RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2871
(178 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 = 146 bits (371), Expect = 1e-46
Identities = 54/78 (69%), Positives = 63/78 (80%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL Y TTD+SL+ +F QWGEI D VVMKDP TKRSRGFGF+T++ A VD AM+
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 78 RPHNIDGRVVETKRAVPR 95
RPH +DGR VE KRAVPR
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
Score = 46.2 bits (110), Expect = 2e-07
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
K+F+GGL + +D L+ YFSQ+G I ++ + T RGF F+ F VD
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDA 56
>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 = 7e-35
Identities = 55/80 (68%), Positives = 65/80 (81%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TYS + VD AM
Sbjct: 2 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61
Query: 76 SNRPHNIDGRVVETKRAVPR 95
+ RPH +DGRVVE KRAV R
Sbjct: 62 NARPHKVDGRVVEPKRAVSR 81
Score = 40.8 bits (95), Expect = 2e-05
Identities = 19/57 (33%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 107 VKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 162
++K+F+GGL + D+ LR +F Q+GT+ ++ + T RGF F+ ++ + VD
Sbjct: 2 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVD 58
>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 = 2e-33
Identities = 51/80 (63%), Positives = 64/80 (80%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
RK+FIGGL + TT+ESL+ ++EQWG++ D VVM+DP +KRSRGFGF+T+S VD AM
Sbjct: 2 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61
Query: 76 SNRPHNIDGRVVETKRAVPR 95
+ RPH IDGRVVE KRAV R
Sbjct: 62 AARPHTIDGRVVEPKRAVAR 81
Score = 40.9 bits (95), Expect = 2e-05
Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
+K+F+GGL + E+ LR Y+ Q+G + ++ + + RGF F+ F+ + VD +
Sbjct: 3 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62
Query: 167 SKITLLLDRRVE 178
++ + R VE
Sbjct: 63 ARPHTIDGRVVE 74
>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 = 111 bits (278), Expect = 1e-32
Identities = 54/80 (67%), Positives = 64/80 (80%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
LRK+FIGGL + TTD+SL+ FE+WG + D VVM+DP TKRSRGFGF+TYS + VD AM
Sbjct: 2 LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61
Query: 76 SNRPHNIDGRVVETKRAVPR 95
S RPH +DGRVVE KRAV R
Sbjct: 62 SARPHKVDGRVVEPKRAVSR 81
Score = 42.8 bits (100), Expect = 5e-06
Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 107 VKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++K+F+GGL + DD LRE+F ++GT+ ++ + +T RGF F+ ++ + VD +
Sbjct: 2 LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61
Query: 166 LSKITLLLDRRVE 178
++ + R VE
Sbjct: 62 SARPHKVDGRVVE 74
>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 = 110 bits (277), Expect = 2e-32
Identities = 38/71 (53%), Positives = 56/71 (78%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRP 79
FIGGL + TT+ESL+ +F ++GE+VD V+MKDPIT RSRGFGF+T+++ VD ++ +P
Sbjct: 2 FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61
Query: 80 HNIDGRVVETK 90
H +DGR ++ K
Sbjct: 62 HVLDGREIDPK 72
Score = 70.7 bits (174), Expect = 6e-17
Identities = 27/70 (38%), Positives = 43/70 (61%), Gaps = 1/70 (1%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
+F+GGL D E+ LREYFS++G + ++ + TG RGF F+ F D VDK++ +K
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 169 ITLLLDRRVE 178
+L R ++
Sbjct: 61 PHVLDGREID 70
>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 = 102 bits (256), Expect = 3e-29
Identities = 41/78 (52%), Positives = 57/78 (73%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
L K+F+GGL+ +T+D L+ F ++G++ + VVM DP TKRSRGFGFIT+S A D+AM
Sbjct: 2 LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
Query: 76 SNRPHNIDGRVVETKRAV 93
+PH+IDG +E KRA
Sbjct: 62 EAQPHSIDGNQIELKRAK 79
Score = 42.9 bits (101), Expect = 4e-06
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 162
K+FVGGL + + LR +F+++G + ++ + T RGF FI F+ D D
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEAD 58
>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 = 102 bits (256), Expect = 4e-29
Identities = 36/80 (45%), Positives = 53/80 (66%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL + TT E+L+ +F Q+GE+VD V+MKD T RSRGFGF+ + + V ++
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 78 RPHNIDGRVVETKRAVPRDE 97
PH +DGR ++ K PR
Sbjct: 61 GPHTLDGRTIDPKPCTPRGM 80
Score = 52.9 bits (127), Expect = 7e-10
Identities = 27/69 (39%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGL + ++ LR YFSQ+G + ++ +K T RGF F++F D + V VL+
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCV-GTVLA 59
Query: 168 KITLLLDRR 176
LD R
Sbjct: 60 GGPHTLDGR 68
>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 = 100 bits (252), Expect = 1e-28
