition to an activating
hnRNP H. It silences exons when bound to exonic elements
in the alternatively spliced transcripts of c-src, HIV,
GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle
between the nucleus and the cytoplasm. Thus, it may be
involved in transport of cellular RNAs, including the
packaging of pre-mRNA into hnRNP particles and transport
of poly A+ mRNA from the nucleus to the cytoplasm. The
cytoplasmic hnRNP A1 has high affinity with AU-rich
elements, whereas the nuclear hnRNP A1 has high affinity
with a polypyrimidine stretch bordered by AG at the 3'
ends of introns. hnRNP A1 is also involved in the
replication of an RNA virus, such as mouse hepatitis
virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 83.5 bits (206), Expect = 2e-20
Identities = 33/77 (42%), Positives = 55/77 (71%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
KK+FVG +++D E L++YF Q+G++ + ++T++ +GKKRGF FV ++D+D VDK +
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60
Query: 160 KGTHLVKGKKVDVKKAL 176
+ H V G +V+KAL
Sbjct: 61 QKYHTVNGHNCEVRKAL 77
Score = 50.0 bits (119), Expect = 3e-08
Identities = 23/77 (29%), Positives = 42/77 (54%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+K+F+GG+ T L+ +FE +G + + +M D + K RGF F+T+ VD
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60
Query: 69 ARPHTIDSKVVEPKRAV 85
+ HT++ E ++A+
Sbjct: 61 QKYHTVNGHNCEVRKAL 77
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 82.5 bits (204), Expect = 3e-20
Identities = 34/74 (45%), Positives = 47/74 (63%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+FVG L + TE+D+K+YF QFG+V L+ +K+T + RGFGFV + D VDK C
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 161 GTHLVKGKKVDVKK 174
H + K V+ KK
Sbjct: 61 HFHEINNKMVECKK 74
Score = 70.9 bits (174), Expect = 5e-16
Identities = 30/74 (40%), Positives = 47/74 (63%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GGL T+ + +K +F +G V D ++M D QT + RGFGF+T+ S +VD
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 70 RPHTIDSKVVEPKR 83
H I++K+VE K+
Sbjct: 61 HFHEINNKMVECKK 74
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to
the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p,
also termed cleavage factor IB (CFIB), is a
sequence-specific trans-acting factor that is essential
for mRNA 3'-end formation in yeast Saccharomyces
cerevisiae. It can be UV cross-linked to RNA and
specifically recognizes the (UA)6 RNA element required
for both, the cleavage and poly(A) addition, steps.
Moreover, Hrp1p can shuttle between the nucleus and the
cytoplasm, and play an additional role in the export of
mRNAs to the cytoplasm. Hrp1p also interacts with
Rna15p and Rna14p, two components of CF1A. In addition,
Hrp1p functions as a factor directly involved in
modulating the activity of the nonsense-mediated mRNA
decay (NMD) pathway. It binds specifically to a
downstream sequence element (DSE)-containing RNA and
interacts with Upf1p, a component of the surveillance
complex, further triggering the NMD pathway. Hrp1p
contains two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an
arginine-glycine-rich region harboring repeats of the
sequence RGGF/Y. .
Length = 76
Score = 82.6 bits (204), Expect = 3e-20
Identities = 32/77 (41%), Positives = 54/77 (70%), Gaps = 1/77 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+FIGGL++ T+ ++L+ +F +G+V D VM+D T +SRGFGF+T+ V++ +
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEV-MKK 59
Query: 71 PHTIDSKVVEPKRAVPR 87
H +D K+++PKRA+PR
Sbjct: 60 EHILDGKIIDPKRAIPR 76
Score = 64.9 bits (158), Expect = 1e-13
Identities = 30/77 (38%), Positives = 51/77 (66%), Gaps = 1/77 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+F+G L + T++ L+EYFGQFGEVT ++ + TG+ RGFGF+ + V++ +K
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEV-MKK 59
Query: 162 THLVKGKKVDVKKALSK 178
H++ GK +D K+A+ +
Sbjct: 60 EHILDGKIIDPKRAIPR 76
>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 = 87.9 bits (218), Expect = 2e-19
Identities = 72/264 (27%), Positives = 111/264 (42%), Gaps = 41/264 (15%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L++ LD + + L+ F +G++ VMKD + +SRGF F+ + +DA A
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKH---EDAAKAV 236
Query: 71 --------PHTIDSKVVEPKRAVPRTE-------------INRPEAGATVKKLFVGSLRD 109
+ K + RA R E R A L+V +L D
Sbjct: 237 EEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMK-AQGVNLYVKNLDD 295
Query: 110 DITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTH--LVKG 167
+T+E L+E F + GE+TS ++ + E G RGFGFV +++ + ++A + H ++ G
Sbjct: 296 TVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRA-VTEMHGRMLGG 353
Query: 168 KKVDVKKALSKEE-MAKLKTRGGFGGNQGGGD--PWGNNGGGGWGG---GGPGPWDQGGS 221
K + V A KE+ A L+ + F Q P G+ GG G G GP Q
Sbjct: 354 KPLYVALAQRKEQRRAHLQDQ--FMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNG 411
Query: 222 S---WGGNSGGGWGGNSGGGWGGN 242
W S GG N
Sbjct: 412 QPLGWPRMSMMPTPMGPGGPLRPN 435
Score = 70.6 bits (173), Expect = 1e-13
Identities = 47/176 (26%), Positives = 85/176 (48%), Gaps = 15/176 (8%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L++G LD + L F+ +G V+ V V +D T++S G+G++ + + DA+ A
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNP---ADAERA- 58
Query: 71 PHTIDSKVVEP--KRAVPRTEINR-PEAGAT-VKKLFVGSLRDDITEEDLKEYFGQFGEV 126
+++ + + + R P + V +FV +L + + L + F +FG +
Sbjct: 59 ---LETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNI 115
Query: 127 TSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK--GTHLVKGKKVDVKKALSKEE 180
S + T+ E GK RG+GFV + + A K G L+ K+V V + + K E
Sbjct: 116 LSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGM-LLNDKEVYVGRFIKKHE 169
Score = 28.6 bits (64), Expect = 4.2
Identities = 11/47 (23%), Positives = 14/47 (29%)
Query: 249 GNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAP 295
G+ GG G + GQG G + M G P
Sbjct: 388 GSPMGGAMGQPPYYGQGPQQQFNGQPLGWPRMSMMPTPMGPGGPLRP 434
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 1 (Musashi-1) and similar
proteins. This subgroup corresponds to the RRM1 of
Musashi-1. The mammalian MSI1 gene encoding Musashi-1
(also termed Msi1) is a neural RNA-binding protein
putatively expressed in central nervous system (CNS)
stem cells and neural progenitor cells and associated
with asymmetric divisions in neural progenitor cells.
Musashi-1 is evolutionarily conserved from
invertebrates to vertebrates. It is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). Musashi-1 has
been implicated in the maintenance of the stem-cell
state, differentiation, and tumorigenesis. It
translationally regulates the expression of a mammalian
numb gene by binding to the 3'-untranslated region of
mRNA of Numb, encoding a membrane-associated inhibitor
of Notch signaling, and further influences neural
development. Moreover, it represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 77
Score = 78.1 bits (192), Expect = 1e-18
Identities = 35/75 (46%), Positives = 52/75 (69%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+FIGGL ++T+ E L+ +F +G+V + +VM+DP TK+SRGFGF+T+ VD A
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 70 RPHTIDSKVVEPKRA 84
H +DSK ++PK A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 57.7 bits (139), Expect = 4e-11
Identities = 32/76 (42%), Positives = 44/76 (57%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+F+G L T+E L+EYFGQFGEV ++ + T + RGFGFV + D VDK +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 161 GTHLVKGKKVDVKKAL 176
H + K +D K A
Sbjct: 62 SRHELDSKTIDPKVAF 77
>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 = 84.9 bits (210), Expect = 1e-18
Identities = 56/231 (24%), Positives = 93/231 (40%), Gaps = 20/231 (8%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R +F+ L + L F G V DV +KD +++S+G ++ + V A A
Sbjct: 90 RTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA 149
Query: 69 A-------RPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFG 121
RP + S E RA + ++P KL+VG+L +ITE++L++ F
Sbjct: 150 LTGQMLLGRPIIVQSSQAEKNRAA-KAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFE 208
Query: 122 QFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHL-VKGKKVDVKKAL-SKE 179
FG++ V L + ETG+ +GFGF++++D + +A + G+ + V A S
Sbjct: 209 PFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTY 268
Query: 180 EMAKLKTRGGFGGNQGGGDPWGNNG----------GGGWGGGGPGPWDQGG 220
+ T Q G G GG
Sbjct: 269 LLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKI 319
Score = 51.1 bits (122), Expect = 3e-07
Identities = 22/106 (20%), Positives = 40/106 (37%), Gaps = 2/106 (1%)
Query: 70 RPHTIDSKVVEPKRAVPRTEINRPEAGATVKKL--FVGSLRDDITEEDLKEYFGQFGEVT 127
+ P A FV L E DL E+F + G+V
Sbjct: 58 YYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVR 117
Query: 128 SVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVK 173
V + ++ + + +G +VE+ D + V KA ++ G+ + V+
Sbjct: 118 DVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ 163
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 77.4 bits (191), Expect = 2e-18
Identities = 34/75 (45%), Positives = 50/75 (66%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+FVG L D+TEE+ KEYF QFG+V L+ + +TG+ RGFGFV ++ V++
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 161 GTHLVKGKKVDVKKA 175
G + GK+V+VK+A
Sbjct: 61 GMLELGGKQVEVKRA 75
Score = 67.8 bits (166), Expect = 9e-15
Identities = 31/75 (41%), Positives = 44/75 (58%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GGL + E K +F +G VVD +M+D T +SRGFGF+T+ S V+ +A
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 70 RPHTIDSKVVEPKRA 84
+ K VE KRA
Sbjct: 61 GMLELGGKQVEVKRA 75
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding
protein Musashi homolog 2 (Musashi-2 ) and similar
proteins. This subgroup corresponds to the RRM2 of
Musashi-2 (also termed Msi2) which has been identified
as a regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Musashi-2 contains two
conserved N-terminal tandem RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains
of unknown function. .
Length = 76
Score = 76.7 bits (188), Expect = 5e-18
Identities = 34/75 (45%), Positives = 54/75 (72%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+FIGGL ++TS ++L+ +F +G++ + +VM+DP TK+SRGFGF+T++ VD A
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 70 RPHTIDSKVVEPKRA 84
H +DSK ++PK A
Sbjct: 61 PHHELDSKTIDPKVA 75
Score = 52.8 bits (126), Expect = 3e-09
Identities = 26/76 (34%), Positives = 42/76 (55%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+F+G L + + L++YF +FGE+ ++ + T + RGFGFV + D VDK +
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 161 GTHLVKGKKVDVKKAL 176
H + K +D K A
Sbjct: 61 PHHELDSKTIDPKVAF 76
>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 = 76.1 bits (188), Expect = 8e-18
Identities = 37/77 (48%), Positives = 52/77 (67%), Gaps = 3/77 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
L+VG+L ++TEEDLK+ FGQFGEVTS ++T++ETG+ RGFGFVE + + A
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 159 LKGTHLVKGKKVDVKKA 175
L GT G+ + V +A
Sbjct: 61 LNGTDF-GGRTLTVNEA 76
Score = 61.9 bits (151), Expect = 1e-12
Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++G L Y + E LK F +G+V V+ D +T +SRGFGF+ +A ++A AA
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETA---EEANAA 57
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 80.4 bits (197), Expect = 2e-17
Identities = 40/166 (24%), Positives = 63/166 (37%), Gaps = 19/166 (11%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS--- 59
K E LF+G L Y + E L+ F+ +G V V +++D +T KSRGF F+ + S
Sbjct: 110 KSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEES 169
Query: 60 AH----------------MVDDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLF 103
A V AQ A + + + L+
Sbjct: 170 AEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLY 229
Query: 104 VGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
VG+L EE+L + F G++ +L K+ + FV
Sbjct: 230 VGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNE 275
Score = 78.1 bits (191), Expect = 2e-16
Identities = 41/113 (36%), Positives = 57/113 (50%), Gaps = 9/113 (7%)
Query: 71 PHTIDSKVVEPKRAVPRTEINRPEAGATVKK------LFVGSLRDDITEEDLKEYFGQFG 124
D + K + + K LFVG+L D+TEEDL+E F +FG
Sbjct: 81 EEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFG 140
Query: 125 EVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--LKGTHLVKGKKVDVKKA 175
V V LV ++ETGK RGF FVE+ + +KA L G L +G+ + V+KA
Sbjct: 141 PVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKEL-EGRPLRVQKA 192
>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 = 73.0 bits (180), Expect = 1e-16
Identities = 30/60 (50%), Positives = 44/60 (73%), Gaps = 3/60 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+ GL RT+ + L++ F +G V +V++MKDP+T +SRGFGF+T+ S V+DA AA
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFES---VEDADAA 59
Score = 61.1 bits (149), Expect = 2e-12
Identities = 32/77 (41%), Positives = 45/77 (58%), Gaps = 3/77 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
KLFV L TE++L+ F +FG V V L+ + ETG+ RGFGFV + + D A
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62
Query: 159 LKGTHLVKGKKVDVKKA 175
L G L +G+ + V+KA
Sbjct: 63 LNGKEL-EGRVIKVEKA 78
>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 = 72.4 bits (178), Expect = 2e-16
Identities = 31/78 (39%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
L V L TE+DLK+YF FGE+ V + + +TG+ +GFGFV + DY+ L
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYE-DQVKVLS 59
Query: 161 GTHLVKGKKVDVKKALSK 178
H++ G+ DVK SK
Sbjct: 60 QRHMIDGRWCDVKIPNSK 77
Score = 65.1 bits (159), Expect = 9e-14
Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + GL ++T+ + LK +F +G+++ V V KDP+T +S+GFGF+ ++ +
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60
Query: 70 RPHTIDSKVVEPKRAVPR 87
R H ID + + K +
Sbjct: 61 R-HMIDGRWCDVKIPNSK 77
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 72.3 bits (177), Expect = 2e-16
Identities = 35/77 (45%), Positives = 51/77 (66%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
VKK+FVG L + TEE ++EYFG+FGE+ ++ L + +T K+RGF F+ + + DPV K
Sbjct: 4 VKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVL 63
Query: 159 LKGTHLVKGKKVDVKKA 175
K H V G K ++K A
Sbjct: 64 EKKFHNVSGSKCEIKVA 80
Score = 51.9 bits (124), Expect = 5e-09
Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 2/82 (2%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
K+P ++K+F+GGL+ + E ++ +F +G++ + + DP+T K RGF FIT+
Sbjct: 1 KDP--VKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDP 58
Query: 63 VDDAQAARPHTIDSKVVEPKRA 84
V + H + E K A
Sbjct: 59 VKKVLEKKFHNVSGSKCEIKVA 80
>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 = 72.0 bits (177), Expect = 3e-16
Identities = 35/74 (47%), Positives = 47/74 (63%), Gaps = 4/74 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CL 159
LFVG+L D TEEDL+E F +FGE+ SV +V +K GK +GF FVE+ + +KA L
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59
Query: 160 KGTHLVKGKKVDVK 173
G L G+K+ V
Sbjct: 60 NGKEL-DGRKLKVS 72
Score = 64.2 bits (157), Expect = 2e-13
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+G L T+ E L+ F +G++ V +++D KS+GF F+ + S +DA+ A
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFES---PEDAEKA 55
>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 = 70.7 bits (174), Expect = 5e-16
Identities = 31/71 (43%), Positives = 46/71 (64%), Gaps = 4/71 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CL 159
LFVG+L D TEEDLK+ F +FG + S+ +V ETG+ +GF FVE+ D + +KA L
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVR-DETGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 160 KGTHLVKGKKV 170
G + G+++
Sbjct: 60 NG-KELGGREL 69
Score = 63.8 bits (156), Expect = 2e-13
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
LF+G L T+ E LK F +G + + +++D +T +S+GF F+ + + A A
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 71 P-HTIDSKVVE 80
+ + +
Sbjct: 60 NGKELGGRELR 70
>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 = 70.7 bits (173), Expect = 6e-16
Identities = 30/74 (40%), Positives = 48/74 (64%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+F+GGL + T+ + LK +F +G+VVD + DP T +SRGFGF+ + A V+ +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 71 PHTIDSKVVEPKRA 84
H +D +V++PKRA
Sbjct: 61 EHKLDGRVIDPKRA 74
Score = 65.3 bits (159), Expect = 7e-14
Identities = 32/74 (43%), Positives = 46/74 (62%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+FVG L D T++DLKEYF +FGEV + + TG+ RGFGFV + D V+K +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 162 THLVKGKKVDVKKA 175
H + G+ +D K+A
Sbjct: 61 EHKLDGRVIDPKRA 74
>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 = 70.0 bits (172), Expect = 2e-15
Identities = 24/61 (39%), Positives = 41/61 (67%), Gaps = 3/61 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
K+F+GGL Y T+ ++L+ +F +G++ + VV+ D QT KSRG+GF+T+ + A+
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDK---ESAER 57
Query: 69 A 69
A
Sbjct: 58 A 58
Score = 69.6 bits (171), Expect = 2e-15
Identities = 29/76 (38%), Positives = 49/76 (64%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
K+FVG L T++ L++YF QFGE+ ++T+++TGK RG+GFV + D + ++AC
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 160 KGTHLVKGKKVDVKKA 175
++ G+K +V A
Sbjct: 61 DPNPIIDGRKANVNLA 76
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 2 (Musashi-2) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 79
Score = 69.3 bits (169), Expect = 2e-15
Identities = 34/76 (44%), Positives = 47/76 (61%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
KK+FVG L + ED+K+YF QFG+V L+ +K T + RGFGFV + + D V+K C
Sbjct: 4 KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63
Query: 160 KGTHLVKGKKVDVKKA 175
H + K V+ KKA
Sbjct: 64 IHFHEINNKMVECKKA 79
Score = 66.2 bits (161), Expect = 4e-14
Identities = 30/76 (39%), Positives = 48/76 (63%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+K+F+GGL T E +K +FE +G V D ++M D T + RGFGF+T+ + +V+
Sbjct: 4 KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63
Query: 69 ARPHTIDSKVVEPKRA 84
H I++K+VE K+A
Sbjct: 64 IHFHEINNKMVECKKA 79
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional and
post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 69.3 bits (169), Expect = 3e-15
Identities = 33/75 (44%), Positives = 46/75 (61%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+FVG L D TEE +KEYFG FGE+ ++ L + +T ++RGF FV Y D +PV K
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 161 GTHLVKGKKVDVKKA 175
H + K ++K A
Sbjct: 61 RYHQIGSGKCEIKVA 75
Score = 50.0 bits (119), Expect = 2e-08
Identities = 27/75 (36%), Positives = 43/75 (57%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GGL T+ E +K +F A+G++ ++ + D +T + RGF F+TY+ V +
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 70 RPHTIDSKVVEPKRA 84
R H I S E K A
Sbjct: 61 RYHQIGSGKCEIKVA 75
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1) and has been implicated in the maintenance of
the stem-cell state, differentiation, and tumorigenesis.
It translationally regulates the expression of a
mammalian numb gene by binding to the 3'-untranslated
region of mRNA of Numb, encoding a membrane-associated
inhibitor of Notch signaling, and further influences
neural development. It represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 74
Score = 69.3 bits (169), Expect = 3e-15
Identities = 33/74 (44%), Positives = 45/74 (60%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+FVG L + T ED+K+YF QFG+V L+ +K T + RGFGFV + D V+K C
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 161 GTHLVKGKKVDVKK 174
H + K V+ KK
Sbjct: 61 HFHEINNKMVECKK 74
Score = 65.0 bits (158), Expect = 8e-14
Identities = 30/74 (40%), Positives = 47/74 (63%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GGL T+ E +K +FE +G V D ++M D T + RGFGF+T+ S +V+
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 70 RPHTIDSKVVEPKR 83
H I++K+VE K+
Sbjct: 61 HFHEINNKMVECKK 74
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long C-terminal glycine-rich
domain that contains a potential ATP/GTP binding loop.
.
Length = 75
Score = 69.2 bits (169), Expect = 3e-15
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GGL + TS + LK +F +G+V D + DP T +SRGFGFI + A V+
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 70 RPHTIDSKVVEPKRA 84
+ H +D ++++PK+A
Sbjct: 61 KEHRLDGRLIDPKKA 75
Score = 65.0 bits (158), Expect = 1e-13
Identities = 32/75 (42%), Positives = 48/75 (64%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+FVG L D +++DLK+YF +FGEVT + + TG+ RGFGF+ + D V+K +
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 161 GTHLVKGKKVDVKKA 175
H + G+ +D KKA
Sbjct: 61 KEHRLDGRLIDPKKA 75
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 68.5 bits (168), Expect = 4e-15
Identities = 31/71 (43%), Positives = 45/71 (63%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
LFVG+L D T EDL +F G SV L+T+K+TGK +G FVE++ + + KA
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 162 THLVKGKKVDV 172
L+KG+K++V
Sbjct: 63 HTLLKGRKINV 73
Score = 48.1 bits (115), Expect = 1e-07
Identities = 20/56 (35%), Positives = 33/56 (58%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
LF+G L Y T++E L +HF+ G V ++ D +T KS+G F+ + +A + A
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA 58
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 68.9 bits (168), Expect = 4e-15
Identities = 31/75 (41%), Positives = 47/75 (62%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+FIGGL + TS + L + +G+V+D + DP T +SRGFGF+ + A VD
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 70 RPHTIDSKVVEPKRA 84
+ H +D K+++PKRA
Sbjct: 61 KEHKLDGKLIDPKRA 75
Score = 62.3 bits (151), Expect = 8e-13
Identities = 32/75 (42%), Positives = 45/75 (60%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+F+G L D +++DL EY +FGEV + T+ TG+ RGFGFV + D VDK
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 161 GTHLVKGKKVDVKKA 175
H + GK +D K+A
Sbjct: 61 KEHKLDGKLIDPKRA 75
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 67.7 bits (165), Expect = 1e-14
Identities = 33/75 (44%), Positives = 46/75 (61%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
K+FVG L D EE ++EYFG FGEV S+ L + +T K+RGF F+ + + +PV K K
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 161 GTHLVKGKKVDVKKA 175
H V K ++K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
Score = 45.4 bits (107), Expect = 9e-07
Identities = 25/75 (33%), Positives = 38/75 (50%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+GGL T E ++ +F A+G+V + + D +T K RGF FIT+ V
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 70 RPHTIDSKVVEPKRA 84
+ H + E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
in the middle and an RGG box rich in glycine and
arginine residues in the C-terminal part. Each of RRMs
can bind solely to the UUAG sequence specifically. .
Length = 74
Score = 66.9 bits (163), Expect = 2e-14
Identities = 31/74 (41%), Positives = 48/74 (64%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+FIGGL + T+ + LK +F +G+VVD + DP T +SRGFGF+ + + VD +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 71 PHTIDSKVVEPKRA 84
H ++ KV++PKRA
Sbjct: 61 EHKLNGKVIDPKRA 74
Score = 63.9 bits (155), Expect = 2e-13
Identities = 32/74 (43%), Positives = 47/74 (63%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+F+G L D T++DLK+YF +FGEV L + TG+ RGFGFV + + + VDK +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 162 THLVKGKKVDVKKA 175
H + GK +D K+A
Sbjct: 61 EHKLNGKVIDPKRA 74
>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 = 66.5 bits (163), Expect = 3e-14
Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
+ +F+ +L D TEE+LKE F QFGEV +V +K TG +G FV++ + K CL
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQK-CL 59
Query: 160 KGT 162
+
Sbjct: 60 EAA 62
Score = 50.7 bits (122), Expect = 1e-08
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R +FI L + + E LK F +G+V ++KD T S+G F+ + + + AQ
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTK---ESAQK 57
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the RRM
of SLIRP, a widely expressed small steroid receptor RNA
activator (SRA) binding protein, which binds to STR7, a
functional substructure of SRA. SLIRP is localized
predominantly to the mitochondria and plays a key role
in modulating several nuclear receptor (NR) pathways. It
functions as a co-repressor to repress SRA-mediated
nuclear receptor coactivation. It modulates SHARP- and
SKIP-mediated co-regulation of NR activity. SLIRP
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is required for SLIRP's corepression activities. .
Length = 73
Score = 66.2 bits (162), Expect = 3e-14
Identities = 31/73 (42%), Positives = 49/73 (67%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLFVG+L + ++LKEYF QFG+V S + +KETG +G+GFV ++ D ++ A K
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 161 GTHLVKGKKVDVK 173
H+++G K+ V+
Sbjct: 61 QKHILEGNKLQVQ 73
Score = 44.6 bits (106), Expect = 2e-06
Identities = 22/70 (31%), Positives = 40/70 (57%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+G L + S+ LK +F +G V V D +T S+G+GF+++SS +++A
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 70 RPHTIDSKVV 79
+ H ++ +
Sbjct: 61 QKHILEGNKL 70
>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 = 66.0 bits (162), Expect = 3e-14
Identities = 28/71 (39%), Positives = 45/71 (63%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGT 162
FVG+L DI EE+L+++F G+V +V +V +++TG +GFG+V + D V A
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62
Query: 163 HLVKGKKVDVK 173
+KG+K+ VK
Sbjct: 63 IKLKGRKIRVK 73
Score = 46.4 bits (111), Expect = 4e-07
Identities = 19/55 (34%), Positives = 31/55 (56%)
Query: 12 FIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
F+G L + E L+ HFE GDV V +++D +T +GFG++ + + V A
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA 57
>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 = 66.0 bits (162), Expect = 4e-14
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 15 GLDYRTSSETLKSHFEAWGDVV--DVVVMKDPQTKKSRGFGFITYSS----AHMVDDAQA 68
GLD T+ E + A V DV +++D T SRGF F+ + S +D
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68
Query: 69 ARPHTIDSKVV 79
P ID +VV
Sbjct: 69 LDPFVIDGRVV 79
Score = 49.1 bits (118), Expect = 6e-08
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 107 LRDDITEEDLKEYFGQFGEVT--SVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L TEED+ + V V L+ +K TG RGF FVE+ ++ A
Sbjct: 10 LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPS---LEDA 59
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein
3 (RBM3) and similar proteins. This subfamily
corresponds to the RRM domain of two structurally
related heterogenous nuclear ribonucleoproteins, CIRBP
(also termed CIRP or A18 hnRNP) and RBM3 (also termed
RNPL), both of which belong to a highly conserved cold
shock proteins family. The cold shock proteins can be
induced after exposure to a moderate cold-shock and
other cellular stresses such as UV radiation and
hypoxia. CIRBP and RBM3 may function in
posttranscriptional regulation of gene expression by
binding to different transcripts, thus allowing the
cell to response rapidly to environmental signals.
However, the kinetics and degree of cold induction are
different between CIRBP and RBM3. Tissue distribution
of their expression is different. CIRBP and RBM3 may be
differentially regulated under physiological and stress
conditions and may play distinct roles in cold
responses of cells. CIRBP, also termed glycine-rich
RNA-binding protein CIRP, is localized in the nucleus
and mediates the cold-induced suppression of cell cycle
progression. CIRBP also binds DNA and possibly serves
as a chaperone that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore,
RBM3 may be essential for cell proliferation and
mitosis. Both, CIRBP and RBM3, contain an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), that
is involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 65.6 bits (160), Expect = 6e-14
Identities = 27/60 (45%), Positives = 42/60 (70%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLFIGGL + T+ ++L+ F +G + +VVV+KD +T++SRGFGF+T+ + DA A
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Score = 52.9 bits (127), Expect = 2e-09
Identities = 26/71 (36%), Positives = 43/71 (60%), Gaps = 4/71 (5%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLF+G L D E+ L++ F ++G+++ V +V ++ET + RGFGFV + + D A +
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 161 GTHLVKGKKVD 171
+ GK VD
Sbjct: 62 ----MNGKSVD 68
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 65.0 bits (159), Expect = 8e-14
Identities = 33/78 (42%), Positives = 44/78 (56%), Gaps = 10/78 (12%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKK--RGFGFVEYNDYDPVDKA 157
+K+FVG L +D+TEEDL++YF QFGEVT V + K R F FV + D +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI-------PKPFRAFAFVTFADPEVAQSL 53
Query: 158 CLKGTHLVKGKKVDVKKA 175
C H++KG V V A
Sbjct: 54 C-GEDHIIKGVSVHVSNA 70
Score = 54.6 bits (132), Expect = 4e-10
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDD 65
RK+F+G L + E L+ +F +G+V DV + K R F F+T++ +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQS 52
>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 = 65.0 bits (159), Expect = 8e-14
Identities = 25/56 (44%), Positives = 35/56 (62%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
FVG++ D TEE L E F + G V S LVT+++TGK +G+GF E+ D + A
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57
Score = 50.3 bits (121), Expect = 2e-08
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 12 FIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
F+G + Y + E L F G VV ++ D T K +G+GF + +D + A
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEF------EDIETAA 54
>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 = 63.0 bits (154), Expect = 6e-13
Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-LK 160
LFV +L D T+E L+E+F + G + +V +K + K RGFG+V + + +A K
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 161 GTHLVKGKKVDVKKALSK 178
G+K+ V+ A K
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
Score = 52.2 bits (126), Expect = 4e-09
Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+ L Y T+ E L+ F G + V+KD +KK RGFG++T++ + +DA+ A
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFA---LEEDAKRA 57
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 68.2 bits (166), Expect = 8e-13
Identities = 46/181 (25%), Positives = 82/181 (45%), Gaps = 15/181 (8%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
++++G + + +T++ F+ +G + + + DP T K +GF F+ Y A
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 70 RPHTI----DSKVVEPK---RAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
+ + KV P +A P ++ + EA +++V S+ D++E D+K F
Sbjct: 169 MNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKK-FNRIYVASVHPDLSETDIKSVFEA 227
Query: 123 FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-------LKGTHLVKGKKVDVKKA 175
FGE+ L +G+GF+EYN+ +A L G +L GK V A
Sbjct: 228 FGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDA 287
Query: 176 L 176
L
Sbjct: 288 L 288
Score = 47.0 bits (111), Expect = 7e-06
Identities = 17/69 (24%), Positives = 38/69 (55%)
Query: 1 ITKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
+ +E + ++++ + S +KS FEA+G++V + + P + +G+GFI Y++
Sbjct: 197 VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNL 256
Query: 61 HMVDDAQAA 69
+A A+
Sbjct: 257 QSQSEAIAS 265
Score = 46.6 bits (110), Expect = 1e-05
Identities = 20/62 (32%), Positives = 38/62 (61%)
Query: 87 RTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFV 146
+ + R +A A + +++VGS+ ++ E+ ++ F FG + S+ + + TGK +GF FV
Sbjct: 95 QRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFV 154
Query: 147 EY 148
EY
Sbjct: 155 EY 156
Score = 28.9 bits (64), Expect = 4.5
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 109 DDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFG----FVEYNDYDPVDKA 157
D+ E +++E G+FG V V + EK+ ++ FVE++D VD+A
Sbjct: 529 DEFLEGEIREECGKFGVVDRVIINFEKQGEEEDAEIIVKIFVEFSDSMEVDRA 581
>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 = 60.7 bits (148), Expect = 3e-12
Identities = 24/56 (42%), Positives = 38/56 (67%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L+VG+L +ITE+DL+ F FGE+ V L + ETG+ +G+GF+++ D + KA
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKA 56
Score = 56.5 bits (137), Expect = 9e-11
Identities = 20/59 (33%), Positives = 39/59 (66%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++G L + + + L+ FE +G++ V + +DP+T +S+G+GFI ++ A +DA+ A
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADA---EDAKKA 56
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP complex,
which is one of the key factors facilitating the
splicing of pre-mRNA via interaction at the 5' splice
site, and is involved in regulation of polyadenylation
of some viral and cellular genes, enhancing or
inhibiting efficient poly(A) site usage. U1-70K plays an
essential role in targeting the U1 snRNP to the 5'
splice site through protein-protein interactions with
regulatory RNA-binding splicing factors, such as the RS
protein ASF/SF2. Moreover, U1-70K protein can
specifically bind to stem-loop I of the U1 small nuclear
RNA (U1 snRNA) contained in the U1 snRNP complex. It
also mediates the binding of U1C, another U1-specific
protein, to the U1 snRNP complex. U1-70K contains a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by an adjacent glycine-rich region at the
N-terminal half, and two serine/arginine-rich (SR)
domains at the C-terminal half. The RRM is responsible
for the binding of stem-loop I of U1 snRNA molecule.
Additionally, the most prominent immunodominant region
that can be recognized by auto-antibodies from
autoimmune patients may be located within the RRM. The
SR domains are involved in protein-protein interaction
with SR proteins that mediate 5' splice site
recognition. For instance, the first SR domain is
necessary and sufficient for ASF/SF2 Binding. The family
also includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but its
SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 60.7 bits (148), Expect = 4e-12
Identities = 29/77 (37%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
K LFV L D TE L+ F ++G + + LV +K+TGK RG+ F+E+ + KA
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDM-KAAY 60
Query: 160 KGTHLVKGKKVDVKKAL 176
K GKK+D ++ L
Sbjct: 61 KY---ADGKKIDGRRVL 74
Score = 54.2 bits (131), Expect = 1e-09
Identities = 27/92 (29%), Positives = 49/92 (53%), Gaps = 9/92 (9%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+ LF+ L+Y T+ L+ FE +G + + +++D +T K RG+ FI + D +A
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHE---RDMKA 58
Query: 69 ARPHTIDSKVVEPKRAVPRTEINRPEAGATVK 100
A + D K ++ +R + ++ R G TVK
Sbjct: 59 AYKY-ADGKKIDGRRVL--VDVER---GRTVK 84
>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 = 60.2 bits (147), Expect = 5e-12
Identities = 22/55 (40%), Positives = 35/55 (63%)
Query: 104 VGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
V +L +D E+DL+E F FG ++ V L +KETG+ RGF FV ++ + ++A
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAI 58
Score = 44.1 bits (105), Expect = 3e-06
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 20 TSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+ L+ F +G + V + KD +T +SRGF F+T+ + +DA+ A
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHT---REDAERA 57
>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 = 59.9 bits (146), Expect = 5e-12
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L VG L ++ ++ LKE F +G V V L ++E RG+ +VE+ + +KA
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKA 56
Score = 36.8 bits (86), Expect = 0.001
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L +G L + + LK F +G V DV + D + RG+ ++ + S +DA+ A
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESP---EDAEKAI 57
Query: 71 PHT----IDSKVV 79
H ID + V
Sbjct: 58 KHMDGGQIDGQEV 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 = 59.5 bits (145), Expect = 7e-12
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++GGL + L + F +GD+ D+ + D +T+K RGF F+ + +DA AA
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEP---EDAAAA 56
Score = 56.8 bits (138), Expect = 9e-11
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
L+VG L +++ E+ L F FG++ + + + ET K RGF FVE+ +
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEE 49
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 59.5 bits (145), Expect = 1e-11
Identities = 30/79 (37%), Positives = 51/79 (64%), Gaps = 4/79 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
++V +L +D+ +E LKE FG++G++TS ++ + + GK +GFGFV + +++ KA L
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62
Query: 160 KGTHLVKGKKVDVKKALSK 178
G V GKK+ V +A K
Sbjct: 63 NG-KEVNGKKLYVGRAQKK 80
Score = 45.3 bits (108), Expect = 1e-06
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+++ L E LK F +G + VMKD KS+GFGF+ + + + AQ A
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENH---EAAQKA 58
>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 = 58.8 bits (143), Expect = 2e-11
Identities = 20/60 (33%), Positives = 37/60 (61%), Gaps = 3/60 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+LF+ L + T+ E L+ FEA+G++ +V + D +TK+S+GF F+++ + A A
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSF---MFPEHAVKA 57
Score = 57.3 bits (139), Expect = 5e-11
Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
+LFV +L TEE+L+E F FGE++ V L +KET + +GF FV + + KA
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAY 58
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by YNL110C
from Saccharomyces cerevisiae, and localizes to the
nucleoplasm and nucleolus. Nop15p has been identified as
a component of a pre-60S particle. It interacts with RNA
components of the early pre-60S particles. Furthermore,
Nop15p binds directly to a pre-rRNA transcript in vitro
and is required for pre-rRNA processing. It functions as
a ribosome synthesis factor required for the 5' to 3'
exonuclease digestion that generates the 5' end of the
major, short form of the 5.8S rRNA as well as for
processing of 27SB to 7S pre-rRNA. Nop15p also play a
specific role in cell cycle progression. Nop15p contains
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 58.7 bits (142), Expect = 2e-11
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+++G L E++LK+YF QFG V +V + K+TG + +GF+++ +P A
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFL--NPEVAAIAAK 59
Query: 162 T---HLVKGKKVDVK 173
+ +L+ GK + V
Sbjct: 60 SMNNYLLMGKVLQVH 74
Score = 34.8 bits (80), Expect = 0.006
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
++IG L + + LK +F +G V +V V + +T S+ +GFI +
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQF 48
>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 = 58.7 bits (142), Expect = 2e-11
Identities = 24/49 (48%), Positives = 34/49 (69%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
+FVG++ + TEE LK+ F + G V S LV ++ETGK +G+GF EY D
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKD 49
Score = 34.8 bits (80), Expect = 0.005
Identities = 17/47 (36%), Positives = 26/47 (55%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+G + Y + E LK F G VV ++ D +T K +G+GF Y
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEY 47
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 58.8 bits (143), Expect = 2e-11
Identities = 24/66 (36%), Positives = 34/66 (51%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
LFVG L TEE L+E F ++G++ + LV + TG +G+ FVEY +A
Sbjct: 4 LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63
Query: 160 KGTHLV 165
LV
Sbjct: 64 DAHKLV 69
Score = 43.0 bits (102), Expect = 9e-06
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA-QAA 69
LF+G L +T+ ETL+ F +GD+ + +++D T S+G+ F+ Y A + A
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65
Query: 70 RPHTIDS 76
ID
Sbjct: 66 HKLVIDG 72
>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 = 58.4 bits (142), Expect = 2e-11
Identities = 26/78 (33%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
++FVG + D TEE+L+++F +FG V V ++T++ G +G+GFV + + +K
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62
Query: 161 GTHLVKGKKVDVKKALSK 178
G +GKK+++ A+ K
Sbjct: 63 GNLNFRGKKLNIGPAIRK 80
Score = 53.4 bits (129), Expect = 1e-09
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
++F+GG+ T+ E L+ F +G V DV ++ D + S+G+GF+T+ + + A
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62
Query: 70 RP 71
Sbjct: 63 GN 64
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM1 of FCA, a gene controlling
flowering time in Arabidopsis, encoding a flowering time
control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains), and
a WW protein interaction domain. .
Length = 80
Score = 58.1 bits (140), Expect = 4e-11
Identities = 24/57 (42%), Positives = 38/57 (66%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
KLFVGS+ ITE++++ F + G V VA++ +K TG ++G FV+Y+ D D+A
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRA 57
Score = 43.0 bits (101), Expect = 7e-06
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+G + + + ++ FE G+V++V ++KD +T +G F+ YS+ D+A A
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYST---RDEADRA 57
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 57.6 bits (140), Expect = 4e-11
Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 3/71 (4%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA- 69
L++ L + E L+ F +G V V ++++ + RGF F+ ++S + A
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58
Query: 70 RPHTIDSKVVE 80
+D + +
Sbjct: 59 NGLVLDGRTLR 69
Score = 56.8 bits (138), Expect = 7e-11
Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK- 160
L+V +L +TEEDL+E+F +G+V V LV K+ + RGF FVE+ + + A K
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58
Query: 161 GTHLVKGKKV 170
++ G+ +
Sbjct: 59 NGLVLDGRTL 68
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 63.0 bits (153), Expect = 4e-11
Identities = 47/222 (21%), Positives = 81/222 (36%), Gaps = 48/222 (21%)
Query: 7 HLRKLFIGGLDYRTSSETLKSHFEA-----------WGDVVDVVVMKDPQTKKSRGFGFI 55
R+L++GG+ E + F G V V K + F F+
Sbjct: 174 QARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSV-----NINKEKNFAFL 228
Query: 56 TYSSAHMVDDAQAA----------------RPHT-IDSKVVEPKRAVPRTEINRPEAGAT 98
+ + V++A A RPH I + P+ + + N
Sbjct: 229 EFRT---VEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKL 285
Query: 99 VK---------KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
V ++++G+L + E+ +KE FG++ + L+ + TG +G+ F EY
Sbjct: 286 VNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYK 345
Query: 150 DYDPVDKAC--LKGTHLVKGKKVDVKKALSKEEMAKLKTRGG 189
D D A L G K+ V++A A + T G
Sbjct: 346 DPSVTDVAIAALNGKDT-GDNKLHVQRACVGANQATIDTSNG 386
Score = 41.4 bits (97), Expect = 4e-04
Identities = 40/192 (20%), Positives = 72/192 (37%), Gaps = 36/192 (18%)
Query: 2 TKEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAH 61
T + +++IG L + +K E++GD+ ++KD T S+G+ F Y
Sbjct: 289 TTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPS 348
Query: 62 MVDDA--------------------QAARPHTIDSK-----VVEPKRAVPRTEINRPEAG 96
+ D A A TID+ V +A+ ++ +
Sbjct: 349 VTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKP 408
Query: 97 ATVKKLFVGSLRDDITE--------EDLKEYFGQFGEVTSVALVTEKETGKK-RGFG--F 145
V +L DD+ + ED+K F ++G + ++ + G G F
Sbjct: 409 TKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVF 468
Query: 146 VEYNDYDPVDKA 157
+EY D +KA
Sbjct: 469 LEYADVRSAEKA 480
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM1 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 76
Score = 57.4 bits (139), Expect = 6e-11
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-L 159
LFVG+L + +E LK F +FG V ++T++ETG+ RGFG+V++ + KA
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 160 KGTHLVKGKKVDVKKA 175
+ G+ ++V +
Sbjct: 61 MDGKELDGRPINVDFS 76
Score = 52.4 bits (126), Expect = 4e-09
Identities = 24/60 (40%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+G L + E LK+ FE +G VV V+ D +T +SRGFG++ + S +DA+ A
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESP---EDAKKA 57
>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 = 56.8 bits (138), Expect = 8e-11
Identities = 19/60 (31%), Positives = 35/60 (58%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+G L + E +++ FE +G++ +V +++D T +S+G F+ +SS A A
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Score = 55.2 bits (134), Expect = 3e-10
Identities = 19/48 (39%), Positives = 32/48 (66%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
KLFVG L TEED++ F ++G + V ++ +K+TG+ +G FV++
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKF 48
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 56.5 bits (137), Expect = 1e-10
Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 7/75 (9%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
+++V S+ D++E+D+K F FG++ S +L + ETGK +G+GF+EY + A
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61
Query: 159 -----LKGTHLVKGK 168
L G L GK
Sbjct: 62 MNLFDLGGQQLRVGK 76
Score = 45.3 bits (108), Expect = 1e-06
Identities = 19/60 (31%), Positives = 34/60 (56%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
++++ + S + +KS FEA+G + + DP+T K +G+GFI Y + DA A+
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 77
Score = 56.1 bits (136), Expect = 1e-10
Identities = 27/77 (35%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
K+F+G L + ++E+ +KE FG++ + LV + TG +G+ F EY D D+A
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 159 LKGTHLVKGKKVDVKKA 175
L G L KK+ V++A
Sbjct: 62 LNGMQL-GDKKLTVQRA 77
Score = 40.3 bits (95), Expect = 6e-05
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
K+FIGGL S + +K E++G + ++KD T S+G+ F Y + D A
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQA 58
>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 = 56.5 bits (137), Expect = 2e-10
Identities = 20/49 (40%), Positives = 33/49 (67%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
+++G L ++TE D+ F Q+GE+ + LV +K+TGK +GF F+ Y D
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYED 60
Score = 49.9 bits (120), Expect = 4e-08
Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
++IGGL Y + + F +G++VD+ +++D +T KS+GF F+ Y
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAY 58
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM2 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 73
Score = 55.8 bits (135), Expect = 2e-10
Identities = 23/56 (41%), Positives = 39/56 (69%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
LFVG+L D E+ + E FG++GE++SV L T+ ++G+ +GFG+VE++ + A
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAA 56
Score = 40.0 bits (94), Expect = 6e-05
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+G L + +++ F +G++ V + DP + + +GFG++ +SS + AQAA
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSS---QEAAQAA 56
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2 of
PHIP1. A. thaliana PHIP1 and its homologs represent a
novel class of plant-specific RNA-binding proteins that
may play a unique role in the polarized mRNA transport
to the vicinity of the cell plate. The family members
consist of multiple functional domains, including a
lysine-rich domain (KRD domain) that contains three
nuclear localization motifs (KKKR/NK), two RNA
recognition motifs (RRMs), and three CCHC-type zinc
fingers. PHIP1 is a peripheral membrane protein and is
localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 55.9 bits (135), Expect = 2e-10
Identities = 26/55 (47%), Positives = 41/55 (74%), Gaps = 1/55 (1%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
++G+L DITE+D++E+F E+TSV L T+KETG+ +GFG V++ D + +D A
Sbjct: 3 YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAA 56
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. This
subfamily also includes some p54nrb/PSF/PSP1 homologs
from invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 55.4 bits (134), Expect = 2e-10
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 9/75 (12%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFV--EYNDYDPVDKAC 158
+LFVG+L +DITEE+ KE F ++GEV+ V L EK GFGF+ + KA
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK------GFGFIRLDTRTNAEKAKAE 56
Query: 159 LKGTHLVKGKKVDVK 173
L G KG+++ V+
Sbjct: 57 LDGIMR-KGRQLRVR 70
Score = 35.7 bits (83), Expect = 0.003
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+LF+G L + E K F +G+V +V + K+ +GFGFI + + A+A
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 55.5 bits (134), Expect = 2e-10
Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V L ++T+++++ F GE+ S L+ +K TG+ G+GFV Y D + +KA
Sbjct: 4 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59
Score = 33.9 bits (78), Expect = 0.010
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 21 SSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+ + ++S F + G++ +++D T +S G+GF+ Y +DA+ A
Sbjct: 14 TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDP---EDAEKA 59
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. This family also includes the sex-lethal
protein (SXL) from Drosophila melanogaster. SXL governs
sexual differentiation and X chromosome dosage
compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own pre-mRNA
and promotes female-specific alternative splicing. It
contains an N-terminal Gly/Asn-rich domain that may be
responsible for the protein-protein interaction, and
tandem RRMs that show high preference to bind
single-stranded, uridine-rich target RNA transcripts. .
Length = 77
Score = 55.4 bits (134), Expect = 2e-10
Identities = 21/56 (37%), Positives = 33/56 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V L D+T+E+L+ F G + S +V ++ TG+ G+GFV+Y D + KA
Sbjct: 3 LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA 58
Score = 40.4 bits (95), Expect = 6e-05
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
L + L + E L+S FEA G + +++D T +S G+GF+ Y +DAQ
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDE---NDAQK 57
Query: 69 A 69
A
Sbjct: 58 A 58
>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 = 55.5 bits (134), Expect = 3e-10
Identities = 25/57 (43%), Positives = 38/57 (66%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+LFVG+L DITE++LKE+F +FG V V + ++ G+ FGFV ++D + V K
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61
Score = 50.1 bits (120), Expect = 3e-08
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 3/77 (3%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+LF+G L + + + LK F+ +G+V++V + + FGF+ + V A
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64
Query: 70 RPHTIDSKV---VEPKR 83
+P VE K+
Sbjct: 65 KPIYFRGDHRLNVEEKK 81
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 55.4 bits (134), Expect = 3e-10
Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
LFVG+L +TEE L E F Q G + V + + GK + F FV + V A L
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62
Query: 160 KGTHLVKGKKVDVK 173
G L G+++ +K
Sbjct: 63 NGIRLF-GRELRIK 75
Score = 45.0 bits (107), Expect = 2e-06
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
R LF+G LD R + E L F G + V + KDP K + F F+T+ V A
Sbjct: 2 RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYA 58
>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 = 55.2 bits (133), Expect = 4e-10
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK- 160
LFV +L +T+EDL ++F + +VT+ ETG+ RG+GFV + + +A K
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 161 GTHLVKGK--KVDVKKA 175
+ G+ ++D+ +
Sbjct: 62 KNKKLHGRILRLDIAER 78
Score = 54.8 bits (132), Expect = 5e-10
Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+ L + + E L F + VV+ DP+T +SRG+GF+T++ M++DAQ A
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFA---MLEDAQEA 57
>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 = 55.1 bits (133), Expect = 4e-10
Identities = 32/80 (40%), Positives = 47/80 (58%), Gaps = 6/80 (7%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
KLFV L +T+E+L++ F + G V SV LVT + +GK +G +VEY + +A L
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVL 61
Query: 160 K--GTHLVKGKKVDVKKALS 177
K GT +K K + V A+S
Sbjct: 62 KMDGTE-IKEKTISV--AIS 78
Score = 37.4 bits (87), Expect = 7e-04
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY------SSAHMV 63
KLF+ GL + + E L+ F+ G V V ++ + ++ K +G ++ Y S A +
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVLK 62
Query: 64 DDAQAARPHTIDSKVVEP 81
D + TI + P
Sbjct: 63 MDGTEIKEKTISVAISNP 80
>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 = 55.0 bits (133), Expect = 4e-10
Identities = 14/70 (20%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVV---MKDPQTKKSRGFGFITYSSAHMVDD 65
R++++ LD++ + L+ F +G+V + + + Q + + GF F+T+ A ++
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60
Query: 66 AQAARPHTID 75
A +
Sbjct: 61 ALQLNGTELG 70
Score = 48.8 bits (117), Expect = 6e-08
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVAL-VTEKETGKK--RGFGFVEYNDYDPVDKA 157
+++V +L + E+DL+ F +FGEV S+ + + E + GF FV + D + A
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 158 CLKGTHLVKGKKVDV 172
+ G+K+ V
Sbjct: 62 LQLNGTELGGRKISV 76
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 54.6 bits (132), Expect = 5e-10
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
LF+ L ++ T++DL + F FG V S + +K TG+ + FGFV Y++ + A +K
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA-IKA 59
Query: 162 --THLVKGKKVDV 172
V GK++ V
Sbjct: 60 MNGFQVGGKRLKV 72
Score = 45.7 bits (109), Expect = 8e-07
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LFI L + + L F +G+V+ V D T +S+ FGF++Y + + AQAA
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNP---ESAQAA 56
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and
similar proteins. PABPs are highly conserved proteins
that bind to the poly(A) tail present at the 3' ends of
most eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. ePABP-2 is
predominantly located in the cytoplasm and PABP-2 is
located in the nucleus. In contrast to the type I PABPs
containing four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), the type II PABPs contains
a single highly-conserved RRM. This subfamily also
includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C)
gene encoding cytoplasmic mRNA-binding protein Rbp29
that binds preferentially to poly(A). Although not
essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 54.2 bits (131), Expect = 7e-10
Identities = 21/70 (30%), Positives = 41/70 (58%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGT 162
FVG++ T E+L+E+F G + + ++ +K TG+ +GF ++E+ D V+ A L
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62
Query: 163 HLVKGKKVDV 172
+G+++ V
Sbjct: 63 SEFRGRQIKV 72
Score = 50.4 bits (121), Expect = 2e-08
Identities = 17/55 (30%), Positives = 33/55 (60%)
Query: 12 FIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
F+G +DY T+ E L+ HF++ G + + ++ D T + +GF +I + V++A
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA 57
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise role
of PPIase remains unclear. PPIase contains a conserved
N-terminal peptidyl-prolyl cistrans isomerase (PPIase)
motif, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 54.6 bits (132), Expect = 7e-10
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
LFV L T+EDL+ F +FG++ S ++ +K+TG + F+E+ + ++A K
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFK 64
Score = 44.9 bits (107), Expect = 2e-06
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 5 PEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVD 64
PE++ LF+ L+ T+ E L+ F +G + V++D +T S + FI + + +
Sbjct: 2 PENV--LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCE 59
Query: 65 DA 66
+A
Sbjct: 60 EA 61
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the
RRM of SRSF2 and SRSF8. SRSF2, also termed protein
PR264, or splicing component, 35 kDa (splicing factor
SC35 or SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of
pre-mRNA. It is also involved in transcription
elongation by directly or indirectly mediating the
recruitment of elongation factors to the C-terminal
domain of polymerase II. SRSF2 is exclusively localized
in the nucleus and is restricted to nuclear processes.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory
elements on the pre-mRNA. The RS domain modulates SRSF2
activity through phosphorylation, directly contacts
RNA, and promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 53.5 bits (129), Expect = 1e-09
Identities = 21/56 (37%), Positives = 34/56 (60%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
L + L YRT+ + L+ FE +G+V DV + +D T++SRGF F+ + +DA
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA 56
Score = 44.6 bits (106), Expect = 2e-06
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CL 159
L V +L T +DL+ F ++GEV V + ++ T + RGF FV + D + A +
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Query: 160 KGTHLVKGKKVDV 172
G + G+++ V
Sbjct: 61 DG-KELDGRELRV 72
>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 = 53.3 bits (129), Expect = 2e-09
Identities = 17/56 (30%), Positives = 29/56 (51%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L+VG L D+TE L E F G V S+ + + T + G+ +V + + ++A
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERA 57
Score = 33.3 bits (77), Expect = 0.022
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++G L + L F G V+ + V +D T++S G+ ++ + + DA+ A
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPA---DAERA 57
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 52.8 bits (127), Expect = 2e-09
Identities = 25/63 (39%), Positives = 43/63 (68%), Gaps = 1/63 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
LFVG+L + TE++L+ +FG+ G + V ++T +++GK +GF FV++ + + A LKG
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNA-LKG 59
Query: 162 THL 164
HL
Sbjct: 60 KHL 62
Score = 38.6 bits (90), Expect = 2e-04
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
LF+G L + T+ + L++HF G + V +M + K +GF F+ +
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF 47
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 52.4 bits (126), Expect = 3e-09
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+FV + +EE L +YF FG V +V + +K+ G + VE++ + VDK +
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNV--IMDKDKGV---YAIVEFDSKEGVDKVLSEP 59
Query: 162 THLVKGKKVDVKKA 175
H + G ++ V+
Sbjct: 60 QHTLNGHRLRVRPR 73
Score = 40.8 bits (96), Expect = 4e-05
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 8 LRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRG-FGFITYSSAHMVDDA 66
R +F+ G TS E L +F A+G V++V++ KD +G + + + S VD
Sbjct: 2 ERSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDKV 55
Query: 67 QAARPHTIDSKVVEPKRA 84
+ HT++ + +
Sbjct: 56 LSEPQHTLNGHRLRVRPR 73
>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 = 52.2 bits (126), Expect = 4e-09
Identities = 18/38 (47%), Positives = 26/38 (68%)
Query: 113 EEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
E +L++YF QFG VT + L K+TGK +G+ FVE+
Sbjct: 13 EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFES 50
Score = 34.1 bits (79), Expect = 0.010
Identities = 13/50 (26%), Positives = 27/50 (54%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
++IG L + L+ +F +G V + + + +T KS+G+ F+ + S
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 52.0 bits (125), Expect = 4e-09
Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+F+G L +ETL++ F +G++ D V+KD QT KS+G+GF+++ DA+ A
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKE---DAENA 57
Score = 50.8 bits (122), Expect = 1e-08
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+FVG L +I E L+ F FGE++ +V + +TGK +G+GFV +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSF 48
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 51.9 bits (125), Expect = 4e-09
Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+L V +L I E+ L++ F FG +T V L K+ GK R FGFV Y + KA
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKA 57
Score = 36.9 bits (86), Expect = 0.001
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 21 SSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAARPH 72
+ L+ FEA+G + DV + K R FGF+ Y + ++AQ A H
Sbjct: 13 KEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTE---EEAQKALKH 60
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 83
Score = 52.3 bits (126), Expect = 4e-09
Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVV-VMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LFIG LD + L F A+G ++ +M+DP T S+GF FI+Y S D A A
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Score = 48.1 bits (115), Expect = 1e-07
Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 4/81 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGE-VTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--C 158
LF+G+L ++ E+ L + F FG + + ++ + +TG +GF F+ Y+ ++ D A
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 159 LKGTHLVKGKKVDVKKALSKE 179
+ G +L + + V A K+
Sbjct: 64 MNGQYLC-NRPITVSYAFKKD 83
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM2 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 74
Score = 52.0 bits (125), Expect = 4e-09
Identities = 18/40 (45%), Positives = 31/40 (77%)
Query: 110 DITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
TEEDL+E F +FG++ V++V +K TG+ +GFG+V+++
Sbjct: 11 SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFH 50
Score = 43.5 bits (103), Expect = 5e-06
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 5/50 (10%)
Query: 21 SSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+ E L+ F+ +GD+ V ++KD T +S+GFG++ + +QAA
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKP-----SQAAV 57
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 51.9 bits (124), Expect = 5e-09
Identities = 26/68 (38%), Positives = 40/68 (58%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
+LFVG+L DI E +LKE+F FG V + + T+ GK FGFV ++D +PV +
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILGA 66
Query: 161 GTHLVKGK 168
+ +G+
Sbjct: 67 KPIMFRGE 74
Score = 30.7 bits (69), Expect = 0.17
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+LF+G L + LK F ++G+VV++ + K FGF+ + + V A
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILGA 66
Query: 70 RP 71
+P
Sbjct: 67 KP 68
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 51.5 bits (124), Expect = 6e-09
Identities = 23/57 (40%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L+V +L D I +E L+E F FG +TS ++T+ E G+ +GFGFV ++ + KA
Sbjct: 3 NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKA 58
Score = 46.8 bits (112), Expect = 4e-07
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++ LD E L+ F +G + VM D + +S+GFGF+ +SS ++A A
Sbjct: 3 NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSP---EEATKA 58
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 72
Score = 51.1 bits (123), Expect = 8e-09
Identities = 22/67 (32%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+FV +L + E++L++ F + GE+T V LV + GK +G+ +VE+ + + V +A
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLD 60
Query: 162 THLVKGK 168
L+KG+
Sbjct: 61 RELIKGR 67
Score = 39.6 bits (93), Expect = 1e-04
Identities = 15/56 (26%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+F+ LDY + L+ F G++ DV ++K+ + KS+G+ ++ + + V +A
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA 56
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM2
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the 35
S pre-rRNA. MRD1 contains 5 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which may play an
important structural role in organizing specific rRNA
processing events. .
Length = 79
Score = 51.2 bits (123), Expect = 8e-09
Identities = 21/58 (36%), Positives = 37/58 (63%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+LFV +L E+DL++ F +FGE++ V + +K++GK +GF +V + D + KA
Sbjct: 3 GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60
Score = 46.6 bits (111), Expect = 3e-07
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+LF+ L Y + L+ F +G++ +V V D ++ KS+GF ++ + +DA A
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF---LDPEDAVKA 60
>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 = 51.1 bits (123), Expect = 8e-09
Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 8/74 (10%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
L+VG L + +TE+DL+++F QFGE+ S+ +V ++ FV + + +KA L
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVVP------RQQCAFVTFTTREAAEKAAERL 57
Query: 160 KGTHLVKGKKVDVK 173
++ G+++ +K
Sbjct: 58 FNKLIINGRRLKLK 71
Score = 31.5 bits (72), Expect = 0.092
Identities = 15/73 (20%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L++GGL R + + L+ HF +G++ + V+ + F+T+++ + A+ A
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTR---EAAEKAA 54
Query: 71 PHTIDSKVVEPKR 83
+ ++ +R
Sbjct: 55 ERLFNKLIINGRR 67
>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 = 51.5 bits (124), Expect = 8e-09
Identities = 27/67 (40%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA-- 157
KL V ++ + T+++L+E F FG+V SV L +K G RGF FVE+ A
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRL-PKKFDGSHRGFAFVEFVTKQEAQNAME 59
Query: 158 CLKGTHL 164
LK THL
Sbjct: 60 ALKSTHL 66
Score = 31.4 bits (72), Expect = 0.092
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KL + + + + + L+ F +G V V + K RGF F+ + + +AQ A
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTK---QEAQNA 57
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 51.4 bits (124), Expect = 8e-09
Identities = 20/46 (43%), Positives = 31/46 (67%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVE 147
LFVG L +TE DL+E F +FG V+ V ++ +K+ G RGF +++
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYID 47
Score = 37.2 bits (87), Expect = 0.001
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
LF+GGL + L+ F +G V DV ++K RGF +I ++
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTS 51
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM3 in
hnRNP R, hnRNP Q, and APOBEC-1 complementation factor
(ACF). hnRNP R is a ubiquitously expressed nuclear
RNA-binding protein that specifically bind mRNAs with a
preference for poly(U) stretches and has been implicated
in mRNA processing and mRNA transport, and also acts as
a regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as a
component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA transport.
ACF is an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members contain three conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains).
Length = 72
Score = 51.1 bits (123), Expect = 9e-09
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 14/74 (18%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKK-RGFGFVEYNDYDPVDKA 157
VK L+V +L TEE L+E F ++GEV V KK + + FV + + D
Sbjct: 1 VKVLYVRNLPLSTTEEQLRELFSEYGEVERV---------KKIKDYAFVHFEERD----D 47
Query: 158 CLKGTHLVKGKKVD 171
+K + GK+++
Sbjct: 48 AVKAMEEMNGKELE 61
Score = 33.4 bits (77), Expect = 0.018
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++ L T+ E L+ F +G+V V +KD + F+ + DDA A
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEER---DDAVKA 51
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 15 GLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
GL T+ L+ F +G + V V+ D +T +SRGFGF+ + S V+DA+ A+
Sbjct: 6 GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES---VEDAKEAK 58
Score = 45.3 bits (108), Expect = 1e-06
Identities = 17/41 (41%), Positives = 27/41 (65%)
Query: 110 DITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
TE DL+E F ++G + V +V +++TG+ RGFGFV +
Sbjct: 10 YTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES 50
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to the
RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contain
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. On the other
hand, both RRM1 and RRM2 of CELF-4 can activate cardiac
troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in
brain, is also known as bruno-like protein 5 (BRUNOL-5),
or CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, strongly
expressed in kidney, brain, and testis, is also known as
bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in an muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In additiona to three highly conserved RRMs,
CELF-6 also possesses numerous potential phosphorylation
sites, a potential nuclear localization signal (NLS) at
the C terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 50.9 bits (122), Expect = 1e-08
Identities = 20/57 (35%), Positives = 34/57 (59%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
KLFVG + ++ E+DL+ F QFG++ + ++ +K TG +G F+ Y + KA
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63
Score = 47.8 bits (114), Expect = 2e-07
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 3 KEPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM 62
K+ + + KLF+G + + L+ FE +G + ++ V+KD T +G F+TY +
Sbjct: 1 KDDDAI-KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARES 59
Query: 63 VDDAQAA 69
AQ+A
Sbjct: 60 ALKAQSA 66
>gnl|CDD|197548 smart00157, PRP, Major prion protein. The prion protein is a major
component of scrapie-associated fibrils in
Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler
syndrome and bovine spongiform encephalopathy.
Length = 218
Score = 53.7 bits (129), Expect = 2e-08
Identities = 34/70 (48%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 205 GGGWGGGG---PGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAW 261
GGGW GG PG GG+ + GGGWG GGGWG GGGWG GGGWG
Sbjct: 7 GGGWNTGGSRYPGQGSPGGNRYPP-QGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGG 65
Query: 262 GGQGGGGFGG 271
G GGG
Sbjct: 66 GWGQGGGTHN 75
Score = 49.5 bits (118), Expect = 4e-07
Identities = 30/75 (40%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 191 GGNQGGGDPW---GNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGW 247
GG GG + G+ GG + G G G WG GGGWG GGGWG GGGW
Sbjct: 8 GGWNTGGSRYPGQGSPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGW 67
Query: 248 GGNSGGGWGGNSAWG 262
G G G ++ W
Sbjct: 68 ----GQGGGTHNQWN 78
Score = 34.8 bits (80), Expect = 0.029
Identities = 28/63 (44%), Positives = 29/63 (46%), Gaps = 15/63 (23%)
Query: 187 RGGFGGN--QGGGDPWGNNGGGGWG---GGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGG 241
+G GGN G WG GGGWG GGG WG GGGWG GGGWG
Sbjct: 20 QGSPGGNRYPPQGGGWGQPHGGGWGQPHGGG----------WGQPHGGGWGQPHGGGWGQ 69
Query: 242 NSG 244
G
Sbjct: 70 GGG 72
Score = 32.1 bits (73), Expect = 0.21
Identities = 25/71 (35%), Positives = 27/71 (38%), Gaps = 5/71 (7%)
Query: 236 GGGW--GGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGG 293
GGGW GG+ G G G + GQ GG G G P GG G GG
Sbjct: 7 GGGWNTGGSRYPGQGSPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGG 66
Query: 294 APYSGGRGGIH 304
G GG H
Sbjct: 67 ---WGQGGGTH 74
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM2 of FCA, a gene
controlling flowering time in Arabidopsis, which
encodes a flowering time control protein that functions
in the posttranscriptional regulation of transcripts
involved in the flowering process. The flowering time
control protein FCA contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 50.6 bits (121), Expect = 2e-08
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 4/60 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
KLF+G L+ + + + ++ F +G V D+ +M+D K+SRG F+ YSS M AQAA
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEM---AQAA 56
Score = 47.5 bits (113), Expect = 2e-07
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--C 158
KLFVG L TE++++E F +G V + ++ + E + RG FV+Y+ + A
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59
Query: 159 LKGTHLVKG 167
L G + ++G
Sbjct: 60 LNGVYTMRG 68
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 80
Score = 50.0 bits (120), Expect = 2e-08
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+FVG L D+T+E+L E F + G++ V L+ K F F+++ +A
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63
Query: 162 THLV-KGKKVDVKK 174
H + K K + V+
Sbjct: 64 NHSMLKNKTMHVQY 77
Score = 41.9 bits (99), Expect = 2e-05
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+F+G L + E L F G +++V ++K + + F FI + A
Sbjct: 4 YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIK--RANHTNAFAFIKFERE---QAAAR 58
Query: 69 A 69
A
Sbjct: 59 A 59
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 49.8 bits (119), Expect = 3e-08
Identities = 27/63 (42%), Positives = 36/63 (57%), Gaps = 5/63 (7%)
Query: 112 TEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGT-HLVKGKKV 170
TEED+ EYFGQFG V V + +KR FGFV + + + V + KG H + G +V
Sbjct: 12 TEEDVSEYFGQFGPVLDVRI----PYQQKRMFGFVTFENAETVKRILSKGNPHFICGSRV 67
Query: 171 DVK 173
VK
Sbjct: 68 RVK 70
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 50.1 bits (119), Expect = 3e-08
Identities = 25/56 (44%), Positives = 34/56 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V L ++T+E+LK FG GE+ S LV +K TG+ G+GFV Y D +KA
Sbjct: 7 LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62
Score = 30.9 bits (69), Expect = 0.15
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
L + L + E LKS F + G++ +++D T +S G+GF+ Y
Sbjct: 7 LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 53
>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 = 49.6 bits (119), Expect = 3e-08
Identities = 30/78 (38%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
+L V +L TE DLK+ F FG V V + K GKK+GF FV++ +KA +K
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKA-IK 58
Query: 161 GT--HLVKGKKVDVKKAL 176
G +KG+ V V A+
Sbjct: 59 GVNGKKIKGRPVAVDWAV 76
Score = 42.6 bits (101), Expect = 8e-06
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
+L + L ++ + LK F +G V +V + + P K +GF F+ ++S
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTS 49
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 49.5 bits (119), Expect = 4e-08
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 8/64 (12%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVV-----MKDPQTKKSRGFGFITYSSAHMVDD 65
LF+ L+++T+ ETLK HFE G V V + K P S G+GF+ + S +
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKS---KEA 59
Query: 66 AQAA 69
AQ A
Sbjct: 60 AQKA 63
Score = 47.2 bits (113), Expect = 2e-07
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 8/79 (10%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKR-----GFGFVEYNDYDPVDK 156
LFV +L TEE LK++F + G V SV + +K+ G+GFVE+ + K
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 157 AC--LKGTHLVKGKKVDVK 173
A L+GT L G +++K
Sbjct: 63 ALKRLQGTVL-DGHALELK 80
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM1 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 49.7 bits (118), Expect = 4e-08
Identities = 25/56 (44%), Positives = 34/56 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V L ++T+E+ K FG GE+ S LV +K TG+ G+GFV Y D + DKA
Sbjct: 6 LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61
Score = 33.6 bits (76), Expect = 0.021
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
L + L + E KS F + G++ +++D T +S G+GF+ Y + D A
Sbjct: 6 LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 51.2 bits (122), Expect = 4e-08
Identities = 40/115 (34%), Positives = 62/115 (53%), Gaps = 10/115 (8%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLF+G L + L++ F FG+V ++ ++ETG+ RGFGFV +ND A +
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
Query: 161 GTHLVKGKKVD---VKKALSKEEMAKLKTRGGFGGNQGGGDPWGNNGGGGWGGGG 212
+ GK+++ ++ + + + + GG GG GGG G GGGG GGGG
Sbjct: 96 ----MDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGG---GGYGGGGDGGGG 143
Score = 42.3 bits (99), Expect = 4e-05
Identities = 24/49 (48%), Positives = 34/49 (69%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
KLFIGGL + T +L+ F +GDVVD V+ D +T +SRGFGF+ ++
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFN 84
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 49.2 bits (118), Expect = 5e-08
Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALV---TEKETGKKRGFGFVEYNDYDPVDKA 157
L+VG+L +TEE L + FG+FG + SV ++ TE+E + R GFV + + ++A
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62
Score = 31.1 bits (71), Expect = 0.15
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVM---KDPQTKKSRGFGFITYSSAHMVDDAQ 67
L++G L+ + + E L F +G + V +M + + +++R GF+ + + DA+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNR---ADAE 60
Query: 68 AARPHTIDSKVVE 80
A +D K V
Sbjct: 61 RAL-DELDGKDVM 72
>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 = 48.8 bits (117), Expect = 6e-08
Identities = 20/51 (39%), Positives = 32/51 (62%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
L++G L + E + F + GEVTSV ++ K+TGK G+GFVE+ ++
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHE 52
Score = 44.6 bits (106), Expect = 2e-06
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L++G L+ + S F G+V V ++++ QT KS G+GF+ +++ + A+ A
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFAT---HEAAEQAL 58
Query: 71 PH 72
Sbjct: 59 QS 60
>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 = 48.8 bits (117), Expect = 6e-08
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 98 TVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
TV FV L + E DL E+F + G+V V ++ ++ + + +G +VE+ D + V A
Sbjct: 1 TV---FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57
Score = 36.8 bits (86), Expect = 0.001
Identities = 12/52 (23%), Positives = 24/52 (46%)
Query: 12 FIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMV 63
F+ L + L F G V DV +++D +++S+G ++ + V
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 48.8 bits (117), Expect = 7e-08
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 8/80 (10%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CL 159
LFV ++ ++ +E+L+ F QFG++ ++ K RGF V Y D +A L
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDIRTLYTAC-----KHRGFIMVSYYDIRAARRAKRAL 58
Query: 160 KGTHLVKGKKVDVKKALSKE 179
+GT L G+K+D+ ++ K+
Sbjct: 59 QGTEL-GGRKLDIHFSIPKD 77
Score = 37.6 bits (88), Expect = 5e-04
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
R LF+ ++ E L++ FE +GD+ + K RGF ++Y
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGDIRTLYT-----ACKHRGFIMVSY 45
>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 = 48.6 bits (116), Expect = 7e-08
Identities = 20/48 (41%), Positives = 31/48 (64%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+LF+ +L TEEDL++ F ++G ++ V L +K T K +GF FV Y
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
Score = 47.0 bits (112), Expect = 3e-07
Identities = 19/48 (39%), Positives = 28/48 (58%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+LFI L Y + E L+ F +G + +V + D TKK +GF F+TY
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 48.6 bits (116), Expect = 8e-08
Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 5/78 (6%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA-- 157
K+L V ++ + DL++ FGQFG + V ++ E G K GFGFV + + D+A
Sbjct: 1 KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIF-NERGSK-GFGFVTFANSADADRARE 58
Query: 158 CLKGTHLVKGKKVDVKKA 175
L GT V+G+K++V A
Sbjct: 59 KLHGTV-VEGRKIEVNNA 75
Score = 37.0 bits (86), Expect = 8e-04
Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 10/84 (11%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
++L + + +R L+ F +G ++DV ++ + + S+GFGF+T++++ DA
Sbjct: 1 KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN--ERGSKGFGFVTFANS---ADADR 55
Query: 69 ARPHTIDSKVVEPKRAVPRTEINR 92
AR + VVE + + E+N
Sbjct: 56 AR-EKLHGTVVEGR----KIEVNN 74
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM1 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 48.4 bits (116), Expect = 8e-08
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 4/60 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
++ + L + + L+ HFE+ G+V DV VM+ KSR FGF+ + S +DAQ A
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSE---EDAQQA 57
Score = 46.8 bits (112), Expect = 3e-07
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
++ V +L +TE+ L+E+F GEVT V ++ ++ GK R FGFV + + +A
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAV 58
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 77
Score = 48.1 bits (115), Expect = 1e-07
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
LFVG+L ++DL+E+F + GEV V + + + G+ +GFG VE+ + KA K
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60
Query: 162 THLVKGKKVDVKKALSK 178
+ G+++ V A +
Sbjct: 61 GEELLGREIRVDLATER 77
Score = 43.8 bits (104), Expect = 4e-06
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+G L + + L+ F+ G+VVDV + +D +S+GFG + +++ + AQ A
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFAT---EEGAQKA 56
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
++VG+L + +TEE L E F Q G V +V + ++ T +G+GFVE+ + D A K
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAI-KI 59
Query: 162 THLVK--GKKVDVKK 174
+++K GK + V K
Sbjct: 60 MNMIKLYGKPIRVNK 74
Score = 35.6 bits (83), Expect = 0.002
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+++G LD + + E L F G VV+V + KD T+ +G+GF+ + S +DA A
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLS---EEDADYA 56
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 48.0 bits (115), Expect = 1e-07
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
L VG+L + T+E +E FG V LV + TG+ +G+GFVEY
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEY 48
Score = 37.6 bits (88), Expect = 6e-04
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L +G L + E + +G V ++ T +S+G+GF+ Y+S A A+
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASK---ASALKAK 58
Query: 71 PHTIDSKVVEPKRA 84
+ +D K + ++
Sbjct: 59 -NQLDGKQIGGRKL 71
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 48.0 bits (115), Expect = 1e-07
Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 102 LFVGSLRDDITEEDLKEYF-GQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+FVG L D+T+ L+E F ++ V +V + TG+ +G+GFV + D D D+A
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60
Score = 31.1 bits (71), Expect = 0.13
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEA-WGDVVDVVVMKDPQTKKSRGFGFITYSS 59
+F+G L + L+ F A + V V+ DP T +S+G+GF+ +
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGD 53
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM1 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells, as well as the
neurite elongation and morphological differentiation.