Identities = 47/71 (66%), Positives = 56/71 (78%), Gaps = 1/71 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGLK D E+DLREYFSQ+G +ESV +VT+KETG KRGFAF+ F+DYD VDKIVL
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 168 KITLLLDRRVE 178
K + RVE
Sbjct: 61 KYHTINGHRVE 71
Score = 60.0 bits (146), Expect = 9e-13
Identities = 27/73 (36%), Positives = 43/73 (58%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL T+E L+ +F Q+G + V ++ D T + RGF F+T+ + VD +
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 78 RPHNIDGRVVETK 90
+ H I+G VE K
Sbjct: 61 KYHTINGHRVEVK 73
>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 = 93.8 bits (233), Expect = 8e-26
Identities = 38/77 (49%), Positives = 58/77 (75%), Gaps = 1/77 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+FIGGL++ TTD+SL+ +F Q+GE+ D VM+D T RSRGFGF+T+ + K V++ M
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60
Query: 79 PHNIDGRVVETKRAVPR 95
H +DG++++ KRA+PR
Sbjct: 61 -HILDGKIIDPKRAIPR 76
Score = 54.5 bits (131), Expect = 1e-10
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
MF+GGL + +D LREYF QFG + ++ + TG RGF F+ F V++++
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVM 57
>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 = 93.3 bits (232), Expect = 1e-25
Identities = 36/74 (48%), Positives = 54/74 (72%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRP 79
FIGGL ++TT E L+ +F ++GEI + +VM+DP TKRSRGFGF+T+S+ VD ++ P
Sbjct: 2 FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGP 61
Query: 80 HNIDGRVVETKRAV 93
H +DG+ ++ K A
Sbjct: 62 HELDGKKIDPKVAF 75
Score = 49.7 bits (119), Expect = 7e-09
Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
MF+GGL Q + LREYFS+FG I+ ++ + T RGF F+ F+D VDK++
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVL 57
>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 = 85.5 bits (212), Expect = 1e-22
Identities = 35/78 (44%), Positives = 50/78 (64%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+K+F+GGL T+ L+ +F Q+G + +VVVM D KR RGFGFIT+ VD ++
Sbjct: 3 KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62
Query: 77 NRPHNIDGRVVETKRAVP 94
H+I+G+ VE KRA P
Sbjct: 63 EHFHDINGKKVEVKRAEP 80
Score = 61.6 bits (150), Expect = 3e-13
Identities = 32/73 (43%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 107 VKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
KK+FVGGL E DLR+YFSQFGT+ V ++ + E RGF FI F D VD++V
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61
Query: 166 LSKITLLLDRRVE 178
+ ++VE
Sbjct: 62 NEHFHDINGKKVE 74
>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 = 82.0 bits (203), Expect = 3e-21
Identities = 31/75 (41%), Positives = 46/75 (61%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL T+E + +F Q+G++VD +M+D T RSRGFGF+T+ V+ S
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 78 RPHNIDGRVVETKRA 92
+ G+ VE KRA
Sbjct: 61 GMLELGGKQVEVKRA 75
Score = 59.7 bits (145), Expect = 1e-12
Identities = 26/71 (36%), Positives = 44/71 (61%), Gaps = 1/71 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGL D E++ +EYFSQFG + ++ + +TG RGF F+ F+ V+++ +
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 168 KITLLLDRRVE 178
+ L ++VE
Sbjct: 61 GMLELGGKQVE 71
>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 = 77.6 bits (191), Expect = 2e-19
Identities = 32/74 (43%), Positives = 52/74 (70%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+GGL + TT + L+ +F ++GE+VD + DP+T RSRGFGF+ + +A V+ + +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 79 PHNIDGRVVETKRA 92
H +DGRV++ KRA
Sbjct: 61 EHKLDGRVIDPKRA 74
Score = 49.5 bits (118), Expect = 9e-09
Identities = 26/60 (43%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
MFVGGL D + DL+EYFS+FG + + + TG RGF F+ F D V+K++ K
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
>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 = 77.4 bits (190), Expect = 3e-19
Identities = 34/75 (45%), Positives = 54/75 (72%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 RPHNIDGRVVETKRA 92
H +D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 46.5 bits (110), Expect = 2e-07
Identities = 25/58 (43%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 109 KMFVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
KMF+GGL Q ++ LREYF QFG ++ ++ + T RGF F+ F D VDK++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>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 = 76.9 bits (189), Expect = 4e-19
Identities = 35/62 (56%), Positives = 49/62 (79%), Gaps = 1/62 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
KK+FVGG+K D EE LR+YF Q+G IE + ++T++ +G KRGFAF+ F+D+D VDKIV+
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60
Query: 167 SK 168
K
Sbjct: 61 QK 62
Score = 52.3 bits (125), Expect = 9e-10