HuD specifically binds poly(A) RNA. Like other Hu
proteins, HuD contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 83
Score = 48.2 bits (114), Expect = 1e-07
Identities = 23/56 (41%), Positives = 33/56 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L V L ++T+E+ + FG GE+ S LV +K TG+ G+GFV Y D +KA
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Score = 28.5 bits (63), Expect = 0.96
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
L + L + E +S F + G++ +++D T +S G+GF+ Y
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 51
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 51.2 bits (122), Expect = 2e-07
Identities = 50/196 (25%), Positives = 81/196 (41%), Gaps = 12/196 (6%)
Query: 25 LKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAARPHTIDSKVVEPKRA 84
L + F G + +M+D +T S G+ F+ + S D+Q A ++ V KR
Sbjct: 124 LYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEA---DSQRA-IKNLNGITVRNKRL 179
Query: 85 VPRTEINRPEAGATVK--KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRG 142
+ RP G ++K L+V +L IT++ L FG++G++ ++ +K TG RG
Sbjct: 180 --KVSYARP-GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRG 236
Query: 143 FGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKEEMAKLKTR---GGFGGNQGGGDP 199
FV +N + +A +++ EE K K G G
Sbjct: 237 VAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMG 296
Query: 200 WGNNGGGGWGGGGPGP 215
GN G G G P
Sbjct: 297 HGNMGMAGGSGMNPPN 312
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 46.9 bits (112), Expect = 3e-07
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CL 159
+FV +L D E L + F FG VT+V ++ + T K +G+GFV +Y+ A L
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63
Query: 160 KGTHL 164
G L
Sbjct: 64 NGYRL 68
Score = 36.5 bits (85), Expect = 0.002
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+F+ L L F +G V +V V++D T K +G+GF+T ++ ++A +A
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTN---YEEAYSA 59
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 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 = 107
Score = 47.6 bits (113), Expect = 3e-07
Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
LFV +L D TEE L +F +FG V V +K TG+ +G GFV + D + ACLK
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN-ACLKN 62
Query: 162 THLVKGKKVDVKKALSKEEMAKL 184
+ +L+ + +
Sbjct: 63 APAAGSTSLLSGSSLTADIGDDV 85
Score = 40.3 bits (94), Expect = 1e-04
Identities = 16/61 (26%), Positives = 29/61 (47%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
LF+ L Y + E+L HF +G V + + D T +++G GF+ + + +
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63
Query: 71 P 71
P
Sbjct: 64 P 64
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 47.0 bits (112), Expect = 3e-07
Identities = 21/57 (36%), Positives = 31/57 (54%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
++V L + T E LK F ++G V V+L K TG +GF F+E+ + KAC
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKAC 58
Score = 38.5 bits (90), Expect = 3e-04
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+++ L + E LK+ F +G VV V + + T +GF FI + + ++AQ A
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETP---EEAQKAC 58
Query: 71 PHTIDSKVVEPKRA 84
H + +
Sbjct: 59 KHLNNPPETATDKP 72
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 46.1 bits (109), Expect = 4e-07
Identities = 28/66 (42%), Positives = 38/66 (57%), Gaps = 8/66 (12%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFV--EYNDYDPVDKAC 158
+LFVG+L DITEED K+ F ++GE + V + + RGFGF+ E + KA
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 56
Query: 159 LKGTHL 164
L GT L
Sbjct: 57 LDGTIL 62
Score = 38.0 bits (88), Expect = 4e-04
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+LF+G L + E K FE +G+ +V + +D RGFGFI S + + A+A
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAE 56
Query: 70 RPHTI 74
TI
Sbjct: 57 LDGTI 61
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 45.7 bits (108), Expect = 9e-07
Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDK 156
+LFVG+L D+ + +LKE+F Q+G V + + GK FGFV ++D +PV K
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQK 57
Score = 31.8 bits (72), Expect = 0.076
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+LF+G L + LK F+ +G+VV+ ++ K FGF+ + + V +
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVE---LRINSGGKLPNFGFVVFDDSEPVQKILSN 61
Query: 70 RPHTIDSKV---VEPKR 83
RP V VE K+
Sbjct: 62 RPIMFRGDVRLNVEEKK 78
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs) connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 45.3 bits (108), Expect = 9e-07
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
K LF+ +L ++ T+E L+ F QF V LV +RG FVE+
Sbjct: 3 KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFET 47
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 45.6 bits (108), Expect = 9e-07
Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAH 61
RKLF+G L + + ++ F +G + + V++D Q +SRG F+T++S
Sbjct: 2 RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQ 53
Score = 37.5 bits (87), Expect = 7e-04
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+KLFVG L E D++ F FG + V + G+ RG FV +
Sbjct: 2 RKLFVGMLSKKCNENDVRIMFAPFGSIEECT-VLRDQNGQSRGCAFVTF 49
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 45.4 bits (108), Expect = 1e-06
Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
FVG+L + + DL F V SV LV +KET K +GF +VE+ D + + +A
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEA 58
>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 = 45.6 bits (108), Expect = 1e-06
Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
++FVG + E DL+++F Q+G V V +V ++ G +G+GFV + + K +
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQE 62
Query: 161 GTHL-VKGKKVDVKKALSK 178
L + KK+++ +A+ K
Sbjct: 63 ANRLCFRDKKLNIGQAIRK 81
Score = 39.0 bits (91), Expect = 2e-04
Identities = 19/58 (32%), Positives = 38/58 (65%), Gaps = 4/58 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQ 67
++F+GG+D++T+ L+ F +G V +V ++ D + S+G+GF+T+ + +DAQ
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQ---EDAQ 57
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to the
RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a TRBP-interacting
domain. RBM4 is a ubiquitously expressed splicing factor
with two isoforms, RBM4A (also known as Lark homolog)
and RBM4B (also known as RBM30), which are very similar
in structure and sequence. RBM4 may also function as a
translational regulator of stress-associated mRNAs as
well as play a role in micro-RNA-mediated gene
regulation. RBM4 contains two N-terminal RRMs, a
CCHC-type zinc finger, and three alanine-rich regions
within their C-terminal regions. This family also
includes Drosophila RNA-binding protein lark (Dlark), a
homolog of human RBM4. It plays an important role in
embryonic development and in the circadian regulation of
adult eclosion. Dlark shares high sequence similarity
with RBM4 at the N-terminal region. However, Dlark has
three proline-rich segments instead of three
alanine-rich segments within the C-terminal region. .
Length = 66
Score = 44.9 bits (107), Expect = 1e-06
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 11/75 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
KLFVG+L D T E+L+ F ++G VT +V + +GFV + + + A +K
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDA-IK 51
Query: 161 GTH--LVKGKKVDVK 173
+ GK+++V+
Sbjct: 52 ALNGYEFMGKRINVE 66
Score = 39.1 bits (92), Expect = 1e-04
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 15/62 (24%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM--VDDAQ 67
KLF+G L T+SE L++ FE +G V + V+K+ +GF+ HM +DA+
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFV-----HMEEEEDAE 47
Query: 68 AA 69
A
Sbjct: 48 DA 49
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation
initiation factor 4B (eIF-4B) and similar proteins.
This subfamily corresponds to the RRM of eIF-4B, a
multi-domain RNA-binding protein that has been primarily
implicated in promoting the binding of 40S ribosomal
subunits to mRNA during translation initiation. It
contains two RNA-binding domains; the N-terminal
well-conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), binds the 18S rRNA of the 40S ribosomal subunit
and the C-terminal basic domain (BD), including two
arginine-rich motifs (ARMs), binds mRNA during
initiation, and is primarily responsible for the
stimulation of the helicase activity of eIF-4A. eIF-4B
also contains a DRYG domain (a region rich in Asp, Arg,
Tyr, and Gly amino acids) in the middle, which is
responsible for both, self-association of eIF-4B and
binding to the p170 subunit of eIF3. Additional research
indicates that eIF-4B can interact with the poly(A)
binding protein (PABP) in mammalian cells, which can
stimulate both, the eIF-4B-mediated activation of the
helicase activity of eIF-4A and binding of poly(A) by
PABP. eIF-4B has also been shown to interact
specifically with the internal ribosome entry sites
(IRES) of several picornaviruses which facilitate
cap-independent translation initiation. .
Length = 77
Score = 45.1 bits (107), Expect = 1e-06
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 2/74 (2%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEK-ETGKKRGFGFVEYNDYDPVDKACLKG 161
++G+L D+TEED+KE+F V+SV L E + G+ RGFG+ E+ D D + +A
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLN 63
Query: 162 THLVKGKKVDVKKA 175
+K +++ V A
Sbjct: 64 DESLKNRRIRVDIA 77
>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 = 45.3 bits (108), Expect = 1e-06
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALV---TEKETGKKRGFGFVEYNDYDPVDKA 157
+L++G+L +TE L + F ++G++ + + G+ RG+ FV + + +KA
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 158 --CLKGTHLVKGKKVDVKKA 175
L G GKK+ V+ A
Sbjct: 61 LKSLNGK-TALGKKLVVRWA 79
Score = 35.3 bits (82), Expect = 0.004
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDV--VDVVVMKD-PQTKKSRGFGFITYSSAHMVDDA 66
+L+IG LD R + L F +G + D + K P + RG+ F+T+ + + A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 48.8 bits (116), Expect = 1e-06
Identities = 35/150 (23%), Positives = 76/150 (50%), Gaps = 11/150 (7%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L + L + E ++S F + G++ +++D T +S G+GF+ Y V A +
Sbjct: 6 LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNY-----VRPEDAEK 60
Query: 71 P-HTIDSKVVEPKRAVPRTEINRPEAGATVK--KLFVGSLRDDITEEDLKEYFGQFGEVT 127
++++ ++ K + RP + ++K L+V L +T+ +L+ F FG++
Sbjct: 61 AVNSLNGLRLQNKTI--KVSYARP-SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQII 117
Query: 128 SVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+ ++++ TG +G GF+ ++ D D+A
Sbjct: 118 TSRILSDNVTGLSKGVGFIRFDKRDEADRA 147
Score = 44.5 bits (105), Expect = 4e-05
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+FV +L D E L + FG FG V +V ++ + T + +G+GFV +YD
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYD 322
Score = 38.8 bits (90), Expect = 0.003
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFIT---YSSAHM 62
+F+ L T L F +G V +V +++D T + +G+GF++ Y A M
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAM 326
Score = 30.7 bits (69), Expect = 0.81
Identities = 20/71 (28%), Positives = 31/71 (43%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L++ GL + L+S F +G ++ ++ D T S+G GFI + D A
Sbjct: 92 LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151
Query: 71 PHTIDSKVVEP 81
T S EP
Sbjct: 152 NGTTPSGCTEP 162
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 44.6 bits (106), Expect = 2e-06
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDY 151
L+VG+L +TE+ L E F Q G + S L+ E + FVEY D+
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDH 47
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 44.6 bits (105), Expect = 2e-06
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD--PVDKA 157
+ LFVG+L + EE L E F Q G +T V + +KE GK + FGFV + + P A
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIA 60
Query: 158 CLKGTHLVKGKKVDVK 173
L G L G+ + V
Sbjct: 61 LLNGIRLY-GRPIKVH 75
Score = 36.1 bits (83), Expect = 0.002
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R LF+G L+ R E L F G + V + KD + K + FGF+ + + V A A
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIA 60
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 44.3 bits (105), Expect = 2e-06
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 9/79 (11%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
L++G+L D+ E DL++ F + S LV KK G+ FV+ D DKA L
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLV------KKGGYAFVDCPDQSWADKAIEKL 54
Query: 160 KGTHLVKGKKVDVKKALSK 178
G L +GK ++V+ ++ K
Sbjct: 55 NGKIL-QGKVIEVEHSVPK 72
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 44.5 bits (106), Expect = 2e-06
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
++FVG L +++T+E L F ++ +V +K TGK +G+GFV ++D
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSD 57
Score = 40.7 bits (96), Expect = 6e-05
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 4 EPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMV 63
R +F+G L + E L F + V++D +T KS+G+GF+++S +
Sbjct: 3 PENDFR-IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN-- 59
Query: 64 DDAQAAR 70
D +A +
Sbjct: 60 DYLKAMK 66
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 44.2 bits (105), Expect = 3e-06
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+++ L + ++ L F +G VV V ++KD +T+KS+G FI + +DA
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLD---REDAHKC 59
Score = 40.8 bits (96), Expect = 5e-05
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
++V +L +T DL + F ++G+V V +V +KET K +G F+ + D + K C+K
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHK-CVKA 62
Query: 162 TH 163
+
Sbjct: 63 LN 64
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 47.4 bits (113), Expect = 3e-06
Identities = 27/59 (45%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 237 GGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAP 295
G GG GG GG GGG GG G GG G G G G GGG GG GG P
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRG-----RGRGGGGGGRGGGGGGGP 54
Score = 45.5 bits (108), Expect = 1e-05
Identities = 34/65 (52%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 229 GGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGG 288
G GG GG GG GGG GG GGG GG G GG G G G GGG RGGGGG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGG----GRGGGRGRGRG-----GGGGGRGGGGG 51
Query: 289 GRSGG 293
G G
Sbjct: 52 GGPGK 56
Score = 43.2 bits (102), Expect = 7e-05
Identities = 24/51 (47%), Positives = 24/51 (47%)
Query: 252 GGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
G G G GG GGG GGG GG GG G GR GG GG GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGG 51
Score = 42.4 bits (100), Expect = 1e-04
Identities = 23/51 (45%), Positives = 24/51 (47%)
Query: 187 RGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGG 237
GG G GG G GGGG GGG G +G GG GGG GG G
Sbjct: 6 FGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
Score = 42.0 bits (99), Expect = 2e-04
Identities = 35/68 (51%), Positives = 35/68 (51%), Gaps = 12/68 (17%)
Query: 204 GGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGG 263
G GG GGG G GG GGG GG GGG GG GGG G GGG GG GG
Sbjct: 1 GMGGGFGGGRG---------GGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGR---GG 48
Query: 264 QGGGGFGG 271
GGGG G
Sbjct: 49 GGGGGPGK 56
Score = 42.0 bits (99), Expect = 2e-04
Identities = 27/54 (50%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 201 GNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGG 254
G GG G G GG G GG GG GGG GG G G GG GG GG GG
Sbjct: 5 GFGGGRGGGRGGGG----GGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGP 54
Score = 40.9 bits (96), Expect = 5e-04
Identities = 29/54 (53%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 219 GGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGG 272
GG GG GG GG GG GG GGG GG G G GG GG GGG GGG
Sbjct: 3 GGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGG---GGGRGGGGGGG 53
Score = 39.3 bits (92), Expect = 0.001
Identities = 28/58 (48%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 245 GGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
G GG GG GG GG GGGG GGG GGG G G G GG GG GG
Sbjct: 1 GMGGGFGGGRGGGR---GGGGGGGRGGG---GRGGGRGGGRGRGRGGGGGGRGGGGGG 52
Score = 32.4 bits (74), Expect = 0.23
Identities = 18/45 (40%), Positives = 18/45 (40%)
Query: 185 KTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGG 229
RGG GG GG G GGG G G G G GG G
Sbjct: 12 GGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM2 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA). However, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 75
Score = 43.7 bits (103), Expect = 4e-06
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+F+G L + TL + F A+ D VM D ++ +SRG+GF+++ S DA+ A
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQ---QDAENA 57
Score = 41.7 bits (98), Expect = 2e-05
Identities = 15/56 (26%), Positives = 29/56 (51%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+FVG L ++T+ L F F + ++ + ++G+ RG+GFV + + A
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENA 57
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 43.2 bits (102), Expect = 5e-06
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 13/71 (18%)
Query: 102 LFVGSLRDD-ITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
LFV EED+++ F FG + + ++ F FVE+ D + KA +
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKAL-E 52
Query: 161 GTHLVKGKKVD 171
H G ++D
Sbjct: 53 ALH---GSRID 60
Score = 29.0 bits (65), Expect = 0.68
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 12/60 (20%)
Query: 11 LFIGGLD-YRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+ G D T E ++ FE +G +V + + F F+ + +DA A
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFED---SEDATKA 50
>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 = 43.4 bits (103), Expect = 5e-06
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQF-GEVTSVALVTEKETGKKRGFGFVEYND 150
+L V +L +TE +LKE+F + GE+T V L+ E GK R F+ Y
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLR-TEDGKSRRIAFIGYKT 51
Score = 39.6 bits (93), Expect = 1e-04
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 10 KLFIGGLDYRTSSETLKSHFEA-WGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+L + L + LK HF G++ DV +++ K SR FI Y + ++AQ
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGK-SRRIAFIGYKTE---EEAQK 57
Query: 69 ARPH 72
A+ +
Sbjct: 58 AKDY 61
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 43.6 bits (103), Expect = 5e-06
Identities = 16/48 (33%), Positives = 31/48 (64%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+++VGS+ ++ E+ +++ F FG + S+ + + T K +GF FVEY
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEY 49
Score = 33.2 bits (76), Expect = 0.019
Identities = 12/48 (25%), Positives = 27/48 (56%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
++++G + + +T++ F +G + + + DP T K +GF F+ Y
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEY 49
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 43.3 bits (102), Expect = 5e-06
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL-- 159
+FVG+L + EE L FG+ G + V +V + +T +GF +V++ D + V+KA L
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61
Query: 160 -KGTHLVKGKKVDVKKA 175
K + +++ V +
Sbjct: 62 EKKFPPMLPRELRVSRC 78
Score = 41.4 bits (97), Expect = 3e-05
Identities = 15/56 (26%), Positives = 29/56 (51%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+F+G L + E L F G + V +++DP+T +GF ++ + + V+ A
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKA 57
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 43.5 bits (103), Expect = 6e-06
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
K F SL +D L E+F GE+T V++ T++ETG +GF ++E+ D V+KA
Sbjct: 5 KGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61
Score = 32.7 bits (75), Expect = 0.032
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 10 KLFIGGLDYRTSSETLKS----HFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDD 65
+F+ G D + ++ HF + G++ V + D +T S+GF +I + S V+
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60
Query: 66 A 66
A
Sbjct: 61 A 61
>gnl|CDD|221868 pfam12938, M_domain, M domain of GW182.
Length = 238
Score = 46.4 bits (110), Expect = 6e-06
Identities = 29/103 (28%), Positives = 33/103 (32%), Gaps = 9/103 (8%)
Query: 206 GGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGG-- 263
G G GP D+ S + + N+ N GGG GG GGG G N
Sbjct: 3 SGMGFAGPFGGDRFPSGGSSVNSPPFSQNNL---PNNLGGGGGGPGGGGGGNNPNLASLS 59
Query: 264 ----QGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
QG G G Q G G GG G G
Sbjct: 60 SLTSQGLGKILSGLQPPPLGNGGGSGAGGPGPVGGGGGPGVAP 102
Score = 40.2 bits (94), Expect = 6e-04
Identities = 21/94 (22%), Positives = 26/94 (27%), Gaps = 5/94 (5%)
Query: 188 GGFGGNQG---GGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNS--GGGWGGNSGGGWGGN 242
G + NN GGG GG G G + +S G G G
Sbjct: 18 SGGSSVNSPPFSQNNLPNNLGGGGGGPGGGGGGNNPNLASLSSLTSQGLGKILSGLQPPP 77
Query: 243 SGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQS 276
G G G +GG G Q+
Sbjct: 78 LGNGGGSGAGGPGPVGGGGGPGVAPNNIQPNAQA 111
Score = 36.4 bits (84), Expect = 0.012
Identities = 23/116 (19%), Positives = 27/116 (23%), Gaps = 9/116 (7%)
Query: 188 GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQG--GSSWGGNSGGGWGGNSGGGWGGN--- 242
G GGD + + G G GG GGG G N +
Sbjct: 4 GMGFAGPFGGDRFPSGGSSVNSPPFSQNNLPNNLGGGGGGPGGGGGGNNPNLASLSSLTS 63
Query: 243 -SGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYS 297
G GN G GG G GG P +
Sbjct: 64 QGLGKILSGLQPPPLGNGGGSGAGGPGPVGGGGGPGVAP---NNIQPNAQAQQPST 116
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 43.3 bits (102), Expect = 6e-06
Identities = 20/71 (28%), Positives = 41/71 (57%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
++VG++ T E+L+ +F G V V ++ +K +G +GF ++E++D + V A
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61
Query: 162 THLVKGKKVDV 172
L +G+++ V
Sbjct: 62 ESLFRGRQIKV 72
Score = 39.8 bits (93), Expect = 1e-04
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+++G +DY ++E L++HF G V V ++ D + +GF +I +S V A A
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALA 59
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM2 of the sex-lethal protein (SXL) which
governs sexual differentiation and X chromosome dosage
compensation in Drosophila melanogaster. It induces
female-specific alternative splicing of the transformer
(tra) pre-mRNA by binding to the tra uridine-rich
polypyrimidine tract at the non-sex-specific 3' splice
site during the sex-determination process. SXL binds
also to its own pre-mRNA and promotes female-specific
alternative splicing. SXL contains an N-terminal
Gly/Asn-rich domain that may be responsible for the
protein-protein interaction, and tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), that show high
preference to bind single-stranded, uridine-rich target
RNA transcripts. .
Length = 79
Score = 43.0 bits (101), Expect = 7e-06
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
L+V +L +TE++L++ F +G + L+ +K TG RG FV Y+
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYD 50
Score = 33.7 bits (77), Expect = 0.014
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L++ L + + + L+ FEA+G++V +++D T RG F+ Y ++AQAA
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKR---EEAQAAI 59
Query: 71 PHTIDSKVVEPKRAVP 86
+ + P +P
Sbjct: 60 SSL--NGTIPPGSTMP 73
>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 = 43.0 bits (102), Expect = 7e-06
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY---ND----YDP 153
+L V +L D+TEEDL+E FG+ GEV V + ++ +G+ G V + D
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60
Query: 154 VDKACLKGTHLV 165
+ L G +
Sbjct: 61 FNGVLLDGQPMQ 72
Score = 31.0 bits (71), Expect = 0.11
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+L + L Y + E L+ F G+V V + D + +S G + + D +A
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFE--KREDAERA 57
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 42.6 bits (100), Expect = 7e-06
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
KLFVG+L + TE++++ F Q+G+V ++ + +GFV +D D+A
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEA 50
Score = 36.4 bits (84), Expect = 0.001
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
KLF+G L + + ++S FE +G V++ ++K+ +GF+ D+A
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEA 50
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 42.6 bits (101), Expect = 8e-06
Identities = 21/76 (27%), Positives = 46/76 (60%), Gaps = 12/76 (15%)
Query: 101 KLFVGSL-RDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
++FVG+L D +++EDL+E F ++G++ ++L +G+GFV++++ + A
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53
Query: 160 KGTH--LVKGKKVDVK 173
G + + G+K+D+
Sbjct: 54 -GENGREIAGQKLDIN 68
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 42.8 bits (100), Expect = 9e-06
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVE-YNDYDPVDKACLK 160
+FVG L +IT ED+K F FG+++ +V + TGK +G+GFV YN D +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 161 GTHLVKGKKV 170
G + G+++
Sbjct: 64 GGQWLGGRQI 73
Score = 35.4 bits (81), Expect = 0.003
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+G L ++E +KS F +G + D V+KD T KS+G+GF+++
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 50
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 42.6 bits (101), Expect = 1e-05
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
K++VG+L T+ +L++ F ++G + SV V GF FVE+ D + A
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSV-WVARNPP----GFAFVEFEDPRDAEDAV 53
Score = 36.1 bits (84), Expect = 0.002
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
K+++G L R + L+ FE +G + V V ++P GF F+ + +DA
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDA 52
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 42.4 bits (100), Expect = 1e-05
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+F+ LDY+ + LK F+ G VV + +D + KSRG G + + H ++ QA
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFE--HPIEAVQA 55
Score = 40.8 bits (96), Expect = 4e-05
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+FV +L + + LKE F G+V + +KE GK RG G V++
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQF 46
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 42.1 bits (99), Expect = 1e-05
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 13/61 (21%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+G +D TS E L++ FEA+G V+ VM+ F F+ H+ +A A
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFV-----HLRGEAAAD 48
Query: 70 R 70
R
Sbjct: 49 R 49
Score = 41.7 bits (98), Expect = 1e-05
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 11/75 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
K+FVG++ +D ++E+L+ F +G V S A++ R F FV D+A
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEE 53
Query: 159 LKGTHLVKGKKVDVK 173
L G + G+K+ V+
Sbjct: 54 LNG-RELHGRKLVVE 67
>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 = 42.6 bits (100), Expect = 1e-05
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
LFV ++ DD EDL+ FG++G + V + + T + RGF +V++ D
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFED 51
Score = 39.6 bits (92), Expect = 1e-04
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
LF+ + T SE L+ F +G +VDV V D T++ RGF ++ + +DA
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL--- 59
Query: 71 PHTIDSKVV 79
H +D K +
Sbjct: 60 -HNLDRKWI 67
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
+FV + ++ EED+ + F +FGE+ ++ L ++ TG +G+ +EY A L
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 160 KGTHLVKGKKVDVKKALSKE 179
G L+ G+ + V A K
Sbjct: 69 NGKELL-GQTISVDWAFVKG 87
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 42.1 bits (99), Expect = 1e-05
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--C 158
K+ V +L + T++D++ F +G++ SV V +K RGF FVE++ A
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMNA 60
Query: 159 LKGTHLV 165
LK THL+
Sbjct: 61 LKDTHLL 67
Score = 33.3 bits (76), Expect = 0.023
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+ + L + + + +++ F ++G + V V K + +RGF F+ +S+A +A A
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFD-QSARGFAFVEFSTAKEALNAMNA 60
Query: 70 RPHT 73
T
Sbjct: 61 LKDT 64
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is an integral part of the U2
small nuclear ribonucleoprotein (snRNP) and the U11/U12
di-snRNP. SF3B is essential for the accurate excision of
introns from pre-messenger RNA and has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 42.2 bits (100), Expect = 1e-05
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
L+V +L I+ E+L + FG++G + + + KET RG FV Y D AC
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNAC 58
Score = 30.3 bits (69), Expect = 0.23
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R L++ L ++ SSE L F +G + + + +T RG F+ Y + DA+
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYED---IYDAKN 56
Query: 69 ARPH 72
A H
Sbjct: 57 ACDH 60
>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 = 42.4 bits (100), Expect = 1e-05
Identities = 15/51 (29%), Positives = 29/51 (56%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
L+V ++ D +DL+ FG++G + V + + T + RGF +V++ D
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFED 51
Score = 41.2 bits (97), Expect = 3e-05
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++ + T + L+ F +G +VDV + D T++ RGF ++ + V DA+ A
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFED---VRDAEDA 58
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins from plants. This
subgroup corresponds to the RRM2 in a family that
represents a novel group of arginine/serine (RS) or
serine/arginine (SR) splicing factors existing in
plants, such as A. thaliana RSp31, RSp35, RSp41 and
similar proteins. Like vertebrate RS splicing factors,
these proteins function as plant splicing factors and
play crucial roles in constitutive and alternative
splicing in plants. They all contain two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
at their N-terminus, and an RS domain at their
C-terminus.
Length = 70
Score = 41.8 bits (98), Expect = 1e-05
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 12/71 (16%)
Query: 11 LFIGGLD-YRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LF+ D T + L+ HFE +G +V+V + R F F+ Y + +DA A
Sbjct: 2 LFVINFDPINTRTRDLERHFEPYGKLVNVRI--------RRNFAFVQYETQ---EDATKA 50
Query: 70 RPHTIDSKVVE 80
T SKV++
Sbjct: 51 LESTNMSKVLD 61
Score = 36.0 bits (83), Expect = 0.002
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 9/54 (16%)
Query: 113 EEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVK 166
DL+ +F +G++ +V + +R F FV+Y + KA L+ T++ K
Sbjct: 14 TRDLERHFEPYGKLVNVRI--------RRNFAFVQYETQEDATKA-LESTNMSK 58
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 41.5 bits (98), Expect = 2e-05
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVD--KACL 159
+++ L + T+EDL++ FG++ S + +K+T K +G+GFV D+D + +
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFV---DFDSPEAALKAI 59
Query: 160 KG 161
+G
Sbjct: 60 EG 61
Score = 32.2 bits (74), Expect = 0.039
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
++I GL T+ E L+ + +G ++ + D +T K +G+GF+ + S + A
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDS---PEAALK 57
Query: 69 A 69
A
Sbjct: 58 A 58
>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM2 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 93
Score = 42.2 bits (100), Expect = 2e-05
Identities = 26/96 (27%), Positives = 40/96 (41%), Gaps = 25/96 (26%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTE----KETGKKRGFGF---------VEY 148
++ G L +T+EDL+E+F + E + KR V
Sbjct: 5 VYCGKLPKKVTDEDLREFFKDYNP-------QEIWIFRTRKSKRNPLQLHRHFTAALVTL 57
Query: 149 NDYDPVDKAC--LKGTHLVKGKKVDVKKA-LSK-EE 180
+ + +D+ LK L GKK+ +K A LSK EE
Sbjct: 58 DTEETLDEIIESLKSKKL-NGKKISLKPAYLSKIEE 92
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 86
Score = 42.0 bits (98), Expect = 2e-05
Identities = 22/51 (43%), Positives = 31/51 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+FV +L D E L + FG FG VT+V ++ + T K +GFGFV +YD
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYD 56
Score = 30.4 bits (68), Expect = 0.26
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
+F+ L L F +G V +V V++D T K +GFGF+T ++
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTN 54
>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown].
Length = 334
Score = 44.9 bits (106), Expect = 2e-05
Identities = 31/64 (48%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 227 SGGGWGGNSGGGWGGNSGG-GWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGG 285
SGG GG S G S G GG SGGG+ G GG GGGFG + GGG GG
Sbjct: 49 SGGRIGGGSFRAPSGYSRGYSGGGPSGGGYSG----GGYSGGGFGFPFIIPGGGG---GG 101
Query: 286 GGGG 289
G GG
Sbjct: 102 GFGG 105
Score = 40.7 bits (95), Expect = 6e-04
Identities = 26/59 (44%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 235 SGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGG 293
SGG GG S G S G GG + GG GGG+ GG FG + GGGGG G
Sbjct: 49 SGGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGG---GFGFPFIIPGGGGGGGFG 104
Score = 35.3 bits (81), Expect = 0.028
Identities = 33/95 (34%), Positives = 37/95 (38%), Gaps = 18/95 (18%)
Query: 218 QGGSSWGGNSGGGWGGNSGG-GWGGNSGGGW-GGN-SGGGWGGNSAWGGQGGGGFGGGYQ 274
+ G GG S G S G GG SGGG+ GG SGGG+G G GGGG GG
Sbjct: 48 RSGGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGGI- 106
Query: 275 QSFG------------GGPMRGGGGGGRSGGAPYS 297
FG G R G G +
Sbjct: 107 --FGILVFGAIANGVVGMMRRNLSSGEARGLSSLG 139
Score = 31.4 bits (71), Expect = 0.48
Identities = 25/71 (35%), Positives = 29/71 (40%), Gaps = 9/71 (12%)
Query: 180 EMAKLKTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNS-GGG 238
A ++ G GG G G G GG S GG SGGG+G G
Sbjct: 43 VAAAARSGGRIGGGSFRA------PSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPG 96
Query: 239 WGGNSGGGWGG 249
GG GGG+GG
Sbjct: 97 GGG--GGGFGG 105
Score = 29.5 bits (66), Expect = 2.4
Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 257 GNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGG----APYSGG 299
+ A + GG GGG ++ G RG GGG SGG YSGG
Sbjct: 41 LSVAAAARSGGRIGGGSFRA-PSGYSRGYSGGGPSGGGYSGGGYSGG 86
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM1 of HuR,
also termed ELAV-like protein 1 (ELAV-1), a ubiquitously
expressed Hu family member. It has a variety of
biological functions mostly related to the regulation of
cellular response to DNA damage and other types of
stress. HuR has an anti-apoptotic function during early
cell stress response; it binds to mRNAs and enhances the
expression of several anti-apoptotic proteins, such as
p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also
has pro-apoptotic function by promoting apoptosis when
cell death is unavoidable. Furthermore, HuR may be
important in muscle differentiation, adipogenesis,
suppression of inflammatory response and modulation of
gene expression in response to chronic ethanol exposure
and amino acid starvation. Like other Hu proteins, HuR
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 41.6 bits (97), Expect = 2e-05
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CL 159
L V L ++T+++L+ F GEV S L+ +K G G+GFV Y + ++A L
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63
Query: 160 KGTHLVKGKKVDVKKA 175
G L + K + V A
Sbjct: 64 NGLRL-QSKTIKVSYA 78
Score = 30.8 bits (69), Expect = 0.18
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L + L + + L+S F + G+V +++D S G+GF+ Y +A DA+ A
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNA---KDAERA 59
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 78
Score = 41.5 bits (97), Expect = 3e-05
Identities = 22/50 (44%), Positives = 32/50 (64%), Gaps = 3/50 (6%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
K LFV L +D TEE LKE F + +VT+++TG +GFGFV+++
Sbjct: 1 KTLFVKGLSEDTTEETLKE---SFDGSIAARIVTDRDTGSSKGFGFVDFS 47
Score = 36.9 bits (85), Expect = 0.001
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+ LF+ GL T+ ETLK F+ + ++ D T S+GFGF+ +SS +DA+A
Sbjct: 1 KTLFVKGLSEDTTEETLKESFDG---SIAARIVTDRDTGSSKGFGFVDFSSE---EDAKA 54
Query: 69 ARPHTIDSKV 78
A+ D ++
Sbjct: 55 AKEAMEDGEI 64
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 41.2 bits (97), Expect = 3e-05
Identities = 16/48 (33%), Positives = 30/48 (62%), Gaps = 5/48 (10%)
Query: 23 ETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+ L+ F +G++ D+ V+KD QTK+S+G ++ ++ A + AAR
Sbjct: 17 DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKA-----SSAAR 59
Score = 40.4 bits (95), Expect = 7e-05
Identities = 14/39 (35%), Positives = 27/39 (69%)
Query: 110 DITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+TE+DL+E F FGE+ + +V +K+T + +G +V++
Sbjct: 13 SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKF 51
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 41.2 bits (96), Expect = 3e-05
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 5/75 (6%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
++FV +L D+T + LKE F Q G V + + E GK +G G V ++ + +KAC
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEI--KMENGKSKGCGTVRFDSPESAEKACRL 58
Query: 159 LKGTHLVKGKKVDVK 173
+ G + G+++DV+
Sbjct: 59 MNGIK-INGREIDVR 72
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. Moreover, hnRNP M is able to
interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. hnRNP M
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 41.3 bits (97), Expect = 3e-05
Identities = 29/76 (38%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYF-GQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
++F+ ++ D+ +DLK+ F + GEVT V L + E GK RG G VE+ D + V KA
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTYVELF-KDEEGKSRGCGVVEFKDKESVQKALE 59
Query: 160 K-GTHLVKGKKVDVKK 174
+ +KG+K+ VK+
Sbjct: 60 TMNRYELKGRKLVVKE 75
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 41.0 bits (97), Expect = 3e-05
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
+F+ +L I + L + F FG + S + T+ E G +G+GFV + + +A +
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63
Query: 160 KGTHLVKGKKVDV 172
G L+ KKV V
Sbjct: 64 NGM-LLNDKKVFV 75
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 43.5 bits (103), Expect = 3e-05
Identities = 28/59 (47%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 220 GSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSA-----WG-GQGGGGFGGG 272
GG GGG+GG GG GG GGG GG GGG SA W GGFGGG
Sbjct: 122 RGGGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGG 180
Score = 43.1 bits (102), Expect = 4e-05
Identities = 25/61 (40%), Positives = 26/61 (42%)
Query: 226 NSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGG 285
S GG GG GGG+GG GG GG GGG GG GG S GG
Sbjct: 120 ASRGGGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGG 179
Query: 286 G 286
G
Sbjct: 180 G 180
Score = 41.6 bits (98), Expect = 1e-04
Identities = 28/61 (45%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 242 NSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRG 301
S GG GG GGG+GG G GGGG GGG GGG AP SGG G
Sbjct: 120 ASRGGGGGGGGGGFGGGGG-GSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFG 178
Query: 302 G 302
G
Sbjct: 179 G 179
Score = 36.2 bits (84), Expect = 0.009
Identities = 23/58 (39%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 188 GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSG-GGWGGNSG 244
GGFGG GG GGGG GGGG G GG+ + W GG+GG
Sbjct: 131 GGFGGGGGGS------GGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGGDD 182
Score = 27.3 bits (61), Expect = 7.1
Identities = 17/45 (37%), Positives = 18/45 (40%)
Query: 258 NSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
A G GGGG GGG+ GG GGGGGG
Sbjct: 118 TRASRGGGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASA 162
>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 = 41.2 bits (97), Expect = 3e-05
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA----- 157
VG + ++E+DLKE+F GEVT V L +++ + F FVE+ D + A
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR--FAFVEFADAESALSALNLSG 61
Query: 158 CLKGTHLVK 166
L G H ++
Sbjct: 62 TLLGGHPLR 70
Score = 34.6 bits (80), Expect = 0.006
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R + +GG+D S + LK F G+V V + D Q F F+ + D A
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR--FAFVEF-----ADAESA 53
Query: 69 AR 70
Sbjct: 54 LS 55
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 41.1 bits (96), Expect = 3e-05
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 8/59 (13%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
VK LFV +L + +TEE L++ FGQFG++ V K + + F+ +++ D KA
Sbjct: 1 VKVLFVRNLANTVTEEILEKAFGQFGKLERVK--------KLKDYAFIHFDERDGAVKA 51
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 41.4 bits (97), Expect = 3e-05
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 102 LFVGSLRDDITEEDLKEYF-GQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+FVG L ++ E DL F +F S ++T+ TG RG+GFV ++D +
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDEN 55
Score = 36.0 bits (83), Expect = 0.002
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 11 LFIGGLDYRTSSETLKSHFEA-WGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+F+G L + L S F++ + +M DP T SRG+GF+ +S +D Q A
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDE---NDQQRA 60
>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 = 41.1 bits (96), Expect = 3e-05
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 112 TEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHL-VKGKKV 170
TE DL+E F ++G + V +V ++ TG+ RGF FV + D +A + + G+++
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71
Query: 171 DVKKALSK 178
V +++K
Sbjct: 72 RVDYSITK 79
Score = 33.4 bits (76), Expect = 0.019
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 15 GLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAARPH 72
GL T+ L+ F +G + V V+ D +T +SRGF F+ + +DD++ A H
Sbjct: 6 GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFER---IDDSKEAMEH 60
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of SXL which governs sexual differentiation
and X chromosome dosage compensation in Drosophila
melanogaster. It induces female-specific alternative
splicing of the transformer (tra) pre-mRNA by binding to
the tra uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 41.2 bits (97), Expect = 4e-05
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L + L +T+E+ + F G V + +V +K TG GFGFV+Y + +A
Sbjct: 3 LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRA 58
Score = 37.0 bits (86), Expect = 0.001
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 21 SSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+ E +S F A G V + +++D +T S GFGF+ Y SA +DAQ A
Sbjct: 13 TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSA---EDAQRA 58
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 44.6 bits (105), Expect = 4e-05
Identities = 58/196 (29%), Positives = 88/196 (44%), Gaps = 25/196 (12%)
Query: 10 KLFIGGL-DYRTSSETLKSHFEAWGDVVDVVVMKDPQTK-KSRGFGFITYSSAHMVDDAQ 67
+LF+GG+ + E L+ + VVDV+V K K+RGF F+ Y S A
Sbjct: 140 RLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAA--AM 197
Query: 68 AAR---PHTID--SKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQ 122
A R P I V+ A P E++ + A VK L+V +L TEE +++ F +
Sbjct: 198 ARRKLMPGRIQLWGHVIAVDWAEPEEEVD-EDVMAKVKILYVRNLMTTTTEEIIEKSFSE 256
Query: 123 F--GEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--LKGTHLVKGKKVDV--KKAL 176
F G+V V K R + FV + D + KA L G L +G +++V K +
Sbjct: 257 FKPGKVERVK--------KIRDYAFVHFEDREDAVKAMDELNGKEL-EGSEIEVTLAKPV 307
Query: 177 SKEEMAKLKTRGGFGG 192
K+ + G G
Sbjct: 308 DKKSYVRYTRGTGGRG 323
Score = 35.4 bits (81), Expect = 0.037
Identities = 33/150 (22%), Positives = 65/150 (43%), Gaps = 13/150 (8%)
Query: 4 EPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMV 63
+P ++F+G + + L FE G + ++ +M D + ++RG+ F+T+
Sbjct: 54 QPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEA 112
Query: 64 DDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQF 123
+A +++ + P R + +LFVG + + E++ E F +
Sbjct: 113 KEAV----KLLNNYEIRPGRLLGVC------ISVDNCRLFVGGIPKNKKREEILEEFSKV 162
Query: 124 GE--VTSVALVTEKETGKKRGFGFVEYNDY 151
E V + + + K RGF FVEY +
Sbjct: 163 TEGVVDVIVYHSAADKKKNRGFAFVEYESH 192
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 40.6 bits (95), Expect = 4e-05
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 9/75 (12%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFV--EYNDYDPVDKAC 158
+LFVG+L DITEE++++ F ++G+ + + K +GFGF+ E + KA
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFI------HKDKGFGFIRLETRTLAEIAKAE 56
Query: 159 LKGTHLVKGKKVDVK 173
L L +GK++ V+
Sbjct: 57 LDNMPL-RGKQLRVR 70
Score = 34.9 bits (80), Expect = 0.004
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+LF+G L + E ++ FE +G ++ + KD +GFGFI + + + A+A
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKA 55
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. Also included in this subfamily is the
sex-lethal protein (SXL) from Drosophila melanogaster.
SXL governs sexual differentiation and X chromosome
dosage compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 41.1 bits (96), Expect = 4e-05
Identities = 14/48 (29%), Positives = 31/48 (64%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
L+V L +T+++L++ F Q+G + + ++ ++ TG RG GF+ ++
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFD 50
Score = 31.8 bits (72), Expect = 0.065
Identities = 17/71 (23%), Positives = 31/71 (43%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L++ GL + + L+ F +G ++ +++D T SRG GFI + ++A
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 71 PHTIDSKVVEP 81
EP
Sbjct: 63 NGQKPEGASEP 73
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 41.2 bits (96), Expect = 4e-05
Identities = 21/51 (41%), Positives = 31/51 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+FV +L + E L + FG FG VT+V ++ + T K +GFGFV +YD
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYD 54
Score = 31.6 bits (71), Expect = 0.084
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
+F+ L L F +G V +V V++D T K +GFGF+T ++
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTN 52
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 40.5 bits (95), Expect = 5e-05
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 7/75 (9%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CL 159
++ G D+K F G V V +++ + F+ + + + A L
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR----TVQPHAFITFENLEAAQLAIETL 57
Query: 160 KGTHLVKGKKVDVKK 174
G V G + V++
Sbjct: 58 NGAS-VDGNCIKVQR 71
>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein. This family of proteins
is greatly expanded in Trichomonas vaginalis. The
proteins are composed of several glycine rich motifs
interspersed through the sequence. Although many
proteins have been annotated by similarity in the family
these annotations given the biased composition of the
sequences these are unlikely to be functionally
relevant.
Length = 248
Score = 43.3 bits (103), Expect = 5e-05
Identities = 45/136 (33%), Positives = 53/136 (38%), Gaps = 25/136 (18%)
Query: 192 GNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGG------------------GWGG 233
G +G + N GG+ GGG G D + G+ GG G GG
Sbjct: 56 GGKGEDNSSNNMVKGGYNGGGDGGNDNSSNDGSGSGGGATDIRLNENSLKSRIIVAGGGG 115
Query: 234 NSGGGWGGNSGGGWGGNSGGGW-------GGNSAWGGQGGGGFGGGYQQSFGGGPMRGGG 286
SG GG+ G G G GGG GG GG+G G G G G GGG
Sbjct: 116 GSGNYNGGSGGFGGGLVGGGGTSNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNGGGGG 175
Query: 287 GGGRSGGAPYSGGRGG 302
GG GG + G GG
Sbjct: 176 GGYFGGGGGHYAGGGG 191
>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 = 40.8 bits (95), Expect = 5e-05
Identities = 19/68 (27%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 112 TEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKGTHL-VKGKKV 170
TE DL+E F ++G + V++V ++++ + RGF FV + + D +A + + + G+++
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 81
Query: 171 DVKKALSK 178
V +++K
Sbjct: 82 RVDFSITK 89
Score = 40.4 bits (94), Expect = 9e-05
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
L + GL T+ L+ F +G + DV ++ D Q+++SRGF F+ + + VDDA+ A+
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN---VDDAKEAK 68
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 40.8 bits (95), Expect = 5e-05
Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVE-YNDYDPVDKACLK 160
+FVG L +IT +D+K F FG ++ +V + TGK +G+GFV +N +D +
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 161 GTHLVKGKKV 170
G + G+++
Sbjct: 64 GGQWLGGRQI 73
Score = 34.7 bits (79), Expect = 0.007
Identities = 16/47 (34%), Positives = 31/47 (65%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+G L +++ +K+ F +G + D V+KD T KS+G+GF+++
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 40.5 bits (95), Expect = 6e-05
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+ LF+G+L T DL+E F +FGE+ + + K+ G + F++Y D V KA
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKA 57
Score = 39.3 bits (92), Expect = 1e-04
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
R LFIG L+ T+ L+ FE +G+++D+ + K + FI Y+
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPA---YAFIQYA 49
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog of
DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 40.6 bits (95), Expect = 7e-05
Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 4/78 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVD-KACLK 160
+FVG + + E +++ +F ++G V V ++T++ TG +G+GFV + YD VD + ++
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSF--YDDVDVQKIVE 64
Query: 161 GTHLVKGKKVDVKKALSK 178
GKK+ + A+ K
Sbjct: 65 SQINFHGKKLKLGPAIRK 82
Score = 36.3 bits (84), Expect = 0.002
Identities = 16/48 (33%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYS 58
+F+GG+D R ++S F +G V +V ++ D +T S+G+GF+++
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFY 54
>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 = 40.0 bits (94), Expect = 7e-05
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 11/77 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
++++G L E D++ +F +G + + L K GFGFVE+ D D A
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYE 52
Query: 159 LKGTHLVKGKKVDVKKA 175
L G L G++V V+ A
Sbjct: 53 LNGKELC-GERVIVEHA 68
Score = 27.7 bits (62), Expect = 1.5
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+++IG L YR ++ F+ +G + ++ + GFGF+ + DDA
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDA 49
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 43.6 bits (103), Expect = 7e-05
Identities = 37/115 (32%), Positives = 42/115 (36%), Gaps = 8/115 (6%)
Query: 193 NQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWG----GNSGGGWGGNSGGGWG 248
G P G G GGGG G GG S G G+ G G G +SG G G
Sbjct: 181 GGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGSG 240
Query: 249 GNSGGGWG-GNSAWGGQGGGGFGG---GYQQSFGGGPMRGGGGGGRSGGAPYSGG 299
G G G G W G G GG G G +++ R G G S S
Sbjct: 241 GTRSGQGGWGPGFWTGLGAGGALGYLFGSRRNNNSSYGRSYGSGSPSYSPSSSSN 295
Score = 40.1 bits (94), Expect = 8e-04
Identities = 26/85 (30%), Positives = 32/85 (37%)
Query: 208 WGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGG 267
GG GP + GG GGG GG GG G G+ + +G + G
Sbjct: 180 CGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGS 239
Query: 268 GFGGGYQQSFGGGPMRGGGGGGRSG 292
G Q +G G G G GG G
Sbjct: 240 GGTRSGQGGWGPGFWTGLGAGGALG 264
Score = 39.3 bits (92), Expect = 0.002
Identities = 25/74 (33%), Positives = 27/74 (36%), Gaps = 4/74 (5%)
Query: 223 WGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQ----GGGGFGGGYQQSFG 278
G GG G GG GGG GG GG G G + G G G +G
Sbjct: 179 SCGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYG 238
Query: 279 GGPMRGGGGGGRSG 292
G R G GG G
Sbjct: 239 SGGTRSGQGGWGPG 252
Score = 29.3 bits (66), Expect = 2.5
Identities = 24/72 (33%), Positives = 25/72 (34%), Gaps = 11/72 (15%)
Query: 239 WGGNSGGGWGGNSG-GGWGGNSAWGGQGGGGFGGGYQ----------QSFGGGPMRGGGG 287
GG GG +G GG GG GG GGG G G GP G G
Sbjct: 180 CGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGS 239
Query: 288 GGRSGGAPYSGG 299
GG G G
Sbjct: 240 GGTRSGQGGWGP 251
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 40.2 bits (95), Expect = 7e-05
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 11 LFIGGLDYRTSSETLKSH----FEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
L+I L+ + + LK F +G V+D+V K T K RG F+ + V+ A
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKD---VESA 55
Query: 67 QAAR 70
A
Sbjct: 56 TNAL 59
Score = 36.7 bits (86), Expect = 0.001
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 7/53 (13%)
Query: 102 LFVGSLRDDITEEDLK----EYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
L++ +L + I +++LK F QFG V + V K T K RG FV + D
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDI--VASK-TLKMRGQAFVVFKD 51
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end)
protein family. This subfamily corresponds to the RRM2
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and component of the NXF1
pathway. It binds to NXF1 and serves as receptor for the
RNA export element RTE. It also possess mRNA export
activity and can facilitate the access of DEAD-box
protein DBP5 to mRNA at the nuclear pore complex (NPC).
RNA-binding protein 15B (RBM15B), also termed one
twenty-two 3 (OTT3), is a paralog of RBM15 and therefore
has post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 39.7 bits (93), Expect = 1e-04
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
LFVG+L ITEE+L+ F ++G V V + G+ + FV++ + D +A
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVD-IKRPPRGQGNAYAFVKFLNLDMAHRA 59
Score = 37.8 bits (88), Expect = 5e-04
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R LF+G L+ + E L+ FE +G V DV + K P + + F+ + + M A+
Sbjct: 3 RTLFVGNLEITITEEELRRAFERYGVVEDVDI-KRPPRGQGNAYAFVKFLNLDMAHRAKV 61
Query: 69 A 69
A
Sbjct: 62 A 62
>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 = 39.6 bits (93), Expect = 1e-04
Identities = 16/56 (28%), Positives = 32/56 (57%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
++VG + TE++++ YF GE+ + L+T +TG+ RG F+ + + +A
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRA 56
Score = 31.2 bits (71), Expect = 0.086
Identities = 14/49 (28%), Positives = 32/49 (65%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
+++GG+ Y ++ + ++S+F G++ ++ +M P T + RG FIT+ +
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKT 49
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 40.0 bits (94), Expect = 1e-04
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGE-VTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
L++G L + E +K F GE V SV ++ K TG G+ FVE+ D ++ K
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61
Score = 25.8 bits (57), Expect = 9.6
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 6/61 (9%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWG-DVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++G L+ +K F + G V+ V ++++ T G+ F+ D+A A
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFV-----EFADEATAE 56
Query: 70 R 70
R
Sbjct: 57 R 57
>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 = 40.0 bits (93), Expect = 1e-04
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK- 160
LFV ++ D EDL+ FG++G + V + + T + RGF ++++ D + A
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 161 GTHLVKGKKVDVKKA 175
V G++++++ A
Sbjct: 63 NRKWVCGRQIEIQFA 77
Score = 39.2 bits (91), Expect = 2e-04
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
LF+ + T E L+ F +G +VDV V D T++ RGF +I + +DA
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDA 58
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 39.4 bits (92), Expect = 1e-04
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
L V +L ++ +DL + FG +GE+ + +ET KR F+E+ D + A LK
Sbjct: 4 LVVFNLDPSVSNDDLHQIFGAYGEIKEI-----RETPNKRHHKFIEFYDVRSAEAA-LKA 57
Query: 162 THL--VKGKKVDVK 173
+ + GK++ ++
Sbjct: 58 LNRSEIAGKRIKLE 71
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 39.6 bits (93), Expect = 1e-04
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 24/67 (35%)
Query: 6 EHLRKLF--IGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMV 63
E L +LF I GL+Y D+ +DP T KS+GF ++TYS+
Sbjct: 14 EQLHRLFDIIPGLEY-----------------CDL--KRDPYTGKSKGFAYVTYSNPAS- 53
Query: 64 DDAQAAR 70
A A+
Sbjct: 54 --AIYAK 58
Score = 30.8 bits (70), Expect = 0.14
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
++LFV + +T+E L F + L + TGK +GF +V Y+
Sbjct: 1 QRLFV-VVSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYS 49
>gnl|CDD|164795 PHA00370, III, attachment protein.
Length = 297
Score = 42.6 bits (100), Expect = 1e-04
Identities = 32/76 (42%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 197 GDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWG 256
G + GGG G GG D GG + GGN+GGG GG GG GG GG+ GGG
Sbjct: 78 GSADKDGDGGGTGEGGS---DTGGDTGGGNTGGGSGGGDTGGSGG------GGSDGGGSE 128
Query: 257 GNSAWGGQGGGGFGGG 272
G S G G G
Sbjct: 129 GGSTGKSLTKEGVGAG 144
Score = 41.1 bits (96), Expect = 4e-04
Identities = 28/73 (38%), Positives = 29/73 (39%)
Query: 214 GPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGY 273
G W GS+ GGG G G GG GG SGGG G S GG GGG GG
Sbjct: 72 GSWKPTGSADKDGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGGS 131
Query: 274 QQSFGGGPMRGGG 286
G G
Sbjct: 132 TGKSLTKEGVGAG 144
Score = 39.5 bits (92), Expect = 0.001
Identities = 28/61 (45%), Positives = 30/61 (49%)
Query: 188 GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGW 247
G GG GG G + GGG GGG G D GGS GG+ GGG G S G G G
Sbjct: 84 GDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEGVGA 143
Query: 248 G 248
G
Sbjct: 144 G 144
Score = 39.5 bits (92), Expect = 0.001
Identities = 26/64 (40%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 195 GGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGG 254
G D G+ GG G GG G GG++ GG+ GG GG+ GGG G GG GG++G
Sbjct: 78 GSADKDGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDG--GGSEGGSTGKS 135
Query: 255 WGGN 258
Sbjct: 136 LTKE 139
Score = 36.0 bits (83), Expect = 0.018
Identities = 26/71 (36%), Positives = 29/71 (40%), Gaps = 3/71 (4%)
Query: 186 TRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGG 245
T GGG G + GG GGG GG GG+ G GG+ GGG G S G
Sbjct: 77 TGSADKDGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGG---GGSDGGGSEGGSTG 133
Query: 246 GWGGNSGGGWG 256
G G G
Sbjct: 134 KSLTKEGVGAG 144
Score = 33.4 bits (76), Expect = 0.11
Identities = 23/61 (37%), Positives = 28/61 (45%)
Query: 241 GNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGR 300
+ GG G G GG++ G GGG GG S GGG GG GG +G + G
Sbjct: 82 KDGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEGV 141
Query: 301 G 301
G
Sbjct: 142 G 142
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells. And it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 86
Score = 39.7 bits (92), Expect = 1e-04
Identities = 21/51 (41%), Positives = 30/51 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+FV +L D E L + FG FG V +V ++ + T K +GFGFV +YD
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYD 56
Score = 30.1 bits (67), Expect = 0.32
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
+F+ L + L F +G V +V V++D T K +GFGF+T ++
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTN 54
>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 = 39.2 bits (92), Expect = 1e-04
Identities = 19/73 (26%), Positives = 42/73 (57%), Gaps = 2/73 (2%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-LK 160
+FV +L +T +DLK+ F + G V + T+ + G+ +GFG V + + +A +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59
Query: 161 GTHLVKGKKVDVK 173
+ ++G++++V+
Sbjct: 60 NGYDLEGRELEVR 72
Score = 32.6 bits (75), Expect = 0.028
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+F+ L + + + LK F G+V+ V D +S+GFG + + S +DAQ A
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESP---EDAQRA 55
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 39.1 bits (92), Expect = 2e-04
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVD-KACLK 160
L+VG+L TEE + E F + G++ + + ++ T GF FVEY Y D + +K
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEY--YTREDAENAVK 58
Query: 161 GTHLVKGKKVD 171
+ G K+D
Sbjct: 59 ---YLNGTKLD 66
Score = 31.4 bits (72), Expect = 0.10
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L++G L + T+ E + F GD+ +++ D TK GF F+ Y + +DA+ A
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTR---EDAENA 56
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 39.0 bits (91), Expect = 2e-04
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 96 GATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
GA+ + +++G+L + +EE+L+E +FG + + +V EK FV +
Sbjct: 1 GAS-RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKEK------NIAFVHF 46
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 39.2 bits (92), Expect = 2e-04
Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 10/69 (14%)
Query: 89 EINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
EI R T+ +VG+L T + L E+F Q GEV V + ET R + FVE+
Sbjct: 2 EIRR-----TI---YVGNLDPTTTADQLLEFFSQAGEVKYVRM-AGDETQPTR-YAFVEF 51
Query: 149 NDYDPVDKA 157
+ V A
Sbjct: 52 AEQTSVINA 60
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding
protein 7 (RBM7). This subfamily corresponds to the RRM
of RBM7, a ubiquitously expressed pre-mRNA splicing
factor that enhances messenger RNA (mRNA) splicing in a
cell-specific manner or in a certain developmental
process, such as spermatogenesis. RBM7 interacts with
splicing factors SAP145 (the spliceosomal splicing
factor 3b subunit 2) and SRp20. It may play a more
specific role in meiosis entry and progression. Together
with additional testis-specific RNA-binding proteins,
RBM7 may regulate the splicing of specific pre-mRNA
species that are important in the meiotic cell cycle.
RBM7 contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. .
Length = 75
Score = 39.1 bits (91), Expect = 2e-04
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+ LFVG+L +TEE + E F Q G V V + +K+ GK + F FV +
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNF 49
Score = 32.6 bits (74), Expect = 0.039
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
R LF+G LD + + E + F G V+ V + KD + K + F F+ +
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNF 49
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 39.1 bits (91), Expect = 2e-04
Identities = 19/75 (25%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAAR 70
+++G +DY +++E L++HF G + V ++ D + +G+ +I +++ V+ A A
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61
Query: 71 PHTIDSKVVE--PKR 83
+ +V++ PKR
Sbjct: 62 ESSFRGRVIKVLPKR 76
Score = 37.5 bits (87), Expect = 6e-04
Identities = 17/71 (23%), Positives = 38/71 (53%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
++VG++ T E+L+ +F G + V ++ +K +G +G+ ++E+ D V+ A
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61
Query: 162 THLVKGKKVDV 172
+G+ + V
Sbjct: 62 ESSFRGRVIKV 72
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 40.0 bits (94), Expect = 2e-04
Identities = 15/93 (16%), Positives = 31/93 (33%), Gaps = 17/93 (18%)
Query: 109 DDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA---------CL 159
+E+ +K YF FGE+ + + T G ++Y Y K +
Sbjct: 12 PSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKY--YGSPGKPDRAAKAALKAV 69
Query: 160 KGTHLVK--GKKV----DVKKALSKEEMAKLKT 186
+ + G + + + ++ KL
Sbjct: 70 RKAQDCRIGGAEFKVELNPNERKLEKIKDKLIK 102
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 40.9 bits (96), Expect = 2e-04
Identities = 31/60 (51%), Positives = 34/60 (56%)
Query: 179 EEMAKLKTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGG 238
++M L RGG GG GGGD G GGGG GGGG G + G G SGGG GG GG
Sbjct: 103 DQMQMLGGRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGA 162
Score = 39.8 bits (93), Expect = 6e-04
Identities = 31/58 (53%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 245 GGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
GG GG+ GGG GG+ G GGGG GGGY GG R GGGGGR+ G G GG
Sbjct: 109 GGRGGSGGGGGGGDEGGYGGGGGGGGGGY-----GGESRSGGGGGRASGGGGGGAGGG 161
Score = 39.4 bits (92), Expect = 7e-04
Identities = 32/71 (45%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 229 GGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGG 288
GG GG+ GGG GG+ GG GG GGG GG GG GG GG G GGG
Sbjct: 109 GGRGGSGGGGGGGDEGGYGGGGGGGG-------GGYGGESRSGGGGGRASGGGGGGAGGG 161
Query: 289 GRSGGAPYSGG 299
AP GG
Sbjct: 162 ASRPSAPAGGG 172
Score = 36.7 bits (85), Expect = 0.006
Identities = 26/52 (50%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 224 GGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQ 275
GG GGG G GGG GG GG G + GG GG + G GGGG GGG +
Sbjct: 115 GGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRA--SGGGGGGAGGGASR 164
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 38.8 bits (90), Expect = 2e-04
Identities = 20/56 (35%), Positives = 30/56 (53%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
LF+ L + T+ DL + F FG V S + +K+T + FGFV Y++ D A
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62
Score = 35.7 bits (82), Expect = 0.003
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LFI L + L F +G+V+ V D QT S+ FGF++Y + D AQAA
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNP---DSAQAA 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 = 38.9 bits (91), Expect = 2e-04
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 111 ITEEDLKEYFGQFG-EVTSVALVTEKETGKKRGFGFVEYN 149
+TEED++ G E V L+ K TG RGF FVE+
Sbjct: 14 VTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFM 53
Score = 34.3 bits (79), Expect = 0.008
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 37 DVVVMKDPQTKKSRGFGFITYSSAH 61
DV +M+ T SRGF F+ + S
Sbjct: 32 DVRLMRRKTTGASRGFAFVEFMSLE 56
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM1
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 74
Score = 38.7 bits (90), Expect = 3e-04
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
L+VG+L +TE+ LK+ F G V +V ++ +K K +GFVEY+
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQ 48
Score = 35.6 bits (82), Expect = 0.003
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
L++G LD R + + LK F+ G V +V ++ D + K +GF+ Y +H + A
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIA 55
>gnl|CDD|227493 COG5164, SPT5, Transcription elongation factor [Transcription].
Length = 607
Score = 41.9 bits (98), Expect = 3e-04
Identities = 20/107 (18%), Positives = 27/107 (25%), Gaps = 11/107 (10%)
Query: 191 GGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGG---WGGNSGG--GWGGNSGG 245
G G P N+ G WG + GS G + W G +
Sbjct: 459 GWKDGPKTPALNDPGIDWGDEKDNWY--KGSLIHALGKGLALEDYRDGLFMTAWKGQATS 516
Query: 246 GWG-GNSGGGWGGNSAWGG---QGGGGFGGGYQQSFGGGPMRGGGGG 288
W +G G G +GG +R G
Sbjct: 517 ASEISFVQPRWNNLVCVLDGEKKGTCGILNGINGDWGGTVIRSTKGS 563
Score = 32.3 bits (73), Expect = 0.38
Identities = 20/105 (19%), Positives = 26/105 (24%), Gaps = 7/105 (6%)
Query: 196 GGDPWGNNGGGGWGGGGPGP-WDQGGSSWGGNSGGGWGGNSGGGWGGNSG-GGWGGNSGG 253
GG G G P W G + N G G+ W S G
Sbjct: 439 GGIAAGAAATSSGLSGYRTPGWKDGPKTPALNDPGIDWGDEKDNWYKGSLIHALGKGLAL 498
Query: 254 GWGGN----SAWGGQGGGGFG-GGYQQSFGGGPMRGGGGGGRSGG 293
+ +AW GQ Q + G + G
Sbjct: 499 EDYRDGLFMTAWKGQATSASEISFVQPRWNNLVCVLDGEKKGTCG 543
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface
Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX)
proteins. This subgroup corresponds to the conserved
RNA recognition motif (RRM) in ECTO-NOX proteins (also
termed ENOX), comprising a family of plant and animal
NAD(P)H oxidases exhibiting both, oxidative and protein
disulfide isomerase-like, activities. They are
growth-related and drive cell enlargement, and may play
roles in aging and neurodegenerative diseases. ENOX
proteins function as terminal oxidases of plasma
membrane electron transport (PMET) through catalyzing
electron transport from plasma membrane quinones to
extracellular oxygen, forming water as a product. They
are also hydroquinone oxidases that oxidize externally
supplied NADH, hence NOX. ENOX proteins harbor a
di-copper center that lack flavin. ENOX proteins display
protein disulfide interchange activity that is also
possessed by protein disulfide isomerase. In contrast to
the classic protein disulfide isomerases, ENOX proteins
lack the double CXXC motif. This family includes two
ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed
candidate growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous and
refractory to drugs. ENOX2, also termed APK1 antigen, or
cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role in
cell proliferation and tumor progression. In contrast to
ENOX1, ENOX2 is drug-responsive and harbors a drug
binding site to which the cancer-specific S-peptide
tagged pan-ENOX2 recombinant (scFv) is directed.
Moreover, ENOX2 is specifically inhibited by a variety
of quinone site inhibitors that have anticancer activity
and is unique to the surface of cancer cells. ENOX
proteins contain many functional motifs.
Length = 84
Score = 38.5 bits (90), Expect = 3e-04
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 92 RPEAGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDY 151
RP TV FVG L ++ TEE ++E F Q GE+ ++ + K+ F + + +
Sbjct: 2 RPPGCKTV---FVGGLPENATEEIIREVFEQCGEIIAIRM-------SKKNFCHIRFAEE 51
Query: 152 DPVDKA 157
VDKA
Sbjct: 52 FAVDKA 57
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 38.0 bits (88), Expect = 4e-04
Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 9/75 (12%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFV--EYNDYDPVDKAC 158
+LFVG+L DITE++ K+ F ++GE V + K +GFGF+ E + KA
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56
Query: 159 LKGTHLVKGKKVDVK 173
L T + +G+++ V+
Sbjct: 57 LDDTPM-RGRQLRVR 70
Score = 30.7 bits (69), Expect = 0.16
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
+LF+G L + + K F +G+ +V + K +GFGFI S + + A+A
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKA 55
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 41.8 bits (98), Expect = 4e-04
Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 210 GGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGG-NSGGGWGGNSGGGWG 256
+ + ++ G GG GGG+GG GGG GG GGGW
Sbjct: 58 SSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGWR 105
Score = 39.5 bits (92), Expect = 0.002
Identities = 20/55 (36%), Positives = 21/55 (38%), Gaps = 6/55 (10%)
Query: 209 GGGGPGPWDQGGSSWGGNSGGGWGG-NSGGGWGGNSGGGWGGNSGGGWGGNSAWG 262
G S GG GGG+GG GGG GG GGGW W A
Sbjct: 65 NGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGW-----RFWLRLFAPA 114
Score = 36.0 bits (83), Expect = 0.022
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 220 GSSWGGNSGGGWGGNSGGGWG--GNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGG 272
+S S +G ++ G GG GGG+GG GG GGGG GG
Sbjct: 50 SASSSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGW 104
Score = 32.9 bits (75), Expect = 0.22
Identities = 16/59 (27%), Positives = 22/59 (37%), Gaps = 6/59 (10%)
Query: 174 KALSKEEMAKLKTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWG 232
+ + + + + G GGGG+GG G GG GG GGGW
Sbjct: 53 SSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFG------GGGGGGGGGGGGWR 105
Score = 32.9 bits (75), Expect = 0.23
Identities = 19/68 (27%), Positives = 25/68 (36%), Gaps = 4/68 (5%)
Query: 218 QGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSF 277
S+ +G ++ GG GGG G GG GG GG GGGG + + F
Sbjct: 56 TSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGG----GGGGGGGGWRFWLRLF 111
Query: 278 GGGPMRGG 285
Sbjct: 112 APADAHAD 119
Score = 31.7 bits (72), Expect = 0.52
Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 235 SGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGG 293
+ S +G +++ GGGG GGG FGG GGGGGG GG
Sbjct: 49 ASASSSATSSSASLVANGAVALLSASAISGGGGGGGGG----FGGFGGGGGGGGGGGGG 103
Score = 31.4 bits (71), Expect = 0.69
Identities = 20/53 (37%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 241 GNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGG 293
+ G S G GG G GGFGGG GG GGGGGG
Sbjct: 62 LVANGAVALLSASAISGGGGGGGGGFGGFGGG------GG---GGGGGGGGWR 105
Score = 29.8 bits (67), Expect = 2.0
Identities = 15/37 (40%), Positives = 18/37 (48%)
Query: 188 GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWG 224
GG GG GG +G GGGG GGGG + +
Sbjct: 78 GGGGGGGGGFGGFGGGGGGGGGGGGGWRFWLRLFAPA 114
Score = 29.4 bits (66), Expect = 2.5
Identities = 17/40 (42%), Positives = 17/40 (42%), Gaps = 11/40 (27%)
Query: 201 GNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWG 240
GGGG GG G G GGG GG GGGW
Sbjct: 77 SGGGGGGGGGFG-----------GFGGGGGGGGGGGGGWR 105
Score = 28.7 bits (64), Expect = 4.8
Identities = 17/54 (31%), Positives = 19/54 (35%), Gaps = 2/54 (3%)
Query: 173 KKALSKEEMAKLKTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGN 226
+L L + G GGG G GG G GGGG G G W
Sbjct: 59 SASLVANGAVALLSASAISGGGGGGG--GGFGGFGGGGGGGGGGGGGWRFWLRL 110
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 86
Score = 38.2 bits (89), Expect = 4e-04
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 10/63 (15%)
Query: 11 LFIGGLDYRTSSETL----KSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+F+ L S + L HF +G +V V V++D + R + F+ +++ DA
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDD---DA 58
Query: 67 QAA 69
+ A
Sbjct: 59 KNA 61
Score = 38.2 bits (89), Expect = 4e-04
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 7/64 (10%)
Query: 102 LFVGSL----RDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+FV SL DD E + E+F ++G + V ++ ++ ++R + FV++ + D A
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVL--RDW-RQRPYAFVQFTNDDDAKNA 61
Query: 158 CLKG 161
KG
Sbjct: 62 LAKG 65
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 38.1 bits (88), Expect = 4e-04
Identities = 20/51 (39%), Positives = 31/51 (60%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+F+ +L D E L + FG FG VT+V ++ + T K +GFGFV +Y+
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYE 54
Score = 30.4 bits (68), Expect = 0.27
Identities = 17/49 (34%), Positives = 26/49 (53%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
+FI L L F +G V +V V++D T K +GFGF+T ++
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTN 52
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 38.0 bits (89), Expect = 5e-04
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 3/76 (3%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA-- 157
+FVG++ + ++++ +++ + G+V S V + TGK + FGF E+ D + +A
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60
Query: 158 CLKGTHLVKGKKVDVK 173
L G L GKK+ VK
Sbjct: 61 LLNGLEL-GGKKLLVK 75
Score = 31.4 bits (72), Expect = 0.11
Identities = 14/52 (26%), Positives = 24/52 (46%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
+F+G + S + ++ E G V+ +KDP T K + FGF +
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDP 52
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM2 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two RRMs.
.
Length = 82
Score = 37.6 bits (88), Expect = 5e-04
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGE-VTSVALVTEKETGKK-RGFGFVEYNDYDPVD--- 155
+LFVG + T+E++ E F + E V V + + K RGF FVEY +
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMAR 62
Query: 156 KACLKGTHLVKGKKVDV 172
+ + G L+ G +V V
Sbjct: 63 RKLVPGRILLWGHEVAV 79
Score = 37.3 bits (87), Expect = 0.001
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGD-VVDVVVMKDPQTK-KSRGFGFITYSS 59
+LF+GG+ + E + F + VVDV+V + P K K+RGF F+ Y S
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYES 54
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 37.2 bits (86), Expect = 6e-04
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 8/57 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
++F+G L E+D++ +F +G + + L KRGFGFVE++D D A
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDA 49
Score = 28.0 bits (62), Expect = 1.5
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
++FIG L+ + ++ F+ +G + D+ + RGFGF+ + DDA
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDA 49
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 38.1 bits (88), Expect = 6e-04
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 95 AGATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
G LF+ L + ++DL + F FG V S + +K+T + FGFV Y++
Sbjct: 3 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 58
Score = 32.7 bits (74), Expect = 0.051
Identities = 18/49 (36%), Positives = 25/49 (51%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
LFI L + L F +G+VV V D QT S+ FGF++Y +
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 58
>gnl|CDD|147458 pfam05268, GP38, Phage tail fibre adhesin Gp38. This family
contains several Gp38 proteins from T-even-like phages.
Gp38, together with a second phage protein, gp57,
catalyzes the organisation of gp37 but is absent from
the phage particle. Gp37 is responsible for receptor
recognition.
Length = 261
Score = 40.2 bits (94), Expect = 7e-04
Identities = 38/93 (40%), Positives = 44/93 (47%), Gaps = 6/93 (6%)
Query: 202 NNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNS------GGGW 255
NNGG GGGG G +SW GN G GG G GG SG G + GGG
Sbjct: 146 NNGGAIAGGGGGGGGASLKNSWRGNGVCGGGGGRPFGAGGKSGSHMSGGNASLTAPGGGS 205
Query: 256 GGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGG 288
G SA+GG GG G +++GG GGG
Sbjct: 206 GTGSAYGGGNGGNVGAAGGRAWGGNGYEYGGGA 238
Score = 37.5 bits (87), Expect = 0.006
Identities = 45/123 (36%), Positives = 50/123 (40%), Gaps = 9/123 (7%)
Query: 189 GFGGNQGGGDPWGNNGGGGWG---GGGPGPWDQGGSSWGGNSGGG------WGGNSGGGW 239
G GGN G + G+NGG GG + G + GG GGG W GN G
Sbjct: 116 GRGGNGSGSNSAGSNGGHCIQNDIGGRLRINNGGAIAGGGGGGGGASLKNSWRGNGVCGG 175
Query: 240 GGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGG 299
GG G GG SG G +A GGG G G G G G GG GG Y G
Sbjct: 176 GGGRPFGAGGKSGSHMSGGNASLTAPGGGSGTGSAYGGGNGGNVGAAGGRAWGGNGYEYG 235
Query: 300 RGG 302
G
Sbjct: 236 GGA 238
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 37.3 bits (87), Expect = 8e-04
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
+FVG L +TE++L+ FG FGE+ V + K G GFV++
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGK------GCGFVQFVH 46
Score = 33.8 bits (78), Expect = 0.013
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 9/59 (15%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+F+GGLD + + L+S F +G++V V K P K G GF+ + A+AA
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYV---KIPPGK---GCGFVQFVHRA---AAEAA 53
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1,
or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3,
or CUG-BP2, or NAPOR) belong to the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family
of RNA-binding proteins that have been implicated in
regulation of pre-mRNA splicing, and control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. The
human CELF-1 is a nuclear and cytoplasmic RNA-binding
protein that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for onset
of type 1 myotonic dystrophy (DM1), a neuromuscular
disease associated with an unstable CUG triplet
expansion in the 3'-UTR (3'-untranslated region) of the
DMPK (myotonic dystrophy protein kinase) gene; it
preferentially targets UGU-rich mRNA elements. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contain three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains): two consecutive RRMs (RRM1
and RRM2) situated in the N-terminal region followed by
a linker region and the third RRM (RRM3) close to the
C-terminus of the protein. The two N-terminal RRMs of
EDEN-BP are necessary for the interaction with EDEN as
well as a part of the linker region (between RRM2 and
RRM3). Oligomerization of EDEN-BP is required for
specific mRNA deadenylation and binding. CELF-2 is
expressed in all tissues at some level, but highest in
brain, heart, and thymus. It has been implicated in the
regulation of nuclear and cytoplasmic RNA processing
events, including alternative splicing, RNA editing,
stability and translation. CELF-2 shares high sequence
identity with CELF-1, but shows different binding
specificity; it binds preferentially to sequences with
UG repeats and UGUU motifs. It has been shown to bind to
a Bruno response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to the
3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2
of CELF-2, can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. This subgroup also
includes Drosophila melanogaster Bruno protein, which
plays a central role in regulation of Oskar (Osk)
expression in flies. It mediates repression by binding
to regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 84
Score = 37.5 bits (87), Expect = 8e-04
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKK--RGFGFVEY 148
K+FVG + +E+DL+E F Q+G V + ++ ++ +G FV +
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52
Score = 34.4 bits (79), Expect = 0.010
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 10 KLFIGGLDYRTSSET-LKSHFEAWGDVVDVVVMKDPQT--KKSRGFGFITYSSAHMVDDA 66
K+F+G + R+ SE L+ FE +G V + V++D +S+G F+T+ + +A
Sbjct: 3 KMFVGQIP-RSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61
Query: 67 QAA 69
Q A
Sbjct: 62 QNA 64
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 37.0 bits (86), Expect = 9e-04
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTE-KETGKKRGFGFVEY---NDYDPVDK 156
K+ V ++ + T ++L+E F FGE+ +V L + TG RGFGFV++ D K
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61
Query: 157 ACLKGTHL 164
A THL
Sbjct: 62 ALCHSTHL 69
Score = 31.2 bits (71), Expect = 0.11
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDP-QTKKSRGFGFITYSSAHMVDDAQA 68
K+ + + + + + L+ F +G++ V + K T RGFGF+ + + DA+
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITK---QDAKR 58
Query: 69 A 69
A
Sbjct: 59 A 59
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including SCAF4,
SCAF8 and similar proteins. The biological role of SCAF4
remains unclear, but it shows high sequence similarity
to SCAF8 (also termed CDC5L complex-associated protein
7, or RNA-binding motif protein 16, or CTD-binding
SR-like protein RA8). SCAF8 is a nuclear matrix protein
that interacts specifically with a highly
serine-phosphorylated form of the carboxy-terminal
domain (CTD) of the largest subunit of RNA polymerase II
(pol II). The pol II CTD plays a role in coupling
transcription and pre-mRNA processing. In addition,
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein domain),
and serine/arginine-rich motifs.
Length = 77
Score = 36.9 bits (86), Expect = 9e-04
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 13/82 (15%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND----YDPVDKA 157
L++G L +TEEDLK F ++GE+ S+ ++ RG +V + + K
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQK- 57
Query: 158 CLKGTHLVKGKKVDVKKALSKE 179
L+ + GKK+ V A +K
Sbjct: 58 -LRN-VKLAGKKIKVAWAPNKG 77
Score = 27.3 bits (61), Expect = 2.3
Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
L+IG L + + E LK+ FE +G++ + ++ RG ++
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCM 45
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 75
Score = 37.0 bits (86), Expect = 0.001
Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L+VG+L +++ EE + E+F ++G V SV ++ ++ + FV++ D KA
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA-AFVDFVDIKSAQKA 56
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes. Since
the Hu proteins share high homology with the Drosophila
embryonic lethal abnormal vision (ELAV) protein, the Hu
family is sometimes referred to as the ELAV family.
Drosophila ELAV is exclusively expressed in neurons and
is required for the correct differentiation and survival
of neurons in flies. The neuronal members of the Hu
family include Hu-antigen B (HuB or ELAV-2 or Hel-N1),
Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D
(HuD or ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Moreover, HuR has an anti-apoptotic
function during early cell stress response. It binds to
mRNAs and enhances the expression of several
anti-apoptotic proteins, such as p21waf1, p53, and
prothymosin alpha. HuR also has pro-apoptotic function
by promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 79
Score = 36.9 bits (86), Expect = 0.001
Identities = 14/56 (25%), Positives = 31/56 (55%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L+V L +T+++L+ F +G + + ++ + TG RG GF+ ++ ++A
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERA 58
Score = 30.0 bits (68), Expect = 0.34
Identities = 14/47 (29%), Positives = 26/47 (55%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
L++ GL + + L++ F +G ++ ++ D T SRG GFI +
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF 49
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 36.9 bits (85), Expect = 0.001
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 12/73 (16%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC 158
VK LFV +L +TEE L++ F +FG++ V K + + FV + + D A
Sbjct: 1 VKVLFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEERD----AA 48
Query: 159 LKGTHLVKGKKVD 171
++ + GK+++
Sbjct: 49 VRAMDEMNGKEIE 61
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 84
Score = 37.0 bits (86), Expect = 0.001
Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 10/82 (12%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKR------GFGFVEYNDYDPV 154
++++ +L +EEDL+E+ F V SV + ++ G + G + E++ +
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPV-SVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59
Query: 155 DKAC--LKGTHLVKGKKVDVKK 174
+K L G + K +K+ VK
Sbjct: 60 EKVVKDLNG-KVFKNRKLFVKL 80
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 90
Score = 37.1 bits (85), Expect = 0.001
Identities = 14/48 (29%), Positives = 31/48 (64%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
L+V L +T+++L++ F Q+G + + ++ ++ TG RG GF+ ++
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 55
Score = 29.4 bits (65), Expect = 0.57
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
L++ GL + + L+ F +G ++ ++ D T SRG GFI +
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 54
>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 = 36.4 bits (85), Expect = 0.001
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 6/49 (12%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSS 59
+++G L + + E L+ F +G + +V V KD +G+ F+ + +
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDT 45
Score = 35.7 bits (83), Expect = 0.003
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 6/47 (12%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
++VG+L +TEE+L+ F FG + V + +K G+ FV +
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRF 43
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 37.0 bits (85), Expect = 0.001
Identities = 14/48 (29%), Positives = 31/48 (64%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
L+V L +T+++L++ F Q+G + + ++ ++ TG RG GF+ ++
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 52
Score = 29.3 bits (65), Expect = 0.56
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
L++ GL + + L+ F +G ++ ++ D T SRG GFI +
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 51
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast
pre-mRNA-splicing factor Cwc2 and similar proteins.
This subfamily corresponds to the RRM of yeast protein
Cwc2, also termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and an intervening loop,
also termed RNA-binding loop or RB loop, between ZnF
and RRM, all of which are necessary and sufficient for
RNA binding. The ZnF is also responsible for mediating
protein-protein interaction. The C-terminal flexible
region of Cwc2 interacts with the WD40 domain of Prp19.
Length = 78
Score = 36.5 bits (85), Expect = 0.001
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 10/53 (18%)
Query: 9 RKLFIGGLDYRTSS----ETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
R L++GG+ ++ E L+ HF WGD+ D+ V+ S+G F+ Y
Sbjct: 2 RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVL------PSKGIAFVRY 48
Score = 28.4 bits (64), Expect = 1.00
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 10/53 (18%)
Query: 100 KKLFVG----SLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+ L+VG EE L+ +FG++G++ + ++ K G FV Y
Sbjct: 2 RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSK------GIAFVRY 48
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 40.0 bits (93), Expect = 0.001
Identities = 14/30 (46%), Positives = 15/30 (50%)
Query: 248 GGNSGGGWGGNSAWGGQGGGGFGGGYQQSF 277
G S GG G G GGGG G GY + F
Sbjct: 513 VGQSYGGRGRTRGRGRGGGGGRGRGYNRGF 542
Score = 39.3 bits (91), Expect = 0.002
Identities = 17/67 (25%), Positives = 24/67 (35%), Gaps = 11/67 (16%)
Query: 166 KGKKVDVKKALSKEEMAKLKTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGG 225
KG V KK+ + + + G G ++ G G G G GG GG
Sbjct: 484 KGNNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGG-----------GG 532
Query: 226 NSGGGWG 232
G G+
Sbjct: 533 GRGRGYN 539
Score = 34.6 bits (79), Expect = 0.052
Identities = 12/36 (33%), Positives = 13/36 (36%), Gaps = 2/36 (5%)
Query: 221 SSWGGNSGGGWGGNSGG--GWGGNSGGGWGGNSGGG 254
S G + G G G G G GGG G G
Sbjct: 506 SGEGISKVGQSYGGRGRTRGRGRGGGGGRGRGYNRG 541
Score = 33.1 bits (75), Expect = 0.18
Identities = 11/30 (36%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 230 GWGGNSGGGWGGNSGG--GWGGNSGGGWGG 257
G G + G G G G G GGG G
Sbjct: 507 GEGISKVGQSYGGRGRTRGRGRGGGGGRGR 536
Score = 31.9 bits (72), Expect = 0.39
Identities = 11/31 (35%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 217 DQGGSSWGGNSGG-GWGGNSGGGWGGNSGGG 246
+ G S+GG G G GGG G G
Sbjct: 511 SKVGQSYGGRGRTRGRGRGGGGGRGRGYNRG 541
Score = 31.2 bits (70), Expect = 0.83
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 166 KGKKVDVKKALSKEEMAKLKTRGGFGGNQGGGDPWGNNGGGGWG-GGGPGPW 216
K + + +K + + G G +G G GGGG G G G W
Sbjct: 492 KSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGGGGRGRGYNRGFW 543
Score = 29.2 bits (65), Expect = 3.2
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 262 GGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGG 293
GQ GG G + GGG GG G G + G
Sbjct: 513 VGQSYGGRGRTRGRGRGGG---GGRGRGYNRG 541
Score = 28.9 bits (64), Expect = 3.9
Identities = 13/39 (33%), Positives = 14/39 (35%), Gaps = 4/39 (10%)
Query: 246 GWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRG 284
G G + G G G G GGG G G RG
Sbjct: 507 GEGISKVGQSYGGRGRTRGRGRGGGGGR----GRGYNRG 541
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 36.4 bits (85), Expect = 0.001
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 14/77 (18%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--- 158
L V +L I++++L+ F QFGEV + +ET + FVE+ YD + A
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEVKDI-----RETPLRPSQKFVEF--YD-IRAAEAAL 55
Query: 159 --LKGTHLVKGKKVDVK 173
L G G ++ VK
Sbjct: 56 DALNGRPF-LGGRLKVK 71
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM,
but unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might
share similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 36.2 bits (84), Expect = 0.002
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
L++ GL T + LK F +G VV ++ + ++ +R FGF+T +S
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASV 51
Score = 36.2 bits (84), Expect = 0.002
Identities = 17/56 (30%), Positives = 25/56 (44%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L+V L DLK+ F ++G+V +VT + R FGFV + K
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKC 57
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
being highly expressed throughout the brain and in
glandular tissues, moderately expressed in heart,
skeletal muscle, and liver, is also known as bruno-like
protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor
4. Like CELF-3, CELF-4 also contain three highly
conserved RRMs. The splicing activation or repression
activity of CELF-4 on some specific substrates is
mediated by its RRM1/RRM2. On the other hand, both RRM1
and RRM2 of CELF-4 can activate cardiac troponin T
(cTNT) exon 5 inclusion. CELF-5, expressed in brain, is
also known as bruno-like protein 5 (BRUNOL-5), or
CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, being strongly
expressed in kidney, brain, and testis, is also known
as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in a muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In addition to three highly conserved RRMs,
CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 36.3 bits (84), Expect = 0.002
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
RKLF+G L + + + ++ FE +G + + +++ P S+G F+ +SS +AQA
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSS---HAEAQA 57
Query: 69 A 69
A
Sbjct: 58 A 58
Score = 33.6 bits (77), Expect = 0.015
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+KLFVG L TE+D++ F FG + ++ + G +G FV++
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKF 49
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM2 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 81
Score = 36.5 bits (84), Expect = 0.002
Identities = 15/62 (24%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
L+V L ++++++++ F Q+G + + ++ ++ TG RG GF+ ++ ++A +KG
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA-IKG 62
Query: 162 TH 163
+
Sbjct: 63 LN 64
Score = 28.4 bits (63), Expect = 1.2
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
L++ GL S + ++ F +G ++ ++ D T SRG GFI + ++A
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA 59
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 36.6 bits (84), Expect = 0.002
Identities = 16/58 (27%), Positives = 31/58 (53%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+ +F L I DL+E+F G+V V +++++ + + +G +VE+ D V A
Sbjct: 2 RTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLA 59
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 77
Score = 36.0 bits (83), Expect = 0.002
Identities = 21/59 (35%), Positives = 30/59 (50%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK 160
L V +L T E+ +E +G + LV + TG +G+GFVEY D KA L+
Sbjct: 2 LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLE 60
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM2 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contains three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains): two consecutive RRMs
(RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The two
N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including
alternative splicing, RNA editing, stability and
translation. CELF-2 shares high sequence identity with
CELF-1, but shows different binding specificity; it
preferentially binds to sequences with UG repeats and
UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 36.2 bits (83), Expect = 0.002
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
RKLFIG + + + ++ F +G + + +++ P SRG F+T+++ M A
Sbjct: 2 RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIK 60
Query: 69 A 69
A
Sbjct: 61 A 61
Score = 33.1 bits (75), Expect = 0.030
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
+KLF+G + E D++ F FG++ ++ + G RG FV +
Sbjct: 2 RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTFT 50
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment
factor B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described
functions in transcriptional repression, RNA splicing
and metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1
has been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
nuclear localization signal (NLS). The C-terminus of
SAFB1 contains Glu/Arg- and Gly-rich regions that might
be involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously
coexpressed and share very high sequence similarity,
suggesting that they might function in a similar
manner. However, unlike SAFB1, exclusively existing in
the nucleus, SAFB2 is also present in the cytoplasm.
The additional cytoplasmic localization of SAFB2
implies that it could play additional roles in the
cytoplasmic compartment which are distinct from the
nuclear functions shared with SAFB1.
Length = 76
Score = 35.9 bits (82), Expect = 0.002
Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
R L++ GL T + LK+ F +G VV V+ + ++ +R +GF+T S++
Sbjct: 2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTS 53
Score = 30.5 bits (68), Expect = 0.22
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
+ L+V L DLK F ++G+V +VT + R +GFV + + K C+
Sbjct: 2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATK-CI 60
Query: 160 KGTH 163
H
Sbjct: 61 NHLH 64
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, a novel
mRNA export factor and component of the NXF1 pathway. It
binds to NXF1 and serves as receptor for the RNA export
element RTE. It also possesses mRNA export activity and
can facilitate the access of DEAD-box protein DBP5 to
mRNA at the nuclear pore complex (NPC). RBM15 belongs to
the Spen (split end) protein family, which contain three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 36.1 bits (83), Expect = 0.002
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
+ LF+G+L +TE DL+ F +FG +T V + G+ +GF+++ + D +A L
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVD-IKRPGRGQTSTYGFLKFENLDMAHRAKL 66
Score = 29.9 bits (67), Expect = 0.34
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R LF+G LD + L+ F+ +G + +V + K P ++ +GF+ + + M A+
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVDI-KRPGRGQTSTYGFLKFENLDMAHRAKL 66
Query: 69 A 69
A
Sbjct: 67 A 67
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 34.8 bits (81), Expect = 0.003
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 116 LKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CLKGTHLVKGKKVDVK 173
L + F FG V + K KK GF FVE++ + +KA L G G+ + V
Sbjct: 1 LYKLFSPFGNVEKI-----KLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLF-GGRPLRVD 54
Query: 174 KA 175
+
Sbjct: 55 YS 56
Score = 34.8 bits (81), Expect = 0.003
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 8/45 (17%)
Query: 25 LKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L F +G+V + ++ KK GF F+ +S+ A+ A
Sbjct: 1 LYKLFSPFGNVEKIKLL-----KKKPGFAFVEFSTEE---AAEKA 37
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 35.5 bits (82), Expect = 0.003
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 12/73 (16%)
Query: 101 KLFVGSL-RDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA-- 157
+LF+G+L +++EDL F +GE+ + L K +GFV+++ + A
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVL--------KNAYGFVQFDSPESCANAIN 52
Query: 158 CLKGTHLVKGKKV 170
C +G +++G+K+
Sbjct: 53 CEQGK-MIRGRKL 64
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 77
Score = 35.7 bits (82), Expect = 0.003
Identities = 18/56 (32%), Positives = 28/56 (50%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L + +L T++ +E FG + LV + TG +G+GFVEY D +A
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARA 57
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 35.2 bits (82), Expect = 0.003
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLK- 160
L+V + + D+++ F Q+GE+ S+ + + K R F +V++ + A
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLR-FNKTRRFCYVQFTSPESAAAAVALL 61
Query: 161 GTHLVKGKKVDVK 173
L +G K+ VK
Sbjct: 62 NGKLGEGYKLVVK 74
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 35.4 bits (81), Expect = 0.004
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 8/83 (9%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA- 157
+ KL++G+L +T EDL++ FG L + K G+ FV+Y D + +A
Sbjct: 1 MNKLYIGNLSPAVTAEDLRQLFGD------RKLPLTGQVLLKSGYAFVDYPDQNWAIRAI 54
Query: 158 -CLKGTHLVKGKKVDVKKALSKE 179
L G + GK ++V ++ K+
Sbjct: 55 ETLSGKVELHGKVMEVDYSVPKK 77
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome
proliferator-activated receptor gamma coactivator 1A
(PGC-1alpha) family of regulated coactivators. This
subfamily corresponds to the RRM of PGC-1alpha,
PGC-1beta, and PGC-1-related coactivator (PRC), which
serve as mediators between environmental or endogenous
signals and the transcriptional machinery governing
mitochondrial biogenesis. They play an important
integrative role in the control of respiratory gene
expression through interacting with a number of
transcription factors, such as NRF-1, NRF-2, ERR, CREB
and YY1. All family members are multi-domain proteins
containing the N-terminal activation domain, an LXXLL
coactivator signature, a tetrapeptide motif (DHDY)
responsible for HCF binding, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In contrast to PGC-1alpha
and PRC, PGC-1beta possesses two glutamic/aspartic
acid-rich acidic domains, but lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 89
Score = 35.4 bits (82), Expect = 0.004
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
++VG + D T +L++ F FGE+ + L ++ G +GFV Y +A G
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITL-HFRDDGDN--YGFVTYRYACDAFRAIEHG 61
Query: 162 THL 164
Sbjct: 62 NDD 64
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 92
Score = 35.7 bits (83), Expect = 0.004
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 7 HLRKLFIGGL--DYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVD 64
H R LF+ L +R S L+ F G + P + RGF F+ Y++A +
Sbjct: 1 HSRCLFVDRLPKTFRDVSI-LRKLFSQVGKPTFCQLAIAPNGQ-PRGFAFVEYATAEDAE 58
Query: 65 DAQAA 69
+AQ A
Sbjct: 59 EAQQA 63
Score = 35.3 bits (82), Expect = 0.005
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 100 KKLFVGSL-RDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA- 157
+ LFV L + L++ F Q G+ T L G+ RGF FVEY + ++A
Sbjct: 3 RCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAI-APNGQPRGFAFVEYATAEDAEEAQ 61
Query: 158 ------CLKGTHL 164
L+G+ +
Sbjct: 62 QALNGHSLQGSPI 74
>gnl|CDD|240932 cd12488, RRM2_hnRNPR, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM2 of hnRNP R, a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. It contains an acidic auxiliary N-terminal
region, followed by two well-defined and one degenerated
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal RGG motif. hnRNP R binds RNA through
its RRM domains. .
Length = 85
Score = 35.5 bits (81), Expect = 0.004
Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGE-VTSVALVTEKETGKK-RGFGFVEYNDYDPVDKA 157
+LFVGS+ + T+E++ E F + E + V L + + KK RGF F+EY D+ +A
Sbjct: 4 RLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQA 62
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 35.3 bits (81), Expect = 0.005
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R LFIG LD+ S L+ F+ +G +++ VV+K P + + F+ + + M A+
Sbjct: 9 RNLFIGNLDHNVSEVELRRAFDKYG-IIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKV 67
Query: 69 A 69
A
Sbjct: 68 A 68
Score = 29.2 bits (65), Expect = 0.73
Identities = 13/58 (22%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+ LF+G+L +++E +L+ F ++G + V ++ G+ + F+++ + D +A
Sbjct: 9 RNLFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKFQNLDMAHRA 65
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein
S1-1 (S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains 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 = 87
Score = 35.4 bits (81), Expect = 0.005
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 37 DVVVMKDPQTKKSRGFGFITYSS----AHMVDDAQAARPH-TIDSKVV 79
+V V+KD QT+ +RGF FI S+ A ++ QA P +ID K +
Sbjct: 33 NVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLSIDGKTI 80
>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 = 35.0 bits (80), Expect = 0.005
Identities = 13/56 (23%), Positives = 33/56 (58%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L++ L +T++D+++ F +FG + + ++ ++ TG RG F+ ++ ++A
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEA 58
Score = 29.2 bits (65), Expect = 0.63
Identities = 15/56 (26%), Positives = 28/56 (50%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
L+I GL + + ++ F +G +++ V+ D T SRG FI + ++A
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEA 58
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 34.9 bits (81), Expect = 0.005
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 9/68 (13%)
Query: 110 DITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--LKGTHLVKG 167
+TEE LK+ F FG + ++++ EKE + GFV + + D+A L GT V+G
Sbjct: 13 GLTEEILKKAFSPFGNIINISM--EKE----KNCGFVTFEKMESADRAIAELNGT-TVQG 65
Query: 168 KKVDVKKA 175
++ V A
Sbjct: 66 VQLKVSLA 73
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 34.9 bits (80), Expect = 0.005
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 11/77 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
++++G L + E+D++ +FG +G++ + L K G+GFVE+ D D A
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYE 52
Query: 159 LKGTHLVKGKKVDVKKA 175
L G L G++V V+ A
Sbjct: 53 LNGKDLC-GERVIVEHA 68
>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 = 34.9 bits (80), Expect = 0.006
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 12/81 (14%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVT--------SVALVTEKETGKKRGFGFVEYNDYDP 153
++V L D++T E+L ++F G V V + T+KETGK +G V Y D P
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYED-PP 61
Query: 154 VDKACLKGTHLVKGKKVDVKK 174
KA ++ GK K
Sbjct: 62 SAKAAVE---WFDGKDFQGSK 79
>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 = 34.5 bits (79), Expect = 0.006
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
++FV +L D T + LK+ F + G V + E GK +G G V + + ++AC
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERACRM 58
Query: 159 LKGTHLVKGKKVDVK 173
+ G L G+++DV+
Sbjct: 59 MNGYKL-NGREIDVR 72
>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 85
Score = 35.1 bits (80), Expect = 0.006
Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGE-VTSVALVTEKETGKK-RGFGFVEYNDYDPVDKA 157
+LFVGS+ T+E + E F + E +T V L + + KK RGF F+EY D+ +A
Sbjct: 4 RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQA 62
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 35.0 bits (81), Expect = 0.006
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQ-FGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
LFVG L D+ + L E+F + + +V + + G RG+GFV ++D +A
Sbjct: 4 LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALTE 62
Query: 159 LKGTHLVKGKKVDVKKALSK 178
++G + GK + V A+ K
Sbjct: 63 MQGASGLGGKPIRVSLAIPK 82
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in the
system using SV40 DNA. MSSP-2 is identical with Scr3, a
human protein which complements the defect of cdc2
kinase in Schizosaccharomyces pombe. MSSP-2 has been
implied in regulating DNA replication, transcription,
apoptosis induction, and cell-cycle movement, via the
interaction with C-MYC, the product of protooncogene
c-myc. MSSP-2 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 75
Score = 34.7 bits (79), Expect = 0.007
Identities = 16/56 (28%), Positives = 31/56 (55%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L++ L T++DL + +G++ S + +K T K +G+GFV+++ KA
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 59
Score = 31.3 bits (70), Expect = 0.12
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L+I GL T+ + L + +G +V + D T K +G+GF+ + S A A
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 62
>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 = 34.1 bits (79), Expect = 0.008
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
L + +L D+TE DL FG+VT+V L+ + + VE + V+ A
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLL------RGKNQALVEMDS---VESAKSMV 52
Query: 162 TH------LVKGKKV 170
+ L++G++V
Sbjct: 53 DYYLTVPALIRGRRV 67
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 34.3 bits (78), Expect = 0.008
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDK--ACL 159
L+VG+L D+TE + + F Q G S ++TE + + FVE+ ++ A +
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59
Query: 160 KGTHLVKGKKVDVKKALS 177
G ++ GK+V V A +
Sbjct: 60 NGRKIL-GKEVKVNWATT 76
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 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 = 86
Score = 34.5 bits (79), Expect = 0.009
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 37 DVVVMKDPQTKKSRGFGFITYSSA----HMVDDAQAARPH-TIDSKVV 79
++ ++KD QT+++RGF F+ SSA ++ QA P ID K +
Sbjct: 33 NIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTI 80
Score = 29.1 bits (65), Expect = 0.66
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 126 VTSVALVTEKETGKKRGFGFVE 147
V+++ L+ +K+T + RGF FV+
Sbjct: 31 VSNIRLIKDKQTQQNRGFAFVQ 52
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 34.2 bits (78), Expect = 0.011
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
++F+G + + L FE G + D+ +M DP T +RG+ F+T+ + +A
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEA 59
Score = 31.9 bits (72), Expect = 0.072
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-L 159
++FVG + D+ E++L F + G + + L+ + TG RG+ FV + + +A L
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62
Query: 160 KGTHLVK-GKKVDV 172
H ++ GK + V
Sbjct: 63 YNNHEIRPGKHIGV 76
>gnl|CDD|226728 COG4278, COG4278, Uncharacterized conserved protein [Function
unknown].
Length = 269
Score = 36.4 bits (84), Expect = 0.011
Identities = 19/60 (31%), Positives = 23/60 (38%), Gaps = 6/60 (10%)
Query: 225 GNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRG 284
G G G +G S G G G GG++ G GG GG FGG P+
Sbjct: 215 KKWMSGCGSYGGKNFG--SPSGVGDMYFHGCGGHTGGDGSFCGGGCGG----FGGDPLGE 268
Score = 33.0 bits (75), Expect = 0.14
Identities = 21/63 (33%), Positives = 25/63 (39%), Gaps = 9/63 (14%)
Query: 209 GGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGG 268
G GG ++G S G G G GG++ GG G GGG GG GG
Sbjct: 215 KKWMSGCGSYGGKNFG--SPSGVGDMYFHGCGGHT-GGDGSFCGGGCGGF------GGDP 265
Query: 269 FGG 271
G
Sbjct: 266 LGE 268
Score = 32.2 bits (73), Expect = 0.25
Identities = 20/61 (32%), Positives = 21/61 (34%), Gaps = 7/61 (11%)
Query: 233 GNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSG 292
G G G +G S G G G GG GG GGG GG GG G
Sbjct: 215 KKWMSGCGSYGGKNFG--SPSGVGDMY---FHGCGGHTGGDGSFCGGGC--GGFGGDPLG 267
Query: 293 G 293
Sbjct: 268 E 268
Score = 32.2 bits (73), Expect = 0.30
Identities = 20/57 (35%), Positives = 24/57 (42%), Gaps = 5/57 (8%)
Query: 201 GNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGG 257
+G G +GG G S G G GG++ GG G GGG GG G G
Sbjct: 217 WMSGCGSYGGKNFGS----PSGVGDMYFHGCGGHT-GGDGSFCGGGCGGFGGDPLGE 268
Score = 29.1 bits (65), Expect = 2.4
Identities = 19/58 (32%), Positives = 21/58 (36%), Gaps = 4/58 (6%)
Query: 241 GNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSG 298
G G G +G S G G GG + G G GGG GG GG P
Sbjct: 215 KKWMSGCGSYGGKNFGSPSGVGDMYFHGCGGH---TGGDGSFCGGGCGG-FGGDPLGE 268
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 34.4 bits (78), Expect = 0.011
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
L++ L + T++DL + +G++ S + +K T K +G+GFV+++ A K
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS----PAAAQKA 65
Query: 162 THLVKGKKVDVKKALSKEE 180
+K V + A +E+
Sbjct: 66 VSALKASGVQAQMAKQQEQ 84
Score = 32.5 bits (73), Expect = 0.043
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L+I GL T+ + L + +G +V + D T K +G+GF+ + S A +A
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSA 68
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable
RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 34.3 bits (78), Expect = 0.011
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC- 158
+ +F L I DL+++F G+V V +++++ + + +G +VE+ + V A
Sbjct: 2 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 61
Query: 159 LKGTHLV 165
L G L+
Sbjct: 62 LTGQRLL 68
Score = 33.9 bits (77), Expect = 0.016
Identities = 15/55 (27%), Positives = 26/55 (47%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMV 63
R +F L R L+ F A G V DV ++ D +++S+G ++ + V
Sbjct: 2 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 56
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 33.9 bits (78), Expect = 0.011
Identities = 16/43 (37%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 96 GATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETG 138
GA+ + +++G++ D +TEE L+ F Q+GE+ SV + EK
Sbjct: 1 GAS-RNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCA 42
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 34.2 bits (78), Expect = 0.012
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA---C 158
L V +L ++ E L++ F QFG V A+V + G+ G GFVE+ KA C
Sbjct: 2 LTVKNLSPVVSNELLEQAFSQFGPVER-AVVIVDDRGRPTGKGFVEFAAKPAARKALERC 60
Query: 159 LKGTHLV 165
G L+
Sbjct: 61 ADGAFLL 67
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 34.3 bits (79), Expect = 0.012
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 8/81 (9%)
Query: 98 TVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
++K F+ + DD+ E +++YF QFG+ SV + + GFV + + +K
Sbjct: 1 SIKSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVN------HRAKCGFVRFETREAAEKF 54
Query: 158 --CLKGTHLVKGKKVDVKKAL 176
+ L G L
Sbjct: 55 AAAISENGLNAGLSRGGLLVL 75
>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-4, can activate cardiac troponin T (cTNT)
exon 5 inclusion. CELF-5, expressed in brain, is also
known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein 6
(BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent manner
and can activate inclusion via multiple copies of a
single element, MSE2. CELF-6 also promotes skipping of
exon 11 of insulin receptor, a known target of CELF
activity that is expressed in kidney. In addition to
three highly conserved RRMs, CELF-6 also possesses
numerous potential phosphorylation sites, a potential
nuclear localization signal (NLS) at the C terminus, and
an alanine-rich region within the divergent linker
region. .
Length = 79
Score = 34.1 bits (78), Expect = 0.013
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
LF+ L + + +L + F FG V S + ++ T + + FGFV +++
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDN 55
Score = 31.7 bits (72), Expect = 0.068
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
LFI L L F +G+V+ V D T +S+ FGF+++ + AQAA
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPA---SAQAA 62
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 33.6 bits (77), Expect = 0.013
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 8/52 (15%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRG--FGFVEYND 150
+++VG+L DI +D+++ F ++G + + L +RG F FVE+ D
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDL------KNRRGPPFAFVEFED 46
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 33.6 bits (77), Expect = 0.013
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
+++VG+L D+ E+DL++ F ++G + + L K F FV + D
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFED 47
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 36.7 bits (85), Expect = 0.013
Identities = 21/67 (31%), Positives = 26/67 (38%), Gaps = 3/67 (4%)
Query: 217 DQGGSSWGGNSGGGW-GGNSGGGWGG--NSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGY 273
G SS G S G NS G + N G + N +GG G GG+GG
Sbjct: 4 TDGSSSNGSVSSGPSNNYNSYGPYPDSSNPYGNYQANHQDNYGGFRPGYGNYSGGYGGFG 63
Query: 274 QQSFGGG 280
S+G
Sbjct: 64 MNSYGSS 70
Score = 30.5 bits (69), Expect = 1.3
Identities = 16/63 (25%), Positives = 22/63 (34%), Gaps = 4/63 (6%)
Query: 240 GGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGG 299
+ G S G +++G G Q+ + GG R G YSGG
Sbjct: 3 STDGSSSNGSVSSGPSNNYNSYGPYPDSSNPYGNYQANH----QDNYGGFRPGYGNYSGG 58
Query: 300 RGG 302
GG
Sbjct: 59 YGG 61
>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 = 33.6 bits (77), Expect = 0.014
Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
++VG+L DI E ++++ F ++G + + L K + G+ F+E+ D
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFED 47
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 34.2 bits (79), Expect = 0.014
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSV----ALVTEKETGKK 140
+FVG+L ++DLK+ F QFG + SV V EK+ KK
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKK 45
>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 33.4 bits (76), Expect = 0.017
Identities = 23/76 (30%), Positives = 44/76 (57%), Gaps = 3/76 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYF-GQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC- 158
++F+ ++ D+ + +K+ + GEVT V L + E GK RG G VE+ D + V KA
Sbjct: 1 RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAE-GKSRGCGVVEFKDEEFVKKALE 59
Query: 159 LKGTHLVKGKKVDVKK 174
+ + + G+ +++K+
Sbjct: 60 VMNKYDLNGRPLNIKE 75
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM1 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding protein
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 33.3 bits (76), Expect = 0.017
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 7/69 (10%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC- 158
+ LFV ++ D+TE L+ F +G+V V TE+ G V + D +A
Sbjct: 2 RSLFVINVPRDVTESTLRRLFEVYGDVRGVQ--TER---ISEGIVTVHFYDIRDAKRAVR 56
Query: 159 -LKGTHLVK 166
L G H+ +
Sbjct: 57 ELCGRHMQQ 65
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 33.5 bits (77), Expect = 0.017
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 8/57 (14%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVT--------SVALVTEKETGKKRGFGFVEYND 150
+FV +L + TE+DL E+FG G + + L +K+TG+ +G V Y+D
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDD 57
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 33.3 bits (77), Expect = 0.017
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+F+G + + L FE G + ++ +M D +RG+ F+TY+ + AQ A
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYT---NKEAAQRA 58
Score = 30.6 bits (70), Expect = 0.16
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CL 159
+FVG + D+ E++L F + G + + L+ + +G RG+ FV Y + + +A L
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDF-SGLNRGYAFVTYTNKEAAQRAVKQL 62
Query: 160 KGTHLVKGKKVDVKK 174
+ GK++ V
Sbjct: 63 HNYEIRPGKRLGVCI 77
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 83
Score = 33.7 bits (77), Expect = 0.017
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 114 EDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CLKGTHLVKGKKVD 171
LK+ FG++G+V + ++ GK GF FV + A G + G+ V
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALENTNGLE-IDGRPVA 73
Query: 172 VKKALSKE 179
V A+ K
Sbjct: 74 VDWAVQKN 81
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 33.3 bits (76), Expect = 0.019
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
+ LFV +L +IT ++LKE F ++ + + G +G ++E+ +KA
Sbjct: 4 RTLFVKNLPYNITVDELKEVFEDAVDIRLPS----GKDGSSKGIAYIEFKTEAEAEKA 57
Score = 31.0 bits (70), Expect = 0.12
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDV-VVMKDPQTKKSRGFGFITYSS 59
R LF+ L Y + + LK FE D VD+ + S+G +I + +
Sbjct: 4 RTLFVKNLPYNITVDELKEVFE---DAVDIRLPSGK--DGSSKGIAYIEFKT 50
>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 = 33.1 bits (76), Expect = 0.019
Identities = 16/50 (32%), Positives = 30/50 (60%), Gaps = 3/50 (6%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
+++VG+L DI E D+++ F ++G + ++ L K + F FVE+ D
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFED 47
>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein CPEB-2, CPEB-3,
CPEB-4 and similar protiens. This subgroup corresponds
to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and
CPEB-4, all well-conserved in both, vertebrates and
invertebrates. Due to the high sequence similarity,
members in this family 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.
Moreover, 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 family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a Zn-finger motif.
In addition, they do have conserved nuclear export
signals that are not present in CPEB-1. .
Length = 92
Score = 33.6 bits (77), Expect = 0.019
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVT 127
+K+FVG L DI E+++ F +FG +
Sbjct: 1 RKVFVGGLPPDIDEDEITASFRRFGPLV 28
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 33.3 bits (76), Expect = 0.020
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
++FVG + D+ E++L F + G++ L+ E +G+ RG+ FV Y
Sbjct: 3 EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEF-SGENRGYAFVMY 49
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 36.0 bits (83), Expect = 0.020
Identities = 27/69 (39%), Positives = 28/69 (40%), Gaps = 17/69 (24%)
Query: 215 PWDQGGSSWGGNSGGGWGGNSGGGWGGNSG------------GGWGGNSGGGWGGNSAWG 262
PW G S GGNSGG GN GG G GG GG G G GG S+
Sbjct: 15 PW--GSSKPGGNSGGN--GNKGGRDQGPPDLDDIFRKLSKKLGGLGGGKGTGSGGGSSSQ 70
Query: 263 GQGGGGFGG 271
G GG
Sbjct: 71 GP-RPQLGG 78
Score = 34.8 bits (80), Expect = 0.046
Identities = 27/74 (36%), Positives = 29/74 (39%), Gaps = 14/74 (18%)
Query: 191 GGNQGGGDPWGN--NGGGGWGGGGPGPWDQGG----------SSWGGNSGGGWGGNSGGG 238
G N DPWG+ GG G G G DQG S G GGG G SGG
Sbjct: 7 GNNGQDRDPWGSSKPGGNSGGNGNKGGRDQGPPDLDDIFRKLSKKLGGLGGGKGTGSGG- 65
Query: 239 WGGNSGGGWGGNSG 252
G +S G G
Sbjct: 66 -GSSSQGPRPQLGG 78
Score = 27.9 bits (62), Expect = 8.1
Identities = 27/83 (32%), Positives = 32/83 (38%), Gaps = 13/83 (15%)
Query: 216 WDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWG------GQGGGGF 269
W+Q G++ G WG + GG NSGG GN GG G + GG
Sbjct: 3 WNQPGNN--GQDRDPWGSSKPGG---NSGGN--GNKGGRDQGPPDLDDIFRKLSKKLGGL 55
Query: 270 GGGYQQSFGGGPMRGGGGGGRSG 292
GGG GGG G G
Sbjct: 56 GGGKGTGSGGGSSSQGPRPQLGG 78
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 33.4 bits (76), Expect = 0.020
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTS--------VALVTEKETGKKRGFGFVEYND 150
+FV L +D+T E + +YF Q G + + + L T++ETGK +G V ++D
Sbjct: 5 IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 61
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 33.1 bits (75), Expect = 0.023
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 13/81 (16%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQF--GEVTSVALVTEKETGKKRGFGFVEYNDYDPVDK 156
VK L+V +L + +E+ +K+ FGQF G V V K R + FV + +
Sbjct: 1 VKILYVRNLMIETSEDTIKKTFGQFNPGCVERVK--------KIRDYAFVHFTSREDAVH 52
Query: 157 AC--LKGTHLVKGKKVDVKKA 175
A L GT L +G ++V A
Sbjct: 53 AMNNLNGTEL-EGSCIEVTLA 72
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, and in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; it binds RNA through its RRM domains. .
Length = 79
Score = 33.0 bits (75), Expect = 0.024
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
++F+G + + L FE G + D+ +M DP + ++RG+ FIT+ +A
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59
Score = 31.9 bits (72), Expect = 0.059
Identities = 14/57 (24%), Positives = 32/57 (56%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
++FVG + D+ E++L F + G + + L+ + +G+ RG+ F+ + + +A
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEA 59
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 80
Score = 33.3 bits (75), Expect = 0.026
Identities = 15/56 (26%), Positives = 31/56 (55%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
L++ L T++DL + +G++ S + +K T + +G+GFV+++ KA
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKA 62
Score = 30.9 bits (69), Expect = 0.14
Identities = 16/59 (27%), Positives = 29/59 (49%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
L+I GL T+ + L + +G +V + D T + +G+GF+ + S A A+
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65
>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 = 32.6 bits (75), Expect = 0.028
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVT 133
+L V +L +TE+D+ E F G + LV
Sbjct: 2 RLVVSNLHPSVTEDDIVELFSAIGALKRARLVR 34
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. The family
also includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 33.0 bits (76), Expect = 0.029
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
L V +L ++ E L++ F QFGEV A+V + G+ G G VE+
Sbjct: 2 LRVKNLSPFVSNELLEQAFSQFGEVER-AVVIVDDRGRSTGEGIVEF 47
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast
nucleolar protein 3 (Npl3p) and similar proteins. This
subfamily corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or
nuclear polyadenylated RNA-binding protein 1. Npl3p is
a major yeast RNA-binding protein that competes with
3'-end processing factors, such as Rna15, for binding
to the nascent RNA, protecting the transcript from
premature termination and coordinating transcription
termination and the packaging of the fully processed
transcript for export. It specifically recognizes a
class of G/U-rich RNAs. Npl3p is a multi-domain protein
containing two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a short
linker and a C-terminal domain rich in glycine,
arginine and serine residues. .
Length = 67
Score = 32.4 bits (74), Expect = 0.030
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 11/61 (18%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+L++ TS ++ F +G V +V ++ F F+ + S + A A
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESL---ESAIRA 49
Query: 70 R 70
+
Sbjct: 50 K 50
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 32.9 bits (76), Expect = 0.031
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 13/78 (16%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVA-------LVTEKETGKKRGFGFVEYNDYD 152
K+L+V +L +TEEDL FG+F + +S L+TE G+ +G FV + +
Sbjct: 2 KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTE---GRMKGQAFVTFPSEE 58
Query: 153 PVDKACLKGTH--LVKGK 168
KA L + ++KGK
Sbjct: 59 IATKA-LNLVNGYVLKGK 75
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 32.2 bits (74), Expect = 0.038
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--L 159
L+VG L + +L+ F +FG + + R + ++EY + A L
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYD------PGRNYAYIEYESIEAAQAAKEAL 54
Query: 160 KGTHL-VKGKKVDV 172
+G L G+++ V
Sbjct: 55 RGFPLGGPGRRLRV 68
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 32.1 bits (73), Expect = 0.038
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 13/60 (21%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
K+F+G + +S+ L+ FE +G VV+ +KD Y+ HM + +A
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-------------YAFVHMEREEEAL 48
Score = 27.9 bits (62), Expect = 1.5
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 11/75 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
K+FVG++ T ++L+ F +FG V E K + + FV + A
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVV--------ECDKVKDYAFVHMEREEEALAAIEA 53
Query: 159 LKGTHLVKGKKVDVK 173
L G VKG++++V+
Sbjct: 54 LNGKE-VKGRRINVE 67
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 35.2 bits (81), Expect = 0.044
Identities = 17/48 (35%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 248 GGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAP 295
GG GG G +GG F G ++ G G R G R G AP
Sbjct: 568 GGERRGGGRGFGGERREGGRNFSGE-RREGGRGDGRRFSGERREGRAP 614
Score = 31.0 bits (70), Expect = 0.92
Identities = 16/46 (34%), Positives = 19/46 (41%)
Query: 256 GGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRG 301
GG GG+G GG ++F G GG G GR GR
Sbjct: 568 GGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRA 613
Score = 30.6 bits (69), Expect = 1.2
Identities = 18/63 (28%), Positives = 22/63 (34%), Gaps = 3/63 (4%)
Query: 240 GGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGG 299
GG GG G G G + G+ G G G + F G R G R +
Sbjct: 568 GGERRGGGRGFGGERREGGRNFSGERREG-GRGDGRRFSGE--RREGRAPRRDDSTGRRR 624
Query: 300 RGG 302
GG
Sbjct: 625 FGG 627
Score = 29.8 bits (67), Expect = 2.2
Identities = 19/59 (32%), Positives = 23/59 (38%), Gaps = 3/59 (5%)
Query: 232 GGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGR 290
GG GG G G G G + G GG+G G G ++ G P R G R
Sbjct: 568 GGERRGGGRGFGGERREG--GRNFSGERREGGRGDGRRFSGERRE-GRAPRRDDSTGRR 623
Score = 27.5 bits (61), Expect = 9.9
Identities = 14/49 (28%), Positives = 17/49 (34%), Gaps = 4/49 (8%)
Query: 199 PWGNNGGGGWGGGGPGPWDQGGSSWGG--NSGGGWGGNSGGGWGGNSGG 245
G GGG G GG +GG ++ G GG G G
Sbjct: 567 TGGERRGGGRGFGGERR--EGGRNFSGERREGGRGDGRRFSGERREGRA 613
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 34.8 bits (80), Expect = 0.048
Identities = 14/61 (22%), Positives = 17/61 (27%), Gaps = 2/61 (3%)
Query: 240 GGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGG 299
G GG G GGG G +G G G + G + G
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPRRGEG--GAKSASAKPAEKPSRRLGDAKPAGEQQRRR 447
Query: 300 R 300
R
Sbjct: 448 R 448
Score = 33.2 bits (76), Expect = 0.14
Identities = 15/40 (37%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 263 GQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
G GG G GGG Q G P RG GG + P
Sbjct: 395 GGGGRGQGGGRGQQ-QGQPRRGEGGAKSASAKPAEKPSRR 433
Score = 30.9 bits (70), Expect = 0.84
Identities = 18/62 (29%), Positives = 18/62 (29%), Gaps = 6/62 (9%)
Query: 203 NGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWG 262
NG GGGG G QGG G G GG S S A
Sbjct: 389 NGRQQRGGGGRG---QGG---GRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGE 442
Query: 263 GQ 264
Q
Sbjct: 443 QQ 444
Score = 30.5 bits (69), Expect = 1.1
Identities = 10/58 (17%), Positives = 13/58 (22%)
Query: 215 PWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGG 272
P G GG G GG G G ++ + G
Sbjct: 386 PIQNGRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQ 443
Score = 29.4 bits (66), Expect = 2.9
Identities = 15/57 (26%), Positives = 15/57 (26%)
Query: 218 QGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQ 274
Q G G G G GG G G G G S G G Q
Sbjct: 388 QNGRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQ 444
Score = 29.0 bits (65), Expect = 3.8
Identities = 11/60 (18%), Positives = 15/60 (25%)
Query: 226 NSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGG 285
N GG G GG G G +++ G + G R
Sbjct: 389 NGRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRR 448
Score = 28.6 bits (64), Expect = 4.0
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 274 QQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
+Q GGG GGG G+ G P G G
Sbjct: 391 RQQRGGGGRGQGGGRGQQQGQPRRGEGGA 419
Score = 28.6 bits (64), Expect = 4.1
Identities = 14/52 (26%), Positives = 17/52 (32%), Gaps = 2/52 (3%)
Query: 187 RGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGG 238
RGG G QGGG G G G G + + G +G
Sbjct: 394 RGGGGRGQGGGR--GQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQ 443
Score = 28.6 bits (64), Expect = 4.4
Identities = 11/54 (20%), Positives = 15/54 (27%)
Query: 201 GNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGG 254
G GG G G G Q GG ++ + G +G
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQ 443
Score = 27.9 bits (62), Expect = 7.8
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 272 GYQQSFGGGPMRGGGGGGRSGGAPYSGGRG 301
G QQ GGG +GGG G + G G
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPRRGEGGA 419
Score = 27.9 bits (62), Expect = 7.8
Identities = 10/50 (20%), Positives = 13/50 (26%)
Query: 188 GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGG 237
G GG +G G GG P ++ G G
Sbjct: 399 RGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRR 448
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 32.2 bits (74), Expect = 0.049
Identities = 12/41 (29%), Positives = 25/41 (60%), Gaps = 5/41 (12%)
Query: 108 RDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
D +E++L++ F ++G+V+ V + + KK+G VE+
Sbjct: 13 NGDYSEDELRKIFSKYGDVSDVVVSS-----KKKGSAIVEF 48
Score = 28.4 bits (64), Expect = 0.95
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 10/56 (17%)
Query: 14 GGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
G DY S + L+ F +GDV DVVV + K +G + ++S A+AA
Sbjct: 12 GNGDY--SEDELRKIFSKYGDVSDVVV-----SSKKKGSAIVEFASKK---AAEAA 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 = 33.0 bits (75), Expect = 0.051
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFG 124
+K+FVG L DITE D+ F +FG
Sbjct: 1 RKVFVGGLPWDITEADILNSFRRFG 25
>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional.
Length = 392
Score = 34.3 bits (79), Expect = 0.059
Identities = 27/62 (43%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 227 SGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGG 286
+GGG+GG G GG G G GG+ G + N + G GG GGG FGG RGGG
Sbjct: 79 AGGGFGGRRFDGGGGFGGFGTGGD-GAEFNLNDLFDAAGRGG-GGGIGDLFGGLFNRGGG 136
Query: 287 GG 288
Sbjct: 137 SA 138
Score = 31.6 bits (72), Expect = 0.54
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 251 SGGGWGGNSAWGGQGGGGFGGGYQ-QSFGGGPMRGGGGGGRSGG 293
+GGG+GG GG G GGFG G F + G G GG
Sbjct: 79 AGGGFGGRRFDGGGGFGGFGTGGDGAEFNLNDLFDAAGRGGGGG 122
Score = 29.3 bits (66), Expect = 2.5
Identities = 24/62 (38%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 243 SGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQS--FGGGPMRGGGGGGRSGGAPYSGGR 300
+GGG+GG G GG +GG G GG G + + F GGGG G G + R
Sbjct: 79 AGGGFGGRRFDGGGG---FGGFGTGGDGAEFNLNDLFDAAGRGGGGGIGDLFGGLF--NR 133
Query: 301 GG 302
GG
Sbjct: 134 GG 135
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 31.9 bits (72), Expect = 0.061
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
++FVG + D+ E++L F G + + L+ + + GK RG+ FV Y
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMY 49
Score = 28.0 bits (62), Expect = 1.7
Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAH 61
++F+G + + L FE+ G + ++ +M D K+RG+ F+ Y+ H
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKH 53
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 32.1 bits (74), Expect = 0.062
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 108 RDDITEEDLKEYFGQFGEVTSVALVTEKETGKK---RGFGFVEYNDYDPVDKACL 159
++I ED+KE G++G+V SV + + G G FVE+ D + KA L
Sbjct: 21 YEEI-LEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQL 74
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 34.5 bits (79), Expect = 0.068
Identities = 15/27 (55%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 220 GSSWGGNSGGGWGGNSGGGWGGNSGGG 246
S +SGGG GG SGGG GG GG
Sbjct: 569 SSRRSSSSGGG-GGFSGGGSGGGGGGA 594
Score = 33.0 bits (75), Expect = 0.20
Identities = 14/32 (43%), Positives = 14/32 (43%), Gaps = 6/32 (18%)
Query: 259 SAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGR 290
S GGG G F GG GGGGG R
Sbjct: 570 SRRSSSSGGGGG------FSGGGSGGGGGGAR 595
Score = 32.6 bits (74), Expect = 0.26
Identities = 14/49 (28%), Positives = 18/49 (36%), Gaps = 7/49 (14%)
Query: 221 SSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGF 269
S N + + +SGGG G + GG GG GGG
Sbjct: 554 SRSFNNLNRAYSAIASSRRSSSSGGGGGFSGGG-------SGGGGGGAR 595
Score = 32.6 bits (74), Expect = 0.27
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 220 GSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGG 254
++ + +SGGG GG SGGG GG GG
Sbjct: 561 NRAYSAIASSRRSSSSGGG-GGFSGGGSGGGGGGA 594
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 34.7 bits (79), Expect = 0.071
Identities = 17/44 (38%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 220 GSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGG 263
SS GGN+ GGN G G G G G GG + GG
Sbjct: 392 SSSIGGNANSSTGGN---GAAGAGGAGAAGKGGGSAAARATVGG 432
Score = 32.0 bits (72), Expect = 0.45
Identities = 17/48 (35%), Positives = 18/48 (37%), Gaps = 4/48 (8%)
Query: 241 GNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGG 288
G GGN+ GGN A G G G G G G R GG
Sbjct: 389 GRPSSSIGGNANSSTGGNGAAGAGGAGAAGKGG----GSAAARATVGG 432
Score = 31.6 bits (71), Expect = 0.57
Identities = 15/36 (41%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 233 GNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGG 268
G GGN+ GGN G GG A G+GGG
Sbjct: 389 GRPSSSIGGNANSSTGGNGAAGAGGAGA-AGKGGGS 423
Score = 31.6 bits (71), Expect = 0.59
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 225 GNSGGGWGGNSGGGWGGN--SGGGWGGNSGGGWGGNSAWGGQGG 266
G GGN+ GGN +G G G +G G G +A GG
Sbjct: 389 GRPSSSIGGNANSSTGGNGAAGAGGAGAAGKGGGSAAARATVGG 432
Score = 27.7 bits (61), Expect = 9.8
Identities = 19/60 (31%), Positives = 23/60 (38%), Gaps = 4/60 (6%)
Query: 172 VKKALSKEEMAKLKTR--GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGG 229
V LS A+L+ R GGN G NG G GG G G ++ GG
Sbjct: 375 VDATLSYVANARLRGRPSSSIGGNANSST--GGNGAAGAGGAGAAGKGGGSAAARATVGG 432
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 31.6 bits (71), Expect = 0.073
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD--PVDKACL 159
L+VG+L D+TE + + F Q G S ++ +T + FVE+ ++ A +
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIM--DTAGNDPYCFVEFFEHRHAAASLAAM 59
Query: 160 KGTHLVKGKKVDVKKA 175
G ++ GK+V V A
Sbjct: 60 NGRKIM-GKEVKVNWA 74
>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 = 31.6 bits (72), Expect = 0.076
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
+L V +L ++ +DLK++ + GEVT K+ + G VE+ Y + +A
Sbjct: 2 RLIVENLSSRVSWQDLKDFMRKAGEVTYAD--AHKQ---RPNEGVVEFATYSDMKRAIEK 56
Query: 159 LKGTHLVKGKKV 170
L GT L G+K+
Sbjct: 57 LDGTEL-NGRKI 67
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers. hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 31.5 bits (71), Expect = 0.078
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
+F+ LDY+ + LK F G VV +++D + KSRG G +T+
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILED-KDGKSRGIGTVTF 48
Score = 28.4 bits (63), Expect = 0.91
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYN 149
+FV +L + + LKE F G V ++ +K+ GK RG G V +
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFE 49
>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 = 31.7 bits (72), Expect = 0.078
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKR 141
K + V +L D+TEED+ + + G + +V + + GKK+
Sbjct: 8 KMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVF--ESNGKKQ 47
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 34.2 bits (78), Expect = 0.085
Identities = 27/104 (25%), Positives = 30/104 (28%), Gaps = 1/104 (0%)
Query: 182 AKLKTRGGFGGNQGGGDPWGNNG-GGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWG 240
L RG G P + G GG G Q S + G G
Sbjct: 115 QSLNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQ 174
Query: 241 GNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRG 284
G +GG G G GQ G GGG Q G G
Sbjct: 175 GQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGG 218
Score = 33.4 bits (76), Expect = 0.15
Identities = 35/138 (25%), Positives = 42/138 (30%), Gaps = 21/138 (15%)
Query: 186 TRGGFGGNQGGGDPWGNNGGGGWGGGGPG-------PWDQGGSSWGGNSGGG---WGGNS 235
T G G Q G G G GGPG + G G +G G
Sbjct: 80 TGQGTRGPQMGPMGPGPGRPMGQQMGGPGTASNLLQSLNVRGQMPMGAAGMGPHQMSRVG 139
Query: 236 GGGWGGNSGGGWGGNSG-GGWGGNSAWGGQGGGGFG--GGYQQSFGGGPMRG-------- 284
GG +GG +SG + G Q G G GG Q G +
Sbjct: 140 TMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQPPQMGQP 199
Query: 285 GGGGGRSGGAPYSGGRGG 302
G GG G G+ G
Sbjct: 200 GMPGGGGQGQMQQQGQPG 217
Score = 28.8 bits (64), Expect = 4.2
Identities = 35/119 (29%), Positives = 39/119 (32%), Gaps = 6/119 (5%)
Query: 191 GGNQGGGDPWG---NNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGN-SGGG 246
G QG DP N G G G GP G G GG G S N G
Sbjct: 64 QGGQGMPDPINALQNLTGQGTRGPQMGPMGPGPGRPMGQQMGGPGTASNLLQSLNVRGQM 123
Query: 247 WGGNSGGG-WGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGGIH 304
G +G G + Q GG GG QQS G P G GG++
Sbjct: 124 PMGAAGMGPHQMSRVGTMQPGGQAGGMMQQS-SGQPQSQQPNQMGPQQGQAQGQAGGMN 181
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The domain,
however, is found in various periplasmic ligand-binding
sensor proteins.
Length = 234
Score = 33.5 bits (77), Expect = 0.086
Identities = 16/59 (27%), Positives = 24/59 (40%)
Query: 187 RGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGG 245
FGG+ + G GG G G D G +++G + GG+ G + GG
Sbjct: 158 ENLFGGHSQPAEIVDAIGEGGDGSGPAPADDTGINNYGDDDSDAAGGDQGSNGDDDDGG 216
Score = 29.3 bits (66), Expect = 2.1
Identities = 33/125 (26%), Positives = 42/125 (33%), Gaps = 20/125 (16%)
Query: 193 NQGGGDPWGNNGG---GGWGGGGPGPWDQGG----SSWGGNSGGGWGGNSGGGWGGNSGG 245
Q ++GG G +GGG P P + G G GG S G G G
Sbjct: 69 AQAQHPQSQSSGGFLSGMFGGGAPRPPPAAPAVQPPAPPARPGWGSGGPSQQGAGQQPGY 128
Query: 246 GWGGNSGGGWGGNS---AWGGQGG--------GGFGGGYQQSFGGGPMRGGGGGGRSGGA 294
G G + G + A G GG FGG Q + + GG G A
Sbjct: 129 AQPG--PGSFLGGAAQTAAGVAGGMLLGNGLENLFGGHSQPAEIVDAIGEGGDGSGPAPA 186
Query: 295 PYSGG 299
+G
Sbjct: 187 DDTGI 191
>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome
proliferator-activated receptor gamma
coactivator-related protein 1 (PRC) and similar
proteins. This subgroup corresponds to the RRM of PRC,
also termed PGC-1-related coactivator, one of the
members of PGC-1 transcriptional coactivators family,
including peroxisome proliferator-activated receptor
gamma coactivators PGC-1alpha and PGC-1beta. Unlike
PGC-1alpha and PGC-1beta, PRC is ubiquitous and more
abundantly expressed in proliferating cells than in
growth-arrested cells. PRC has been implicated in the
regulation of several metabolic pathways, mitochondrial
biogenesis, and cell growth. It functions as a
growth-regulated transcriptional cofactor activating
many nuclear genes specifying mitochondrial respiratory
function. PRC directly interacts with nuclear
transcriptional factors implicated in respiratory chain
expression including nuclear respiratory factors 1 and
2 (NRF-1 and NRF-2), CREB (cAMP-response
element-binding protein), and estrogen-related receptor
alpha (ERRalpha). It interacts indirectly with the
NRF-2beta subunit through host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. Furthermore, like
PGC-1alpha and PGC-1beta, PRC can transactivate a
number of NRF-dependent nuclear genes required for
mitochondrial respiratory function, including those
encoding cytochrome c, 5-aminolevulinate synthase,
Tfam, and TFB1M, and TFB2M. Further research indicates
that PRC may also act as a sensor of metabolic stress
that orchestrates a redox-sensitive program of
inflammatory gene expression. PRC is a multi-domain
protein containing an N-terminal activation domain, an
LXXLL coactivator signature, a central proline-rich
region, a tetrapeptide motif (DHDY) responsible for HCF
binding, a C-terminal arginine/serine-rich (SR) domain,
and an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 91
Score = 31.8 bits (72), Expect = 0.089
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
R ++IG + R + LK F +G++ + + + +GF+TY ++A A
Sbjct: 3 RVVYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSE---GDNYGFVTYRYT---EEAFA 56
Query: 69 A 69
A
Sbjct: 57 A 57
Score = 28.7 bits (64), Expect = 1.2
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
+++G + +T +LK+ F FGE+ + E +GFV Y
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDN---YGFVTY 48
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and
U3 small nucleolar RNAs (snoRNAs). MRD1 is essential
for the initial processing at the A0-A2 cleavage sites
in the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which may play an important structural role in
organizing specific rRNA processing events. .
Length = 84
Score = 31.7 bits (72), Expect = 0.091
Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 6/80 (7%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKK-----SRGFGFITYSSAHMVDD 65
LF+ L++ T+++ L F+ V V P K+ S GFGF+ + +
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 66 AQAARP-HTIDSKVVEPKRA 84
A A +D + K +
Sbjct: 63 ALKAMDGFVLDGHTLVVKFS 82
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 31.0 bits (71), Expect = 0.10
Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 110 DITEEDLKEYFGQFGEVTSVALVTEKETGKK-RGFGFVEYNDYDPVDK 156
D T +D++E+F +FG+V ++ + ++ KK +G FVE+ + K
Sbjct: 10 DATLDDIQEFFEKFGKVNNIRM--RRDLDKKFKGSVFVEFKTEEDAKK 55
>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 = 31.8 bits (73), Expect = 0.11
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 15/56 (26%)
Query: 110 DITEEDLKEYF---------GQFGEVTSVALVTEKE------TGKKRGFGFVEYND 150
+ E+ LKE F + ++ V ++ + + GK +G+GFVE+ +
Sbjct: 11 SVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTN 66
>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar
proteins. This subgroup corresponds to the RRM of
PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect
modulator 6, a member of a family of transcription
coactivators that plays a central role in the regulation
of cellular energy metabolism. As an inducible
transcription coactivator, PGC-1alpha can interact with
a broad range of transcription factors involved in a
wide variety of biological responses, such as adaptive
thermogenesis, skeletal muscle fiber type switching,
glucose/fatty acid metabolism, and heart development.
PGC-1alpha stimulates mitochondrial biogenesis and
promotes oxidative metabolism. It participates in the
regulation of both carbohydrate and lipid metabolism and
plays a role in disorders such as obesity, diabetes, and
cardiomyopathy. PGC-1alpha is a multi-domain protein
containing an N-terminal activation domain region, a
central region involved in the interaction with at least
a nuclear receptor, and a C-terminal domain region. The
N-terminal domain region consists of three leucine-rich
motifs (L1, NR box 2 and 3), among which the two last
are required for interaction with nuclear receptors,
potential nuclear localization signals (NLS), and a
proline-rich region overlapping a putative repression
domain. The C-terminus of PGC-1alpha is composed of two
arginine/serine-rich regions (SR domains), a putative
dimerization domain, and an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). PGC-1alpha could interact
favorably with single-stranded RNA. .
Length = 91
Score = 31.4 bits (71), Expect = 0.11
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
++VG +R D T +L++ F FGE+ V ++ G +GF+ Y
Sbjct: 5 IYVGKIRPDTTRTELRDRFEVFGEIEE-CTVNLRDDGDS--YGFITY 48
Score = 28.8 bits (64), Expect = 0.94
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEAWGDVVDVVV-MKDPQTKKSRGFGFITY 57
R +++G + T+ L+ FE +G++ + V ++D +GFITY
Sbjct: 3 RVIYVGKIRPDTTRTELRDRFEVFGEIEECTVNLRD----DGDSYGFITY 48
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains 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 = 85
Score = 31.6 bits (71), Expect = 0.11
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 112 TEEDLKEYFGQFG-EVTSVALVTEKETGKKRGFGFVEYN 149
TE D++ + G + V L+ K +G+ RGF FVE+N
Sbjct: 15 TETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFN 53
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). SNF contains two RNA recognition motifs (RRMs);
it can self-associate through RRM1, and each RRM can
recognize poly(U) RNA binding independently. .
Length = 78
Score = 31.0 bits (70), Expect = 0.12
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 11 LFIGGLDYRTSSETLKSH----FEAWGDVVDVVVMKDPQTKKSRGFGFITY 57
++I L+ + E LK F +G ++D+V +K T K RG F+ +
Sbjct: 2 IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVALK---TLKMRGQAFVVF 49
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 33.5 bits (77), Expect = 0.12
Identities = 19/54 (35%), Positives = 21/54 (38%), Gaps = 7/54 (12%)
Query: 243 SGGGWGGNSGG-------GWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGG 289
SGG GG S +S GG G GGG+ F GGGGG
Sbjct: 4 SGGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGGG 57
Score = 33.5 bits (77), Expect = 0.12
Identities = 29/104 (27%), Positives = 38/104 (36%), Gaps = 22/104 (21%)
Query: 205 GGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGG-NSGGGWGGNSAWGG 263
GG GGG + +S GGG+ G+ GGG+G +G +GG
Sbjct: 5 GGRIGGGS------FRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFG----FGG 54
Query: 264 QGG-------GGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGR 300
GG G +F GGGGG A S G+
Sbjct: 55 GGGLFGLLILMAIAGVLVNAF----RSAGGGGGGLSSAGRSNGK 94
Score = 27.7 bits (62), Expect = 7.9
Identities = 13/42 (30%), Positives = 13/42 (30%), Gaps = 8/42 (19%)
Query: 266 GGGFGGGYQQSFGG-----GPMRGGGGGGRSGGAPYSGGRGG 302
GG GGG SF R GG GG G
Sbjct: 5 GGRIGGG---SFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGF 43
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 31.1 bits (71), Expect = 0.13
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
KL V +L ++++D+KE F +FG + A V +G+ G V +
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEFGALKKAA-VHYDRSGRSLGTADVVF 48
>gnl|CDD|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM2 of RBM46, also termed
cancer/testis antigen 68 (CT68). It is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 85
Score = 31.1 bits (70), Expect = 0.13
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 10 KLFIGGL-DYRTSSETLKSHFEAWGDVVDVVVMKDPQTK-KSRGFGFITYSS 59
+LFIG + + E L+ + V+DV+V + K+RGF F+ Y S
Sbjct: 4 RLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYES 55
Score = 29.2 bits (65), Expect = 0.68
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETG--KKRGFGFVEYNDYDPVDKA- 157
+LF+GS+ + +E++ E + E +V T K RGF FVEY + A
Sbjct: 4 RLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRAAAMAR 63
Query: 158 --CLKGTHLVKGKKVDVKKA 175
+ GT + G + V A
Sbjct: 64 RKLIPGTFQLWGHTIQVDWA 83
>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 = 31.4 bits (72), Expect = 0.14
Identities = 24/86 (27%), Positives = 37/86 (43%), Gaps = 11/86 (12%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEK--------ETGKKRGFGFVEYNDY 151
++V L DIT E+ E F + G + T K E G +G Y
Sbjct: 2 TNVYVSGLPLDITVEEFVEVFSKCG-IIKEDPETGKPKIKLYRDENGNLKGDALCCYLKE 60
Query: 152 DPVDKAC--LKGTHLVKGKKVDVKKA 175
+ V+ A L GT + +G K+ V++A
Sbjct: 61 ESVELAIQLLDGTEIGRGYKMKVERA 86
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM2 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 30.6 bits (69), Expect = 0.14
Identities = 13/47 (27%), Positives = 27/47 (57%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEY 148
++V +TEE L+E FGQ ++ ++ L + +GK + F+++
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKF 47
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM2 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 30.8 bits (69), Expect = 0.14
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 15/62 (24%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHM--VDDAQ 67
KL +G + +++ L++ FE +G V++ ++KD Y+ HM +DA
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD-------------YAFVHMERAEDAV 48
Query: 68 AA 69
A
Sbjct: 49 EA 50
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup
corresponds to the RRM2 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 = 86
Score = 31.1 bits (70), Expect = 0.14
Identities = 12/26 (46%), Positives = 20/26 (76%)
Query: 35 VVDVVVMKDPQTKKSRGFGFITYSSA 60
V ++ ++KD QT+++RGF F+ SSA
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQLSSA 56
Score = 29.9 bits (67), Expect = 0.39
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 126 VTSVALVTEKETGKKRGFGFVE 147
V ++ L+ +K+T + RGF FV+
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQ 52
>gnl|CDD|234526 TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein.
Members of this protein family average 125 in length,
roughly half of which is the repetitive and extremely
Gly-rich C-terminal region. Virtually all members occur
in the Cyanobacteria, in a neighborhood that includes a
radical SAM/SPASM domain, often a marker of peptide
modification systems.
Length = 119
Score = 31.6 bits (72), Expect = 0.15
Identities = 27/78 (34%), Positives = 28/78 (35%), Gaps = 19/78 (24%)
Query: 196 GGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGW 255
GN GWG GG G GWG GG N GGGWG GGW
Sbjct: 61 LAGADGNLIARGWGNGG---------------GRGWGNGGSGGGWVNGGGGWG---NGGW 102
Query: 256 GGNSAWGGQGGGGFGGGY 273
W G GGF +
Sbjct: 103 VNGGGW-RNGYGGFANRW 119
Score = 28.9 bits (65), Expect = 1.3
Identities = 21/53 (39%), Positives = 22/53 (41%)
Query: 236 GGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGG 288
G G GWG G GWG + GG GG G G GG R G GG
Sbjct: 62 AGADGNLIARGWGNGGGRGWGNGGSGGGWVNGGGGWGNGGWVNGGGWRNGYGG 114
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 30.7 bits (69), Expect = 0.16
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
++++G L E D++ +F +G++ V L K G+GFVE++D D A
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDA 49
Score = 27.6 bits (61), Expect = 1.7
Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
+++IG L Y+ ++ F+ +G +++V + G+GF+ + DDA
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDA 49
>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of
uncharacterized plant proteins similar to fission yeast
Vip1. This subfamily corresponds to the Vip1-like,
uncharacterized proteins found in plants. Although their
biological roles remain unclear, these proteins show
high sequence similarity to the fission yeast Vip1. Like
Vip1 protein, members in this family contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 69
Score = 30.5 bits (69), Expect = 0.16
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 104 VGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
V +L TE D+ ++F G++ V + E + +V + D + A L
Sbjct: 3 VTNLSPKATERDIYDFFSFSGDIEYVEIQRSGEQSQ---TAYVTFKDPQAQETALL 55
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 32.9 bits (75), Expect = 0.16
Identities = 21/53 (39%), Positives = 24/53 (45%)
Query: 225 GNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSF 277
GGG+GG GG GG GG G GG +GG G G G Y Q +
Sbjct: 184 APGGGGYGGGGGGMGGGGGGGMGEMGGMGPQGGGGGYGGMGAPGQGNAYNQGY 236
Score = 30.2 bits (68), Expect = 1.2
Identities = 27/82 (32%), Positives = 29/82 (35%), Gaps = 2/82 (2%)
Query: 192 GNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNS 251
GN N GG PG Q G + G G GG G GG GG GG
Sbjct: 2 GNMQNYPQAMNPQMGGGNYPAPGQPAQQGYANQGMGGPVGGGGGPGAGGGAPGGPVGG-- 59
Query: 252 GGGWGGNSAWGGQGGGGFGGGY 273
GGG G GG+ G
Sbjct: 60 GGGGSGGPPGGGEVAGEAEDAM 81
Score = 28.7 bits (64), Expect = 3.6
Identities = 24/56 (42%), Positives = 24/56 (42%)
Query: 237 GGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSG 292
GG GGG GG GGG GG GG G G GGGY G G R G
Sbjct: 184 APGGGGYGGGGGGMGGGGGGGMGEMGGMGPQGGGGGYGGMGAPGQGNAYNQGYRQG 239
Score = 28.7 bits (64), Expect = 3.7
Identities = 26/68 (38%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 228 GGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGG 287
GG + G + G GG GGG GG A GG GG GGG GGP GG
Sbjct: 17 GGNYPAPGQPAQQGYANQGMGGPVGGG-GGPGAGGGAPGGPVGGG--GGGSGGPPGGGEV 73
Query: 288 GGRSGGAP 295
G + A
Sbjct: 74 AGEAEDAM 81
Score = 27.5 bits (61), Expect = 8.5
Identities = 24/51 (47%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 250 NSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGR 300
N+ G GG GG GGG GGG + G GP GGGGG GAP G
Sbjct: 182 NNAPGGGGYGGGGGGMGGGGGGGMGEMGGMGPQ-GGGGGYGGMGAPGQGNA 231
>gnl|CDD|227642 COG5337, CotH, Spore coat assembly protein [Cell envelope
biogenesis, outer membrane].
Length = 473
Score = 33.0 bits (75), Expect = 0.17
Identities = 18/47 (38%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 255 WGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRG 301
W N AWG G G G + GG G G R GG S RG
Sbjct: 312 WDYNLAWGRDGHGERGAADEVRIGG----FGTLGMRPGGLDESEFRG 354
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response element
(IGFRE). Moreover, PSF functions as a transcriptional
repressor interacting with Sin3A and mediating silencing
through the recruitment of histone deacetylases (HDACs)
to the DNA binding domain (DBD) of nuclear hormone
receptors. PSF is an essential pre-mRNA splicing factor
and is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. PSF
forms a heterodimer with the nuclear protein p54nrb,
also known as non-POU domain-containing octamer-binding
protein (NonO). The PSF/p54nrb complex displays a
variety of functions, such as DNA recombination and RNA
synthesis, processing, and transport. PSF contains two
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which are responsible for interactions with
RNA and for the localization of the protein in speckles.
It also contains an N-terminal region rich in proline,
glycine, and glutamine residues, which may play a role
in interactions recruiting other molecules. .
Length = 80
Score = 30.8 bits (69), Expect = 0.17
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA---C 158
L V +L ++ E L+E F QFG V A+V + G+ G G VE+ KA C
Sbjct: 2 LSVRNLSPYVSNELLEEAFSQFGPVER-AVVIVDDRGRSTGKGIVEFASKPAARKAFERC 60
Query: 159 LKGTHLV 165
+G L+
Sbjct: 61 TEGVFLL 67
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a specific
inhibitory effect on oestrogen action, SLTM is shown to
exert a generalized inhibitory effect on gene expression
associated with induction of apoptosis in a wide range
of cell lines. .
Length = 74
Score = 30.4 bits (68), Expect = 0.19
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFV 146
L+V L + DLK FG++G+V S +VT + + +G V
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIV 46
Score = 29.3 bits (65), Expect = 0.54
Identities = 14/50 (28%), Positives = 29/50 (58%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
L++ GL T + LK+ F +G V+ V+ + ++ ++ +G +T SS+
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSS 51
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 32.7 bits (75), Expect = 0.20
Identities = 18/37 (48%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 225 GNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAW 261
+SG G G SGGG G G GG+SGGG G + +W
Sbjct: 236 RSSGSGGSGGSGGGSSGGGFSGGGGSSGGG-GASGSW 271
Score = 30.4 bits (69), Expect = 0.92
Identities = 18/43 (41%), Positives = 19/43 (44%), Gaps = 10/43 (23%)
Query: 248 GGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGR 290
G+ G G G GG GGGF S GGG GGG G
Sbjct: 238 SGSGGSGGSG----GGSSGGGF------SGGGGSSGGGGASGS 270
Score = 30.0 bits (68), Expect = 1.3
Identities = 18/44 (40%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 229 GGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGG 272
W G +SG G G SGGG G G GGG GGG
Sbjct: 224 DRWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSG--GGGSSGGG 265
Score = 29.2 bits (66), Expect = 2.7
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 188 GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGW 231
G + G G G+ GG GG G GGSS GG + G W
Sbjct: 232 GRRRRSSGSGGSGGSGGGSSGGGFSGG----GGSSGGGGASGSW 271
Score = 27.7 bits (62), Expect = 6.6
Identities = 19/40 (47%), Positives = 19/40 (47%), Gaps = 10/40 (25%)
Query: 265 GGGGFGGGYQQSFGGGPMRGG--GGGGRSGGAPYSGGRGG 302
G G GG GGG GG GGGG SGG GG G
Sbjct: 238 SGSGGSGG----SGGGSSGGGFSGGGGSSGG----GGASG 269
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase,
or COMPASS component SET1, or lysine
N-methyltransferase 2, or Set1 complex component, is
encoded by SET1 from the fission yeast S. pombe. It is
essential for the H3 lysine-4 methylation. in vivo, and
plays an important role in telomere maintenance and DNA
repair in an ATM kinase Rad3-dependent pathway. spSet1p
is the homology counterpart of Saccharomyces cerevisiae
Set1p (scSet1p). However, it is more closely related to
Set1 found in mammalian. Moreover, unlike scSet1p,
spSet1p is not required for heterochromatin assembly in
fission yeast. spSet1p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a conserved SET domain that may play a role in DNA
repair and telomere function. .
Length = 86
Score = 30.4 bits (69), Expect = 0.22
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+ I GL T+ + ++ HF +G++ + + DP+T +S G +T+ AA
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTF--RGDPLRPSAA 57
>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM2 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 89
Score = 30.4 bits (68), Expect = 0.24
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 10 KLFIGGL-DYRTSSETLKSHFEAWGDVVDVVVMKDPQTK-KSRGFGFITYSS 59
+LFIGG+ + E L+ + V+DV+V K K+RGF F+ Y S
Sbjct: 3 RLFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYES 54
>gnl|CDD|240934 cd12490, RRM2_ACF, RNA recognition motif 2 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM2 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 85
Score = 30.4 bits (68), Expect = 0.24
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 10 KLFIGGLDYRTSSETLKSHFEAWGD-VVDVVVMKDPQTK-KSRGFGFITYSS 59
+LF+GG+ E + + + D V+DV+V K K+RGF F+ Y S
Sbjct: 4 RLFVGGIPKTKKREEILAEMKKVTDGVLDVIVYPSAADKAKNRGFAFVEYES 55
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 30.2 bits (68), Expect = 0.25
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDV 38
L I LD SSETL+S F+ +GDV ++
Sbjct: 4 LVIFNLDPTVSSETLRSIFQVYGDVKEL 31
>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 = 30.4 bits (69), Expect = 0.25
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 8/48 (16%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTS--------VALVTEKETGKKR 141
+++ L DD+TE+ L E FG G + + + T+KET K
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKG 48
>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 = 29.9 bits (68), Expect = 0.28
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 97 ATVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPV 154
TVK V +L D TE ++++F GE+ V +V E E G +E+ D
Sbjct: 1 LTVK---VKNLPKDTTENKIRQFFKDCGEIREVKIV-ESEGGL---VAVIEFETEDEA 51
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 31.3 bits (71), Expect = 0.30
Identities = 15/40 (37%), Positives = 17/40 (42%)
Query: 228 GGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGG 267
G G GG GGG GG +G + G A G GG
Sbjct: 116 GRGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGN 155
Score = 30.9 bits (70), Expect = 0.45
Identities = 16/41 (39%), Positives = 16/41 (39%)
Query: 252 GGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSG 292
G G GG GGG FG G P GGGG S
Sbjct: 118 GEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGNFSR 158
Score = 30.2 bits (68), Expect = 0.75
Identities = 18/44 (40%), Positives = 20/44 (45%)
Query: 228 GGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGG 271
G G GGG G + GGG G+SG GG GGG F
Sbjct: 115 DGRGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGNFSR 158
Score = 29.0 bits (65), Expect = 2.1
Identities = 19/41 (46%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 262 GGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
G+G GG GGG GGG G G R G P S G GG
Sbjct: 115 DGRGEGGGGGGGGDDGGGGDF-GSSGPSRGGPRPASSGGGG 154
Score = 27.5 bits (61), Expect = 6.6
Identities = 12/41 (29%), Positives = 15/41 (36%)
Query: 219 GGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNS 259
G GG GGG GG +G + G GG +
Sbjct: 115 DGRGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGN 155
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 29.9 bits (68), Expect = 0.31
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 107 LRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC--LKGTHL 164
L + +TE+ L +F ++G V V + ++RG V ++ + A +KG L
Sbjct: 15 LDESVTEQYLTRHFSRYGPVVHVVI------DRQRGQALVFFDKVEAAQAAVNEMKGRKL 68
Query: 165 VKGK-KVD 171
K +VD
Sbjct: 69 GGRKLQVD 76
Score = 27.6 bits (62), Expect = 2.0
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
+++ GLD + + L HF +G VV VV+ + RG + + V+ AQAA
Sbjct: 10 VWLDGLDESVTEQYLTRHFSRYGPVVHVVI------DRQRGQALVFFDK---VEAAQAA 59
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 29.9 bits (68), Expect = 0.32
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALV-TEKETGKKRGFGFVEYNDYDP----VDK 156
L + + + EDLKE F +FGEV V + E G+V + + + ++K
Sbjct: 4 LHFSGVGEQTSREDLKEAFEEFGEVAWVDFARGQTE-------GYVRFKEENAAKEALEK 56
Query: 157 ACLKGTHLVKGKKVDVK 173
+KG +V VK
Sbjct: 57 LKEAKNLKIKGSEVTVK 73
>gnl|CDD|241121 cd12677, RRM4_Nop4p, RNA recognition motif 4 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM4 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 = 156
Score = 31.1 bits (70), Expect = 0.35
Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 124 GEVTSVALVTEKE---TGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVKKALSKE 179
G V + TEK G+ RG+GF+E+ + K L + G V VKK + E
Sbjct: 69 GVVKQAKVETEKAGSTAGRSRGYGFMEFISH----KYALMALRWLNGHAVTVKKIIDAE 123
>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM2 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4), a splicing
regulatory serine/arginine (SR) protein that plays an
important role in both constitutive splicing and
alternative splicing of many pre-mRNAs. For instance, it
interacts with heterogeneous nuclear ribonucleoproteins,
hnRNP G and hnRNP E2, and further regulates the 5'
splice site of tau exon 10, whose misregulation causes
frontotemporal dementia. SFRS4 also induces production
of HIV-1 vpr mRNA through the inhibition of the
5'-splice site of exon 3. In addition, SRSF4 activates
splicing of the cardiac troponin T (cTNT) alternative
exon by direct interactions with the cTNT exon 5
enhancer RNA. SRSF4 can shuttle between the nucleus and
cytoplasm. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine-rich region, an
internal region homologous to the RRM, and a very long,
highly phosphorylated C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 29.7 bits (66), Expect = 0.35
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
+L V +L + +DLK+Y Q GEVT + G+K G +E+ Y + +A
Sbjct: 2 RLIVENLSSRCSWQDLKDYMRQAGEVT----YADAHKGRKNE-GVIEFRSYSDMKRALEK 56
Query: 159 LKGTHLVKGKKV 170
L GT V G+K+
Sbjct: 57 LDGTE-VNGRKI 67
>gnl|CDD|217596 pfam03515, Cloacin, Colicin-like bacteriocin tRNase domain. The
C-terminal region of colicin-like bacteriocins is either
a pore-forming or an endonuclease-like domain. Cloacin
and Pyocins have similar structures and activities to
the colicins from E coli and the klebicins from
Klebsiella spp. Colicins E5 and D cleave the anticodon
loops of distinct tRNAs of Escherichia coli both in vivo
and in vitro. The full-length molecule has an N-terminal
translocation domain and a middle, double alpha-helical
region which is receptor-binding.
Length = 279
Score = 31.7 bits (72), Expect = 0.41
Identities = 16/40 (40%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 203 NGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGN 242
G GWG G PW GG S GG+ G G GG
Sbjct: 6 GDGIGWGSEG-TPWGPGGGSPGGDYNPGGGSGVGGSGNDG 44
Score = 30.9 bits (70), Expect = 0.68
Identities = 18/53 (33%), Positives = 19/53 (35%), Gaps = 7/53 (13%)
Query: 222 SWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQ 274
S G GWG + G WG GG S GG G GG G G
Sbjct: 2 SDIPGDGIGWG-SEGTPWGP------GGGSPGGDYNPGGGSGVGGSGNDGLSY 47
Score = 27.5 bits (61), Expect = 9.7
Identities = 15/49 (30%), Positives = 16/49 (32%), Gaps = 3/49 (6%)
Query: 214 GPWDQGGSSWGGNSGGGWGGNSG--GGWGGNSGGGWGGNSGGGWGGNSA 260
G WG + G WG G GG GG G SG S
Sbjct: 2 SDIPGDGIGWG-SEGTPWGPGGGSPGGDYNPGGGSGVGGSGNDGLSYSP 49
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 29.5 bits (67), Expect = 0.42
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 102 LFVGSLRDDITEEDLKEYFGQF 123
LFV +L + TEE+L++ F +
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQ 26
>gnl|CDD|240430 PTZ00473, PTZ00473, Plasmodium Vir superfamily; Provisional.
Length = 420
Score = 31.7 bits (72), Expect = 0.42
Identities = 28/111 (25%), Positives = 39/111 (35%), Gaps = 6/111 (5%)
Query: 200 WGNNGGGGWGGGGPGPWDQGGSS----WGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGW 255
W N G G Q S S G+ +S +GG+S G +S +
Sbjct: 307 WRNMGHDSRGPYNANYGGQFNSRSGRTGSSESIRGFTYDSSTTYGGSSYGTSQTDSTSTY 366
Query: 256 GGNSAWGGQGGGGFGGGYQQSFGGGPMRGG--GGGGRSGGAPYSGGRGGIH 304
G S + GGG G ++GG G G S G Y G + +
Sbjct: 367 GSRSTFDSSTGGGSQSGGGSTYGGSSTFDGSSRGSSDSFGVSYFGPQQTVG 417
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 29.4 bits (66), Expect = 0.43
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 8/51 (15%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
+ +F G+ D + +++ FG++G V V + K GF FV D
Sbjct: 1 RPVFCGNFEYDARQSEIERLFGKYGRVDRVDM--------KSGFAFVYMED 43
>gnl|CDD|233829 TIGR02349, DnaJ_bact, chaperone protein DnaJ. This model
represents bacterial forms of DnaJ, part of the
DnaK-DnaJ-GrpE chaperone system. The three components
typically are encoded by consecutive genes. DnaJ
homologs occur in many genomes, typically not near DnaK
and GrpE-like genes; most such genes are not included by
this family. Eukaryotic (mitochondrial and chloroplast)
forms are not included in the scope of this family.
Length = 354
Score = 31.8 bits (73), Expect = 0.43
Identities = 20/53 (37%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 246 GWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSG 298
G+ G GGG GG + + G FG + FGGG GG G R P G
Sbjct: 68 GFNGGGGGGGGGFNGFDIGFFGDFGDIFGDFFGGG----GGSGRRRRSGPRRG 116
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 29.5 bits (67), Expect = 0.44
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 9/56 (16%)
Query: 14 GGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQAA 69
GGL S E L FE +G V D+V+ K + F++YSS ++DA AA
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVMPPG----KP--YCFVSYSS---IEDAAAA 55
>gnl|CDD|237657 PRK14281, PRK14281, chaperone protein DnaJ; Provisional.
Length = 397
Score = 31.7 bits (72), Expect = 0.48
Identities = 26/69 (37%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 233 GNSGGGWGGNSGGGWGGNSGGGWGGN---SAW------GGQGGGGFGGGYQQSFGGGPMR 283
G++G G SGGG G GGG N SA+ G + GGG G++ FGGG R
Sbjct: 69 GHAGVGSSAASGGG-PGYGGGGGDFNDIFSAFNDMFGGGARRGGGSPFGFEDVFGGGGRR 127
Query: 284 GGGGGGRSG 292
G G
Sbjct: 128 RRASAGIPG 136
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 29.5 bits (67), Expect = 0.49
Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 14/67 (20%)
Query: 4 EPEHLRKLFIGGLDYRTSSETLKSHFEAWGDVVDVVV-MKDPQTKKSRGFGFITYSSAHM 62
E L KL + L+ F +G V + M +T K++G+ F+ +++
Sbjct: 13 GEEKLEKLK----------KVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATP-- 60
Query: 63 VDDAQAA 69
++A+ A
Sbjct: 61 -EEAKEA 66
Score = 29.5 bits (67), Expect = 0.51
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 120 FGQFGEVTSVAL-VTEKETGKKRGFGFVEYNDYDPVDKACLKGTHLVKGKKVDVK 173
F +FG V + + ETGK +G+ FVE+ + +A K + G K+D K
Sbjct: 28 FSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAV-KALN---GYKLDKK 78
>gnl|CDD|237541 PRK13881, PRK13881, conjugal transfer protein TrbI; Provisional.
Length = 472
Score = 31.7 bits (72), Expect = 0.54
Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 6/60 (10%)
Query: 178 KEEMAKLKTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGG 237
+ +A+L+ G GG GGG GG P S G NS +GGN G
Sbjct: 208 QARLAQLRGMGVGGGMAAPA------GGGMGAGGAPQLLQTSTSGGGRNSYAQFGGNGQG 261
>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family. This family of
proteins includes several glycine rich proteins as well
as two nodulins 16 and 24. The family also contains
proteins that are induced in response to various
stresses.
Length = 91
Score = 29.3 bits (66), Expect = 0.58
Identities = 26/45 (57%), Positives = 29/45 (64%)
Query: 228 GGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGG 272
GGG GG GGG GG GGG+ G GG GG + G GGGG+GGG
Sbjct: 46 GGGGGGYGGGGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYGGG 90
Score = 27.0 bits (60), Expect = 4.5
Identities = 24/46 (52%), Positives = 27/46 (58%)
Query: 236 GGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGP 281
GGG GG GGG GG GGG+ G G GGGG+ GG +GGG
Sbjct: 46 GGGGGGYGGGGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYGGGG 91
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 28.8 bits (65), Expect = 0.63
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
Query: 116 LKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA--CLKGTHLVKGKKVDV 172
L++ F +FG + V LV + +G+ +Y D + ++A L G V G K+ V
Sbjct: 16 LEDVFCRFGGLIDVYLV------PGKNYGYAKYADRESAERAITTLHG-KEVNGVKLKV 67
>gnl|CDD|185087 PRK15133, PRK15133, microcin C ABC transporter permease YejB;
Provisional.
Length = 364
Score = 31.3 bits (71), Expect = 0.63
Identities = 14/39 (35%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 263 GQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRG 301
GQ GG G G G G G + Y GGRG
Sbjct: 45 GQAGGLPGAG---GEGVRASHAQTGVGNISDSNYRGGRG 80
Score = 27.8 bits (62), Expect = 7.4
Identities = 11/39 (28%), Positives = 14/39 (35%)
Query: 214 GPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSG 252
GP DQ ++ GG G G G + GN
Sbjct: 33 GPVDQAIAAIEFGQAGGLPGAGGEGVRASHAQTGVGNIS 71
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 31.4 bits (72), Expect = 0.65
Identities = 15/50 (30%), Positives = 16/50 (32%), Gaps = 2/50 (4%)
Query: 189 GFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGG 238
F +G G G GG G G PG Q G G G G
Sbjct: 614 QFNAQRGEQQ--GQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGS 661
Score = 31.4 bits (72), Expect = 0.68
Identities = 12/38 (31%), Positives = 12/38 (31%)
Query: 262 GGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGG 299
G QG GG G G G G GG G
Sbjct: 624 GQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGS 661
Score = 30.3 bits (69), Expect = 1.5
Identities = 29/140 (20%), Positives = 32/140 (22%), Gaps = 32/140 (22%)
Query: 187 RGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGG--------------------N 226
+G G G G G G G G G
Sbjct: 623 QGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQQALRDELGRQRGGLPG 682
Query: 227 SGGGWGGNSGGGWG--GNSGGGWGGNSGGGWGGNSAWGGQ---------GGGGFGGGYQQ 275
GG G + G G + GG G G A Q G G Q
Sbjct: 683 MGGEAGEAARDALGRAGRAMGGAEEALGQGDLA-EAVDRQGRALEALREGARALGEAMAQ 741
Query: 276 SFGGGPMRGGGGGGRSGGAP 295
G G GR GG
Sbjct: 742 QQGQQQGGQGQQQGRQGGNG 761
Score = 28.3 bits (64), Expect = 5.3
Identities = 13/40 (32%), Positives = 14/40 (35%)
Query: 256 GGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAP 295
G GQGG G G QQ G + G G G
Sbjct: 620 GEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQ 659
Score = 27.9 bits (63), Expect = 8.4
Identities = 10/41 (24%), Positives = 11/41 (26%)
Query: 262 GGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
Q G G Q G G G G+ G G
Sbjct: 616 NAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQ 656
Score = 27.9 bits (63), Expect = 8.9
Identities = 26/76 (34%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 224 GGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFG--GGP 281
G G GG G G G G G GGQGG G QQ+ G
Sbjct: 616 NAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQQALRDELGR 675
Query: 282 MRGG--GGGGRSGGAP 295
RGG G GG +G A
Sbjct: 676 QRGGLPGMGGEAGEAA 691
>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 = 29.2 bits (65), Expect = 0.66
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQF-GEVTSVALVTEKETGKKRGFGFVEY 148
K + + L +ITE D++E F G + + +++TG RGF FVE+
Sbjct: 6 KTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEF 55
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. Structurally related CFIm68 and
CFIm59, also termed cleavage and polyadenylation
specificity factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59), are functionally redundant. Both contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. Their N-terminal RRM mediates the interaction
with CFIm25, and also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 76
Score = 28.8 bits (65), Expect = 0.66
Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 5/76 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFG--EVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACL 159
L+VG+L T+EDL+ + G +V S+ K GK +GF +VE+ A
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAA-AAVK 59
Query: 160 KGTH--LVKGKKVDVK 173
+ GKK V
Sbjct: 60 EKLEGREFNGKKCVVT 75
Score = 27.3 bits (61), Expect = 2.3
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWG--DVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQA 68
L++G L + T+ E L+ G DV + + KS+GF ++ ++S + A A
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFAS----EAAAA 56
Query: 69 ARPHTIDSKVVEPKRAV 85
A ++ + K+ V
Sbjct: 57 AVKEKLEGREFNGKKCV 73
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 30.8 bits (70), Expect = 0.78
Identities = 22/62 (35%), Positives = 26/62 (41%), Gaps = 11/62 (17%)
Query: 237 GGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPY 296
G G N G G G GG+ G+ G GGF + F GGGG R+ AP
Sbjct: 69 GAAGANGGFGGGAGGFGGFDGSG-----GFGGFEDIFSSFF------GGGGARRNPNAPR 117
Query: 297 SG 298
G
Sbjct: 118 QG 119
>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin.
This subfamily corresponds to the RRM1 of ubiquitously
expressed protein nucleolin, also termed protein C23.
Nucleolin is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. RRM1,
together with RRM2, binds specifically to RNA stem-loops
containing the sequence (U/G)CCCG(A/G) in the loop. .
Length = 75
Score = 28.6 bits (64), Expect = 0.82
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-LK 160
LFVG+L + ++LK +F ++A V + G + FG+V++ + ++KA L
Sbjct: 3 LFVGNLNPNKDFDELKTAISEFFSKKNLA-VQDVRIGSSKKFGYVDFESAEDLEKALELT 61
Query: 161 GTHLVKGKKVDVKKA 175
G L+ G ++ ++KA
Sbjct: 62 GKKLL-GNEIKLEKA 75
Score = 25.9 bits (57), Expect = 6.9
Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
LF+G L+ + LK+ + ++ V +D + S+ FG++ + SA ++ A
Sbjct: 3 LFVGNLNPNKDFDELKTAISEFFSKKNLAV-QDVRIGSSKKFGYVDFESAEDLEKA 57
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for growth.
Srp1p is closely related to the SR protein family found
in metazoa. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine hinge and a RS
domain in the middle, and a C-terminal domain. Some
family members also contain another RRM domain.
Length = 78
Score = 28.6 bits (64), Expect = 0.84
Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 5/82 (6%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
L+V + DL F ++G + + + T + R F FVEY +
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPR-TFQSRPFAFVEYES----HRDAEDA 56
Query: 162 THLVKGKKVDVKKALSKEEMAK 183
+ G++ + AK
Sbjct: 57 YEEMHGRRFPDTGDTLHVQWAK 78
Score = 27.8 bits (62), Expect = 1.7
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDA 66
L++ G T + L FE +G +V + P+T +SR F F+ Y S +DA
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDI-PPPRTFQSRPFAFVEYESHRDAEDA 56
>gnl|CDD|215441 PLN02825, PLN02825, amino-acid N-acetyltransferase.
Length = 515
Score = 30.9 bits (70), Expect = 0.88
Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 7/68 (10%)
Query: 174 KALSKEEMAKLKTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGG 233
KA+ E+ + G + P+ NNG G WG G Q G G ++G G G
Sbjct: 249 KAVGGEDYSYSL-----GLDSVNTTPFNNNGRGFWGSGSATDSFQNGV--GFDNGNGLSG 301
Query: 234 NSGGGWGG 241
G GG
Sbjct: 302 EQGFAIGG 309
>gnl|CDD|234046 TIGR02877, spore_yhbH, sporulation protein YhbH. This protein
family, typified by YhbH in Bacillus subtilis, is found
in nearly every endospore-forming bacterium and in no
other genome (but note that the trusted cutoff score is
set high to exclude a single high-scoring sequence from
Nitrosococcus oceani ATCC 19707, which is classified in
the Gammaproteobacteria). The gene in Bacillus subtilis
was shown to be in the regulon of the sporulation sigma
factor, sigma-E, and its mutation was shown to create a
sporulation defect [Cellular processes, Sporulation and
germination].
Length = 371
Score = 30.9 bits (70), Expect = 0.92
Identities = 15/32 (46%), Positives = 17/32 (53%)
Query: 192 GNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSW 223
GN+ GD G GG GGGG G DQ G +
Sbjct: 78 GNEKVGDVIGRERAGGEGGGGKGAGDQEGEDY 109
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 28.5 bits (64), Expect = 0.93
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 101 KLFVGSLRDDITEEDLKEYF-GQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
K+ V +L D+TE ++EYF Q G + V L E GK G + + KA
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSY-NEGGKSTGIANITFKRAGDATKA 57
>gnl|CDD|143480 cd06664, IscU_like, Iron-sulfur cluster scaffold-like proteins.
IscU_like and NifU_like proteins. IscU and NifU function
as a scaffold for the assembly of [2Fe-2S] clusters
before they are transferred to apo target proteins. They
are highly conserved and play vital roles in the ISC and
NIF systems of Fe-S protein maturation. NIF genes
participate in nitrogen fixation in several isolated
bacterial species. The NifU domain, however, is also
found in bacteria that do not fix nitrogen, so it may
have wider significance in the cell. Human IscU
interacts with frataxin, the Friedreich ataxia gene
product, and incorrectly spliced IscU has been shown to
disrupt iron homeostasis in skeletal muscle and cause
myopathy.
Length = 123
Score = 29.5 bits (67), Expect = 1.00
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 162 THLVKGKKVDVKKALSKEEMAKLKTRGGFGGNQGGGDP 199
T L+KGK +D L +++A L + G G P
Sbjct: 69 TELIKGKTLDEALKLLNKDIAMLDGKEELAALAGVGLP 106
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an N-terminal
C4C4 type RING finger motif, followed by a RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The RING
fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 29.0 bits (66), Expect = 1.0
Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 112 TEEDLK--EYFGQFGEVTSVAL 131
EE LK EYFGQ+G++ + +
Sbjct: 19 DEEVLKKPEYFGQYGKIKKIVI 40
>gnl|CDD|227606 COG5281, COG5281, Phage-related minor tail protein [Function
unknown].
Length = 833
Score = 30.8 bits (69), Expect = 1.1
Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 4/70 (5%)
Query: 232 GGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRS 291
G G +GG G GG++ G G + G G GG + + GG + ++
Sbjct: 690 VGLVGSAFGGALSG--GGSASTGAGSVFHFAAGGVYGSGGLPEYA--GGVVSSPTVFTKA 745
Query: 292 GGAPYSGGRG 301
G G G
Sbjct: 746 AGLGLMGEAG 755
>gnl|CDD|219481 pfam07596, SBP_bac_10, Protein of unknown function (DUF1559). A
large family of paralogous proteins apparently unique to
planctomycetes.
Length = 255
Score = 30.1 bits (68), Expect = 1.2
Identities = 16/65 (24%), Positives = 21/65 (32%), Gaps = 3/65 (4%)
Query: 204 GGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGG 263
GG G G D G G ++ G SG GG+ N+ +G
Sbjct: 174 GGLADSGSGGTGGDAADGGGGWGGGTTTTTSTNGSTPATSGPPGGGD---NGAANNGFGS 230
Query: 264 QGGGG 268
GG
Sbjct: 231 AHPGG 235
>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM1 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. IGF2BP1 promotes mRNA
stabilization; it functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD and stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus (HCV)
5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing
HCV internal ribosome entry site (IRES)-mediated
translation initiation via the 3'-UTR. IGF2BP1 contains
four hnRNP K-homology (KH) domains, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a RGG RNA-binding
domain. It also contains two putative nuclear export
signals (NESs) and a putative nuclear localization
signal (NLS). .
Length = 77
Score = 28.1 bits (62), Expect = 1.4
Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 8/83 (9%)
Query: 99 VKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA- 157
+ KL++G+L + +T DL++ F S + K G+ FV+ D KA
Sbjct: 1 MNKLYIGNLNESVTPADLEKVFEDHKISYSGQFLV------KSGYAFVDCPDEQWAMKAI 54
Query: 158 -CLKGTHLVKGKKVDVKKALSKE 179
G + GK+++++ ++ K+
Sbjct: 55 ETFSGKVELHGKRLEIEHSVPKK 77
>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 = 28.3 bits (64), Expect = 1.5
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 9/55 (16%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEK-------ETGKKRGFGFVE 147
++L+VG+L ITEE+L ++F Q + + L + ++ F FVE
Sbjct: 2 RRLYVGNLPPGITEEELVDFFNQ--AMLAAGLNQAPGNPVLSVQINPEKNFAFVE 54
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living cells.
RRM2/3 are implicated in ACF interaction with APOBEC-1.
.
Length = 78
Score = 28.0 bits (62), Expect = 1.5
Identities = 12/50 (24%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
++F+G L D+ E++L + G++ + ++ + G RG+ FV +++
Sbjct: 3 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSN 51
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 28.5 bits (64), Expect = 1.5
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKR 141
L L + ED+KE F Q GEV V + + G R
Sbjct: 4 LKFSGLNKPTSREDIKEAFSQHGEVKYVDFLEGDKEGYVR 43
>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
Length = 371
Score = 30.1 bits (69), Expect = 1.5
Identities = 18/38 (47%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 262 GGQGGGGFGG--GYQQSFG---GGPMRGGGGGGRSGGA 294
G GGGGFGG G+ FG G GG GGGR
Sbjct: 76 QGGGGGGFGGGGGFGDIFGDIFGDIFGGGRGGGRQRAR 113
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily corresponds
to the RRM2 of La and LARP7. La is a highly abundant
nuclear phosphoprotein and well conserved in eukaryotes.
It specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. LARP7
is an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
of 7SK RNA. It is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP), intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. LARP7 plays an essential role in the inhibition
of positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
Both La and LARP7 contain an N-terminal La motif (LAM),
followed by two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 27.7 bits (62), Expect = 1.8
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 106 SLRDDITEEDLKEYFGQFGEVTSVALVTEKETG 138
S+ +T ED+K F QFGEV V +TG
Sbjct: 8 SIGPGVTREDIKAVFAQFGEVKYVDFTEGADTG 40
>gnl|CDD|173940 cd08181, PPD-like, 1,3-propanediol dehydrogenase-like (PPD).
1,3-propanediol dehydrogenase-like (PPD). This family is
a member of the iron-containing alcohol dehydrogenase
superfamily, and exhibits a dehydroquinate synthase-like
fold. Protein sequence similarity search and other
biochemical evidences suggest that they are close to the
iron-containing 1,3-propanediol dehydrogenase (EC
1.1.1.202). 1,3-propanediol dehydrogenase catalyzes the
oxidation of propane-1,3-diol to 3-hydroxypropanal with
the simultaneous reduction of NADP+ to NADPH. The
protein structure of Thermotoga maritima TM0920 gene
contains one NADP+ and one iron ion.
Length = 357
Score = 29.9 bits (68), Expect = 1.8
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 125 EVTSVALVTEKETGKKRGFG 144
EVT +++T+ E G K+GFG
Sbjct: 139 EVTQYSVLTDHEEGTKKGFG 158
>gnl|CDD|218350 pfam04959, ARS2, Arsenite-resistance protein 2. Arsenite is a
carcinogenic compound which can act as a co-mutagen by
inhibiting DNA repair. Arsenite-resistance protein 2 is
thought to play a role in arsenite resistance.
Length = 211
Score = 29.4 bits (66), Expect = 2.0
Identities = 16/58 (27%), Positives = 17/58 (29%), Gaps = 7/58 (12%)
Query: 245 GGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRS-GGAPYSGGRG 301
G G G Q +G PM G G GG Y GGRG
Sbjct: 137 KPDPGGLAPGLPGYPPQTPQALMPYG------QPRPPMMGYGRGGPPFPPNQYGGGRG 188
>gnl|CDD|227938 COG5651, COG5651, PPE-repeat proteins [Cell motility and
secretion].
Length = 490
Score = 29.5 bits (66), Expect = 2.1
Identities = 34/122 (27%), Positives = 41/122 (33%), Gaps = 9/122 (7%)
Query: 188 GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQG----GSSWGGNSGGGWGGNSGGGWGGNS 243
G GG G G G G G + G G + G S G N+GG GN+
Sbjct: 372 GLGNNPGGGLGGKPLGGTGNGGIGASGIGNTGYGNSGIANAGLSNAG-SNNAGGENAGNA 430
Query: 244 GGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPM-RGGGGGGRSGGAPYSGGRGG 302
GGN G G+ G G G G S+ G + G G G S G
Sbjct: 431 NNTGGGNVGLWNAGDFNAGAAGTGFTNNG---SYNTGFLNFGNDNTGIFNGGNTSNGTFN 487
Query: 303 IH 304
Sbjct: 488 QG 489
Score = 28.0 bits (62), Expect = 8.3
Identities = 24/115 (20%), Positives = 30/115 (26%), Gaps = 1/115 (0%)
Query: 188 GGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGW 247
G G G G G G G+ + G+ G +G G
Sbjct: 279 GNIGATNIGLAAAGTGNIGSGNAVDSGGSALVGAIGQTSQATANAGSVNATGGAAAGSG- 337
Query: 248 GGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
+ +G G G S G G GG GG P G G
Sbjct: 338 NLGVANSGSAAAPFGIAGANQAALGGANSGAGNFGLGNNPGGGLGGKPLGGTGNG 392
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 29.2 bits (66), Expect = 2.2
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 98 TVKKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
TVK V ++ TE D+KE+F G++ V + +E E + +V + D + A
Sbjct: 6 TVK---VSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQ---IAYVTFKDPQGAETA 59
Query: 158 CL 159
L
Sbjct: 60 LL 61
>gnl|CDD|224378 COG1461, COG1461, Predicted kinase related to dihydroxyacetone
kinase [General function prediction only].
Length = 542
Score = 29.6 bits (67), Expect = 2.2
Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 4/76 (5%)
Query: 64 DDAQAARPHTIDSKVVEPKRAVPRTEINRPEAGATVKKLFVGSLRDDITEEDLKEYFGQF 123
+ A K E G + F+ +L TE++ +E +
Sbjct: 204 GEPVAKLIADKSISEEHHKDLAEHIATEEIEFGYCTE--FIIALGSKKTEDEFREKLSKL 261
Query: 124 GEVTSVALVTEKETGK 139
G+ S+ + +++ K
Sbjct: 262 GD--SLVVANDEDIVK 275
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 27.7 bits (61), Expect = 2.2
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 11 LFIGGLDYRTSSETLKSHFEAWGDVVDVVVMKDPQTKKSRGFGFITYSSA 60
+F+ LD++ + LK F G V + +D + KSRG G +T+
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKED-KDGKSRGMGTVTFEQP 51
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 29.5 bits (67), Expect = 2.3
Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 1/100 (1%)
Query: 204 GGGGWGGGGPGPWDQGGSSWGGNSGGGWG-GNSGGGWGGNSGGGWGGNSGGGWGGNSAWG 262
GGG GG +GG++ G + + G +GG G GG + G ++
Sbjct: 297 GGGAAAAGGAAAAARGGAAAAGGASSAYSAGAAGGSGAAGVAAGLGGVARAGASAAASPL 356
Query: 263 GQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
+ + SF G GGG G + A +G
Sbjct: 357 RRAASRAAESMKSSFRAGARSTGGGAGGAAAAAAAGAAAA 396
Score = 28.0 bits (63), Expect = 7.1
Identities = 15/59 (25%), Positives = 21/59 (35%)
Query: 236 GGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGA 294
G +G G G G +A +GG GG ++ G G G G + G
Sbjct: 283 GAAVAAAAGAGLAAGGGAAAAGGAAAAARGGAAAAGGASSAYSAGAAGGSGAAGVAAGL 341
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 27.7 bits (61), Expect = 2.4
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYND 150
K++VG+L ++ + +L+ FG +G + SV + GF FVE+ D
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFED 50
>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subgroup corresponds to the RRM of SCAF8 (also
termed CDC5L complex-associated protein 7, or
RNA-binding motif protein 16, or CTD-binding SR-like
protein RA8), a nuclear matrix protein that interacts
specifically with a highly serine-phosphorylated form of
the carboxy-terminal domain (CTD) of the largest subunit
of RNA polymerase II (pol II). The pol II CTD plays a
role in coupling transcription and pre-mRNA processing.
SCAF8 co-localizes primarily with transcription sites
that are enriched in nuclear matrix fraction, which is
known to contain proteins involved in pre-mRNA
processing. Thus, SCAF8 may play a direct role in
coupling with both, transcription and pre-mRNA
processing, processes. SCAF8, together with SCAF4,
represents a new class of SCAFs (SR-like CTD-associated
factors). They contain a conserved N-terminal
CTD-interacting domain (CID), an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and
serine/arginine-rich motifs.
Length = 79
Score = 27.3 bits (60), Expect = 2.5
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALV 132
L+VG + T++DL F +FG++ S+ ++
Sbjct: 5 LWVGQVDKKATQQDLTNLFEEFGQIESINMI 35
>gnl|CDD|173939 cd08180, PDD, 1,3-propanediol dehydrogenase (PPD) catalyzes the
reduction of 3-hydroxypropionaldehyde (3-HPA) to
1,3-propanediol in glycerol metabolism. 1,3-propanediol
dehydrogenase (PPD) plays a role in glycerol metabolism
of some bacteria in anaerobic conditions. In this
degradation pathway, glycerol is converted in a two-step
process to 1,3-propanediol (1,3-PD) which is then
excreted into the extracellular medium. The first
reaction involves the transformation of glycerol into
3-hydroxypropionaldehyde (3-HPA) by a coenzyme
B-12-dependent dehydratase. The second reaction involves
the dismutation of the 3-hydroxypropionaldehyde (3-HPA)
to 1,3-propanediol by the NADH-linked 1,3-propanediol
dehydrogenase (PPD). The enzyme require iron ion for its
function. Because many genes in this pathway are
present in the pdu (propanediol utilisation) operon,
they are also named pdu genes. PPD is a member of the
iron-containing alcohol dehydrogenase superfamily. The
PPD structure has a dehydroquinate synthase-like fold.
Length = 332
Score = 29.4 bits (67), Expect = 2.5
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 125 EVTSVALVTEKETGKK 140
EVTS A++T+ ETG K
Sbjct: 124 EVTSFAVITDPETGVK 139
>gnl|CDD|241210 cd12766, RRM2_SRSF6, RNA recognition motif 2 found in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subgroup corresponds to the RRM2 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, an essential splicing
regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 27.3 bits (60), Expect = 2.6
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKAC-- 158
+L V +L + +DLK++ Q GEVT E+ G +E+ Y + +A
Sbjct: 2 RLIVENLSSRCSWQDLKDFMRQAGEVTYADAHKERANE-----GVIEFRSYSDMKRALEK 56
Query: 159 LKGTHLVKGKKV 170
L GT + G+K+
Sbjct: 57 LDGTE-INGRKI 67
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 29.1 bits (65), Expect = 2.7
Identities = 14/42 (33%), Positives = 16/42 (38%), Gaps = 3/42 (7%)
Query: 219 GGSSWGGNS---GGGWGGNSGGGWGGNSGGGWGGNSGGGWGG 257
GG S G N+ GGG S G G G G + G
Sbjct: 266 GGLSSGKNAPKTGGGAKNASSQGSGAAKNSGASGADIDQYAG 307
>gnl|CDD|237658 PRK14284, PRK14284, chaperone protein DnaJ; Provisional.
Length = 391
Score = 29.0 bits (65), Expect = 3.1
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 204 GGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSG--GGWGGNSGGGWGGNSGGG 254
G GG+GG G G + ++ G GG +GG G G G +G G
Sbjct: 74 GAGGFGGAGMGNMEDALRTFMGAFGGEFGGGGSFFEGLFGGLGEAFGMRGGPA 126
Score = 29.0 bits (65), Expect = 3.6
Identities = 23/63 (36%), Positives = 27/63 (42%), Gaps = 9/63 (14%)
Query: 238 GWGGNSGGGWGGNSG------GGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRS 291
G GG G G G G +GG GG G GG ++FG MRGG G R
Sbjct: 74 GAGGFGGAGMGNMEDALRTFMGAFGGEFGGGGSFFEGLFGGLGEAFG---MRGGPAGARQ 130
Query: 292 GGA 294
G +
Sbjct: 131 GAS 133
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 29.0 bits (65), Expect = 3.2
Identities = 23/100 (23%), Positives = 40/100 (40%), Gaps = 15/100 (15%)
Query: 104 VGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG-- 161
V +L D+ E DL E FG V+ V ++ + VE+ D + KAC+
Sbjct: 7 VRNLPQDVVEADLVEALIPFGPVSYVMML------PGKRQALVEFEDEESA-KACVNFAT 59
Query: 162 --THLVKGKKVDVKKALSKEEMAKLKTRGGFGGNQGGGDP 199
++G+ + S+E +K G + G +
Sbjct: 60 SVPIYIRGQPAFFNYSTSQE----IKRDGNSDFDSAGPNK 95
>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 = 27.1 bits (60), Expect = 3.5
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 100 KKLFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEK-------ETGKKRGFGFV 146
K L++ +L D T+ +L+ +F Q+G V VA T K + K GF
Sbjct: 1 KVLYISNLPPDTTQLELESWFTQYG-VRPVAFWTLKTPDEDAYVSSKDSISGFA 53
>gnl|CDD|237665 PRK14295, PRK14295, chaperone protein DnaJ; Provisional.
Length = 389
Score = 29.0 bits (65), Expect = 3.5
Identities = 20/53 (37%), Positives = 25/53 (47%)
Query: 207 GWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNS 259
G GG PGP GG + + G +GG + GG G GGG G GG +
Sbjct: 79 GNGGFRPGPGGGGGGGFNFDLGDLFGGGAQGGGGAGGGGGLGDVFGGLFNRGG 131
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM3
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 73
Score = 26.9 bits (59), Expect = 3.6
Identities = 11/56 (19%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
++ G + +TE+ +++ F FG++ + + EK G+ F+ ++ ++ A
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPEK------GYSFIRFSTHESAAHA 52
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 26.9 bits (59), Expect = 3.6
Identities = 13/56 (23%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKA 157
++ G + +TE+ +++ F FG++ V + +K G+ FV +N ++ A
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDK------GYSFVRFNSHESAAHA 52
>gnl|CDD|241167 cd12723, RRM1_CPEB1, RNA recognition motif 1 in cytoplasmic
polyadenylation element-binding protein 1 (CPEB-1) and
similar proteins. This subgroup corresponds to the RRM2
of CPEB-1 (also termed CPE-BP1 or CEBP), 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 bound 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. CPEB-1
contains an N-terminal unstructured region, two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. Both of the RRMs and the Zn finger are
required for CPEB-1 to bind CPE. The N-terminal
regulatory region may be responsible for CPEB-1
interacting with other proteins. .
Length = 100
Score = 27.4 bits (61), Expect = 3.7
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 101 KLFVGSLRDDITEEDLKEYFGQFGEVT 127
K+F+G + DITE L F FG V+
Sbjct: 4 KVFLGGVPWDITEAGLINTFKPFGSVS 30
>gnl|CDD|223560 COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn
finger domain [Posttranslational modification, protein
turnover, chaperones].
Length = 371
Score = 28.7 bits (65), Expect = 3.9
Identities = 18/45 (40%), Positives = 20/45 (44%), Gaps = 9/45 (20%)
Query: 258 NSAWGGQGGGGFGGGYQ----QSFGGGPMRGGGGGGRSGGAPYSG 298
+GG G GGFGG + FGGG GGG R P G
Sbjct: 76 AGGFGGFGFGGFGGDFGDIFEDFFGGG-----GGGRRRPNRPRRG 115
>gnl|CDD|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator of
basal transcription 1 (ABT1) and similar proteins. This
subfamily corresponds to the RRM of novel nuclear
proteins termed ABT1 and its homologous counterpart,
pre-rRNA-processing protein ESF2 (eighteen S factor 2),
from yeast. ABT1 associates with the TATA-binding
protein (TBP) and enhances basal transcription activity
of class II promoters. Meanwhile, ABT1 could be a
transcription cofactor that can bind to DNA in a
sequence-independent manner. The yeast ABT1 homolog,
ESF2, is a component of 90S preribosomes and 5'
ETS-based RNPs. It is previously identified as a
putative partner of the TATA-element binding protein.
However, it is primarily localized to the nucleolus and
physically associates with pre-rRNA processing factors.
ESF2 may play a role in ribosome biogenesis. It is
required for normal pre-rRNA processing, as well as for
SSU processome assembly and function. Both ABT1 and ESF2
contain an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 98
Score = 27.2 bits (61), Expect = 3.9
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 116 LKEYFGQFGEVTSVALVTEKETGKKR 141
L++ Q+GEV + L E +KR
Sbjct: 17 LRQLLSQYGEVGRIYLQPEDPAKRKR 42
>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein.
Length = 582
Score = 28.7 bits (64), Expect = 4.1
Identities = 21/110 (19%), Positives = 28/110 (25%), Gaps = 2/110 (1%)
Query: 185 KTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGG--WGGNSGGGWGGN 242
+ R + + N G GP QGG + + +GG G W N
Sbjct: 471 RGRQSSQPPRQQQNRSNQNNQRQSQGPNQGPRGQGGYNLRPRTYQPQRYGGGQGRRWNPN 530
Query: 243 SGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSG 292
G G G G Q G R G +
Sbjct: 531 PYRQSGQGRSQQQQPQPEARGNQSRTPGPGRGQGGRGNQNRNQRSGNNTV 580
Score = 28.3 bits (63), Expect = 5.1
Identities = 18/70 (25%), Positives = 19/70 (27%), Gaps = 7/70 (10%)
Query: 190 FGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGG 249
+GG QG N G G Q GN G G G GN
Sbjct: 519 YGGGQGRRW---NPNPYRQSGQGRSQQQQPQPEARGNQSRTPGPGRGQGGRGNQ----NR 571
Query: 250 NSGGGWGGNS 259
N G S
Sbjct: 572 NQRSGNNTVS 581
>gnl|CDD|241170 cd12726, RRM2_CPEB2_like, RNA recognition motif 2 found in
cytoplasmic polyadenylation element-binding protein
CPEB-2, CPEB-3, CPEB-4 and similar protiens. This
subgroup corresponds to the RRM2 of the paralog
proteins CPEB-2, CPEB-3 and CPEB-4, all well conserved
in both, vertebrates and invertebrates. Due to the high
sequence similarity, members in this family 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. Moreover, 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 family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a Zn-finger
motif. In addition, they do have conserved nuclear
export signals that are not present in CPEB-1. .
Length = 81
Score = 26.7 bits (59), Expect = 4.3
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 9 RKLFIGGLDYRTSSETLKSHFEA-WGDVVDVVVMKDPQTKKSRGFGFITYSSAHMVDDAQ 67
+ +F+GG+ + L + +G V + DP+ K +G G + +S+ A
Sbjct: 1 KTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAI 60
Query: 68 AAR 70
+AR
Sbjct: 61 SAR 63
>gnl|CDD|184611 PRK14297, PRK14297, chaperone protein DnaJ; Provisional.
Length = 380
Score = 28.6 bits (64), Expect = 4.4
Identities = 19/53 (35%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 246 GWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSG 298
G GG GG+GG + GGFG + FGG G G R P G
Sbjct: 76 GAGGFGSGGFGG---FDFSDMGGFGDIFDSFFGG----GFGSSSRRRNGPQRG 121
>gnl|CDD|240227 PTZ00009, PTZ00009, heat shock 70 kDa protein; Provisional.
Length = 653
Score = 28.6 bits (64), Expect = 4.6
Identities = 14/29 (48%), Positives = 15/29 (51%)
Query: 224 GGNSGGGWGGNSGGGWGGNSGGGWGGNSG 252
GG GG GG GG GG G G +SG
Sbjct: 618 GGMPGGMPGGMPGGMPGGAGPAGAGASSG 646
Score = 28.2 bits (63), Expect = 6.9
Identities = 16/38 (42%), Positives = 16/38 (42%), Gaps = 3/38 (7%)
Query: 185 KTRGGFGGNQGGGDPWGNNGGGGWGGGGPGPWDQGGSS 222
K GG GG P G GG GG GP G SS
Sbjct: 611 KMYQAAGGGMPGGMP-GGMPGGMPGGAGPAG--AGASS 645
Score = 28.2 bits (63), Expect = 7.0
Identities = 16/41 (39%), Positives = 17/41 (41%), Gaps = 10/41 (24%)
Query: 204 GGGGWGGGGPGPWDQGGSSWGGNSGGGWGGNSGGGWGGNSG 244
GGG GG P GG GG GG G G +SG
Sbjct: 616 AGGGMPGGMP----------GGMPGGMPGGAGPAGAGASSG 646
>gnl|CDD|227690 COG5403, COG5403, Uncharacterized conserved protein [Function
unknown].
Length = 285
Score = 28.4 bits (63), Expect = 4.7
Identities = 20/67 (29%), Positives = 21/67 (31%), Gaps = 6/67 (8%)
Query: 230 GWGGNSGGGWGGNSGGGW----GGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGG 285
G GG GG + GG G GGG G Q GG G M GG
Sbjct: 140 AQMGQMGGNMGGQNPGGMSLPQGMGGGGGGALGPILGPQLGGPADNPLGSVLQG--MFGG 197
Query: 286 GGGGRSG 292
G
Sbjct: 198 GQAQAQM 204
>gnl|CDD|227270 COG4934, COG4934, Predicted protease [Posttranslational
modification, protein turnover, chaperones].
Length = 1174
Score = 28.6 bits (64), Expect = 5.2
Identities = 20/74 (27%), Positives = 24/74 (32%), Gaps = 14/74 (18%)
Query: 236 GGGWGGNSGGGWGGNSGG--GWGGNSAWGGQGGGGFGGGYQQSFG-----GGPMRGGGG- 287
GG N+ S WG + G G G GGGY F GP G
Sbjct: 394 GGYPISNAKFT-SNGSFTETAWGYS--SYGPGSVGSGGGYSIFFPRPWYQDGPSVPSTGR 450
Query: 288 ---GGRSGGAPYSG 298
+ PY+G
Sbjct: 451 LIPDVVAIANPYTG 464
>gnl|CDD|239152 cd02751, MopB_DMSOR-like, The MopB_DMSOR-like CD contains
dimethylsulfoxide reductase (DMSOR), biotin sulfoxide
reductase (BSOR), trimethylamine N-oxide reductase
(TMAOR) and other related proteins. DMSOR catalyzes the
reduction of DMSO to dimethylsulfide, but its cellular
location and oligomerization state are
organism-dependent. For example, in Rhodobacter
sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa
monomeric soluble protein found in the periplasmic
space; in E. coli, it is membrane-bound and exists as a
heterotrimer. BSOR catalyzes the reduction of biotin
sulfixode to biotin, and is unique among Mo enzymes
because no additional auxiliary proteins or cofactors
are required. TMAOR is similar to DMSOR, but its only
natural substrate is TMAO. Also included in this group
is the pyrogallol-phloroglucinol transhydroxylase from
Pelobacter acidigallici. Members of the MopB_DMSOR-like
CD belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 609
Score = 28.3 bits (64), Expect = 5.3
Identities = 18/26 (69%), Positives = 18/26 (69%)
Query: 263 GQGGGGFGGGYQQSFGGGPMRGGGGG 288
G GGGFG GY S GGGP RGG GG
Sbjct: 340 GLPGGGFGFGYGYSNGGGPPRGGAGG 365
>gnl|CDD|185641 PTZ00462, PTZ00462, Serine-repeat antigen protein; Provisional.
Length = 1004
Score = 28.5 bits (63), Expect = 5.4
Identities = 14/46 (30%), Positives = 16/46 (34%), Gaps = 11/46 (23%)
Query: 225 GNSGGGWGGNSGGGWGGNSGGGWGGNSGG-----------GWGGNS 259
GN GGG G +GG GN G GN G +
Sbjct: 31 GNIGGGQAGGTGGDNAGNIDGSPIGNLDANIHASFGADPKESSGAN 76
>gnl|CDD|233001 TIGR00509, bisC_fam, molybdopterin guanine dinucleotide-containing
S/N-oxide reductases. This enzyme family shares
sequence similarity and a requirement for a molydenum
cofactor as the only prosthetic group. The form of the
cofactor is a single molybdenum atom coordinated by two
molybdopterin guanine dinucleotide molecules. Members of
the family include biotin sulfoxide reductase,
dimethylsulfoxide reductase, and trimethylamine-N-oxide
reductase, although a single member may show all those
activities and related activities; it may not be
possible to resolve the primary function for members of
this family by sequence comparison alone. A number of
similar molybdoproteins in which the N-terminal region
contains a CXXXC motif and may bind an iron-sulfur
cluster are excluded from this set, including formate
dehydrogenases and nitrate reductases. Also excluded is
the A chain of a heteromeric, anaerobic DMSO reductase,
which also contains the CXXXC motif.
Length = 770
Score = 28.6 bits (64), Expect = 5.4
Identities = 18/45 (40%), Positives = 18/45 (40%), Gaps = 5/45 (11%)
Query: 263 GQGGGGFGGGYQQSFGG-----GPMRGGGGGGRSGGAPYSGGRGG 302
G GGGFG Y S GG GP G S AP GG
Sbjct: 338 GLPGGGFGFSYHYSGGGTPSASGPALSQGSNSVSTKAPEWLDDGG 382
>gnl|CDD|218967 pfam06273, eIF-4B, Plant specific eukaryotic initiation factor 4B.
This family consists of several plant specific
eukaryotic initiation factor 4B proteins.
Length = 496
Score = 28.5 bits (63), Expect = 5.5
Identities = 38/134 (28%), Positives = 44/134 (32%), Gaps = 19/134 (14%)
Query: 174 KALSKEEMAKLKTRGGFGGNQGGGDPW--GNNGGGGWGGGGPGPWDQGGSSWGGNSGGGW 231
K L++EEM +L T G Q + G GGG GG + G +GG
Sbjct: 83 KGLTQEEMMQLPT----GPRQRSEEEMQRGRLGGGFRSYGGNRSYGGGRRPYGGGFDDDR 138
Query: 232 GGNSGGGWGGNSGG------GWGGN-----SGGGWGGNSAWGGQGGGGFGGGYQQSFGGG 280
G WG G GGG FGGG GGG
Sbjct: 139 RGWGPRVSDFPQPSRADEIDDWGRGKKSTPLPSFDQGRQGRYPSGGGAFGGG--GGGGGG 196
Query: 281 PMRGGGGGGRSGGA 294
R GG S GA
Sbjct: 197 GERRSGGFRDSPGA 210
Score = 27.7 bits (61), Expect = 9.5
Identities = 32/132 (24%), Positives = 40/132 (30%), Gaps = 15/132 (11%)
Query: 177 SKEEMAKLKTRGGFGGNQGGGDPWGNNG--GGGWGGGGPGPWDQGG-----------SSW 223
S+EEM + + GGF G G GGG+ G + W
Sbjct: 101 SEEEMQRGRLGGGFRSYGGNRSYGGGRRPYGGGFDDDRRGWGPRVSDFPQPSRADEIDDW 160
Query: 224 GGNSGGGWGGNSGGGWGG--NSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGP 281
G + G G SGGG G GGG GG G G +G
Sbjct: 161 GRGKKSTPLPSFDQGRQGRYPSGGGAFGGGGGGGGGGERRSGGFRDSPGADDSDRWGRKK 220
Query: 282 MRGGGGGGRSGG 293
+ G G
Sbjct: 221 VETFGSAFGENG 232
>gnl|CDD|176535 cd08593, PI-PLCc_delta, Catalytic domain of metazoan
phosphoinositide-specific phospholipase C-delta. This
subfamily corresponds to the catalytic domain present in
metazoan phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11)-delta isozymes. PI-PLC is a
signaling enzyme that hydrolyzes the membrane
phospholipids phosphatidylinositol-4,5-bisphosphate
(PIP2) to generate two important second messengers in
eukaryotic signal transduction cascades, Inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which then phosphorylates other
molecules, leading to altered cellular activity. Calcium
is required for the catalysis. PLC-delta represents a
class of mammalian PI-PLC that has an N-terminal
pleckstrin homology (PH) domain, an array of EF hands, a
PLC catalytic core domain, and a C-terminal C2 domain.
This CD corresponds to the catalytic domain which is a
TIM barrel with two highly conserved regions (X and Y)
split by a highly degenerate linker sequence. There are
three PI-PLC-delta isozymes (1,3 and 4). PI-PLC-delta1
is relatively well characterized. It is activated by
high calcium levels generated by other PI-PLC family
members, and therefore functions as a calcium amplifier
within the cell. Different PI-PLC-delta isozymes have
different tissue distribution and different subcellular
locations. PI-PLC-delta1 is mostly a cytoplasmic
protein, PI-PLC-delta3 is located in the membrane, and
PI-PLC-delta4 is predominantly detected in the cell
nucleus. Aside from three PI-PLC-delta isozymes
identified in mammals, some eukaryotic PI-PLC-delta
homologs have been classified to this CD.
Length = 257
Score = 28.1 bits (63), Expect = 5.6
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 159 LKGTHLVKGKKVDVKKALS 177
LKG LVKGKK+ + K LS
Sbjct: 137 LKGKILVKGKKLKLAKELS 155
>gnl|CDD|233907 TIGR02517, type_II_gspD, type II secretion system protein D. In
Gram-negative bacteria, proteins that have first crossed
the inner member by Sec-dependent protein transport can
be exported across the outer membrane by type II
secretion, also called the main terminal branch of the
general secretion pathway. Members of this family are
general secretion pathway protein D. In Yersinia
enterocolitica, a second member of this family is part
of a novel second type II secretion system specifically
associated with virulence (See PMID:12654803). This
family is closely homologous to the type IV pilus outer
membrane secretin PilQ (TIGR02515) and to the type III
secretion system pore YscC/HrcC (TIGR02516) [Protein
fate, Protein and peptide secretion and trafficking].
Length = 594
Score = 28.5 bits (64), Expect = 5.8
Identities = 18/67 (26%), Positives = 21/67 (31%), Gaps = 3/67 (4%)
Query: 228 GGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGG 287
G W GG S G S G ++ G G G S GG G
Sbjct: 350 GVQWLIAGTGGGVNFSTGSPNSGSLLGASASAISLGSAGIGLLVT---SSSTTSGVGGTG 406
Query: 288 GGRSGGA 294
GG + G
Sbjct: 407 GGPNLGV 413
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 26.4 bits (58), Expect = 6.0
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDKACLKG 161
+++ +L ++ +LK+ F FGE+ ++ K G+K +GF+ Y + + KG
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLI-KSRGEK--YGFITYRHSEHAALSLGKG 61
Query: 162 THLVKGKK 169
L K +
Sbjct: 62 ASLRKRNE 69
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 26.3 bits (58), Expect = 6.1
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYD 152
+VG++ T+ DL F FG + + RGF FV+ + ++
Sbjct: 4 YVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHE 47
>gnl|CDD|233311 TIGR01208, rmlA_long, glucose-1-phosphate thymidylylransferase,
long form. The family of known and putative
glucose-1-phosphate thymidyltransferase (also called
dTDP-glucose synthase) shows a deep split into a short
form (see TIGR01207) and a long form described by this
model. The homotetrameric short form is found in
numerous bacterial species that incorporate
dTDP-L-rhamnose, which it helps synthesize, into the
cell wall. It is subject to feedback inhibition. This
form, in contrast, is found in many species for which it
serves as a sugar-activating enzyme for antibiotic
biosynthesis and or other, unknown pathways, and in
which dTDP-L-rhamnose is not necessarily produced.
Alternate name: dTDP-D-glucose synthase.
Length = 353
Score = 27.8 bits (62), Expect = 6.9
Identities = 12/54 (22%), Positives = 21/54 (38%)
Query: 103 FVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETGKKRGFGFVEYNDYDPVDK 156
FV L D++ ++ + + F E AL+ + FG D + K
Sbjct: 101 FVVYLGDNLIQDGISRFVKSFEEKDYDALILLTKVRDPTAFGVAVLEDGKRILK 154
>gnl|CDD|220755 pfam10439, Bacteriocin_IIc, Bacteriocin class II with
double-glycine leader peptide. This is a family of
bacteriocidal bacteriocins secreted by Streptococcal
species in order to kill off closely-related competitor
Gram-positives. The sequence includes the peptide
precursor, this being cleaved off proteolytically at the
double-glycine. The family does not carry the YGNGVXC
motif characteristic of pediocin-like Bacteriocins,
Bacteriocin_II pfam01721. The producer bacteria are
protected from the effects of their own bacteriocins by
production of a specific immunity protein which is
co-transcribed with the genes encoding the bacteriocins,
eg family EntA_Immun pfam08951. The bacteriocins are
structurally more specific than their immunity-protein
counterparts. Typically, production of the bacteriocin
gene is from within an operon carrying up to 6 genes
including a typical two-component regulatory system (R
and H), a small peptide pheromone (C), and a dedicated
ABC transporter (A and -B) as well as an immunity
protein. The ABC transporter is thought to recognise the
N termini of both the pheromone and the bacteriocins and
to transport these peptides across the cytoplasmic
membrane, concurrent with cleavage at the conserved
double-glycine motif. Cleaved extracellular C can then
bind to the sensor kinase, H, resulting in activation of
R and up-regulation of the entire gene cluster via
binding to consensus sequences within each promoter. It
seems likely that this whole regulon is carried on a
transmissible plasmid which is passed between closely
related Firmicute species since many clinical isolates
from different Firmicutes can produce at least two
bacteriocins. and the same bacteriocins can be produced
by different species.
Length = 65
Score = 25.8 bits (57), Expect = 7.0
Identities = 17/40 (42%), Positives = 21/40 (52%)
Query: 218 QGGSSWGGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGG 257
+GG+SWG GG GG + G G +GGG G G G
Sbjct: 17 EGGNSWGKCVGGIGGGAAAGAVAGAAGGGPVGGLAGALVG 56
>gnl|CDD|226365 COG3846, TrbL, Type IV secretory pathway, TrbL components
[Intracellular trafficking and secretion].
Length = 452
Score = 27.8 bits (62), Expect = 7.1
Identities = 16/80 (20%), Positives = 21/80 (26%)
Query: 224 GGNSGGGWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMR 283
GG G +G + G G G G + G S
Sbjct: 283 GGPQVGAGAVGAGVAISLKATGAAGAALAGARGATAGASLASSVTALGTSMASAAASAFA 342
Query: 284 GGGGGGRSGGAPYSGGRGGI 303
G G SG + G G +
Sbjct: 343 SGRKGSGSGAFGTAAGVGDV 362
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 28.0 bits (62), Expect = 7.2
Identities = 12/36 (33%), Positives = 12/36 (33%), Gaps = 3/36 (8%)
Query: 266 GGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRG 301
GGG G G GGGG R G R
Sbjct: 433 GGGRSGPGG---GSRSGSVGGGGRRDGAGADGKPRP 465
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 28.2 bits (64), Expect = 7.3
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 116 LKEYFGQFGEVTSVALVTEKETGKKR 141
LK+ G VAL+T GK+R
Sbjct: 330 LKKLLEPLG--IRVALLTGSLKGKER 353
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces
cerevisiae protein Nrd1, Schizosaccharomyces pombe
Rpb7-binding protein seb1 and similar proteins. This
subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1
is a novel heterogeneous nuclear ribonucleoprotein
(hnRNP)-like RNA-binding protein encoded by gene NRD1
(for nuclear pre-mRNA down-regulation) from yeast S.
cerevisiae. It is implicated in 3' end formation of
small nucleolar and small nuclear RNAs transcribed by
polymerase II, and plays a critical role in pre-mRNA
metabolism. Nrd1 contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a short arginine-, serine-,
and glutamate-rich segment similar to the regions rich
in RE and RS dipeptides (RE/RS domains) in many metazoan
splicing factors, and a proline- and glutamine-rich
C-terminal domain (P+Q domain) similar to domains found
in several yeast hnRNPs. Disruption of NRD1 gene is
lethal to yeast cells. Its N-terminal domain is
sufficient for viability, which may facilitate
interactions with RNA polymerase II where Nrd1 may
function as an auxiliary factor. By contrast, the RRM,
RE/RS domains, and P+Q domain are dispensable. Seb1 is
an RNA-binding protein encoded by gene seb1 (for seven
binding) from fission yeast S. pombe. It is essential
for cell viability and bound directly to Rpb7 subunit of
RNA polymerase II. Seb1 is involved in processing of
polymerase II transcripts. It also contains one RRM
motif and a region rich in arginine-serine dipeptides
(RS domain).
Length = 79
Score = 26.0 bits (57), Expect = 7.5
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 102 LFVGSLRDDITEEDLKEYFGQFGEVTSVALVTEKETG 138
LF G + ++ E DL+ FG+FGEV S L +K
Sbjct: 6 LFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHA 42
>gnl|CDD|218573 pfam05387, Chorion_3, Chorion family 3. This family consists of
several Drosophila chorion proteins S36 and S38. The
chorion genes of Drosophila are amplified in response to
developmental signals in the follicle cells of the
ovary.
Length = 277
Score = 27.8 bits (61), Expect = 8.0
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 230 GWGGNSGGGWGGNSGGGWGGNSGGGWGGNSAWGG-QGGGGFGGGYQQSFGGGP 281
+G GGG G+ G G ++G N+A GG Q GG G Q P
Sbjct: 19 SYGSAGGGGGHGSGQYGAGASAGLEEYVNAAAGGAQPSGGNIIGAQAEIQPTP 71
Score = 27.4 bits (60), Expect = 8.6
Identities = 13/57 (22%), Positives = 18/57 (31%)
Query: 246 GWGGNSGGGWGGNSAWGGQGGGGFGGGYQQSFGGGPMRGGGGGGRSGGAPYSGGRGG 302
+G GGG G+ +G G + GG GG G + G
Sbjct: 19 SYGSAGGGGGHGSGQYGAGASAGLEEYVNAAAGGAQPSGGNIIGAQAEIQPTPEEAG 75
>gnl|CDD|237515 PRK13805, PRK13805, bifunctional acetaldehyde-CoA/alcohol
dehydrogenase; Provisional.
Length = 862
Score = 27.8 bits (63), Expect = 9.9
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 125 EVTSVALVTEKETGKK 140
EVT A++T+ +TG K
Sbjct: 607 EVTPFAVITDDKTGVK 622
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
0.312 0.140 0.449
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,364,250
Number of extensions: 1648409
Number of successful extensions: 6263
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4000
Number of HSP's successfully gapped: 1070
Length of query: 304
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 208
Effective length of database: 6,679,618
Effective search space: 1389360544
Effective search space used: 1389360544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 59 (26.7 bits)