Identities = 24/77 (31%), Positives = 47/77 (61%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F+T+ + VD +
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60
Query: 77 NRPHNIDGRVVETKRAV 93
+ H ++G E ++A+
Sbjct: 61 QKYHTVNGHNCEVRKAL 77
>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 = 75.9 bits (186), Expect = 9e-19
Identities = 33/62 (53%), Positives = 50/62 (80%), Gaps = 1/62 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
KK+FVGG+K D EE LR+YF ++G I+++ ++T++++G KRGF F+ F+D+D VDKIVL
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60
Query: 167 SK 168
K
Sbjct: 61 QK 62
Score = 52.8 bits (126), Expect = 6e-10
Identities = 25/79 (31%), Positives = 49/79 (62%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+K+F+GG+ T + L+ +FE++G+I + ++ D + + RGFGF+T+ + VD +
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60
Query: 77 NRPHNIDGRVVETKRAVPR 95
+ H I+G E ++A+ R
Sbjct: 61 QKYHTINGHNAEVRKALSR 79
>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 = 75.9 bits (186), Expect = 9e-19
Identities = 33/75 (44%), Positives = 55/75 (73%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL ++T+ +SL+ +F ++GEI + +VM+DP TKRSRGFGF+T+++ VD ++
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 78 RPHNIDGRVVETKRA 92
H +D + ++ K A
Sbjct: 61 PHHELDSKTIDPKVA 75
Score = 49.3 bits (117), Expect = 1e-08
Identities = 26/58 (44%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 109 KMFVGGLKDQEE-DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
KMF+GGL Q D LR+YFS+FG I ++ + T RGF F+ F D VDK++
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 75.3 bits (186), Expect = 1e-18
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+G L TT+E L+ F ++G++ V +++D T +S+GF F+ + + + A+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 78 -RPHNIDGRVVE 88
+DGR ++
Sbjct: 61 LNGKELDGRPLK 72
Score = 65.3 bits (160), Expect = 8e-15
Identities = 28/58 (48%), Positives = 40/58 (68%), Gaps = 1/58 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+FVG L D E++LRE FS+FG +ESV +V +KETG +GFAF+EF + +K +
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58
>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 = 75.4 bits (185), Expect = 1e-18
Identities = 34/74 (45%), Positives = 53/74 (71%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+FIGGL + TT + L+ +F ++GE+VD + DPIT RSRGFGF+ + E++ VD M +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 79 PHNIDGRVVETKRA 92
H ++G+V++ KRA
Sbjct: 61 EHKLNGKVIDPKRA 74
Score = 47.7 bits (113), Expect = 5e-08
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
MF+GGL D + DL++YFS+FG + + + TG RGF F+ F + + VDK++ K
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in
eukaryotic RNA-binding protein RBM24, RBM38 and similar
proteins. This subfamily corresponds to the RRM of
RBM24 and RBM38 from vertebrate, SUPpressor family
member SUP-12 from Caenorhabditis elegans and similar
proteins. Both, RBM24 and RBM38, are preferentially
expressed in cardiac and skeletal muscle tissues. They
regulate myogenic differentiation by controlling the
cell cycle in a p21-dependent or -independent manner.
RBM24, also termed RNA-binding region-containing
protein 6, interacts with the 3'-untranslated region
(UTR) of myogenin mRNA and regulates its stability in
C2C12 cells. RBM38, also termed CLL-associated antigen
KW-5, or HSRNASEB, or RNA-binding region-containing
protein 1(RNPC1), or ssDNA-binding protein SEB4, is a
direct target of the p53 family. It is required for
maintaining the stability of the basal and
stress-induced p21 mRNA by binding to their 3'-UTRs. It
also binds the AU-/U-rich elements in p63 3'-UTR and
regulates p63 mRNA stability and activity. SUP-12 is a
novel tissue-specific splicing factor that controls
muscle-specific splicing of the ADF/cofilin pre-mRNA in
C. elegans. All family members contain a conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 75.3 bits (186), Expect = 1e-18
Identities = 32/76 (42%), Positives = 48/76 (63%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+F+GGL Y TTD+SL+ +F Q+GEI + VV+ D T +SRG+GF+T+ + + + A
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 77 NRPHNIDGRVVETKRA 92
+ IDGR A
Sbjct: 61 DPNPIIDGRKANVNLA 76
Score = 57.6 bits (140), Expect = 7e-12
Identities = 25/53 (47%), Positives = 36/53 (67%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+FVGGL +D LR+YFSQFG IE ++T+++TG RG+ F+ F D +
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKE 53
>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 = 75.3 bits (185), Expect = 1e-18
Identities = 33/71 (46%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGLK E DL E+FSQFG +E ++ +K+TG KRGF F+ F ++D DK +
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 168 KITLLLDRRVE 178
K + RVE
Sbjct: 61 KFHPINGHRVE 71
Score = 56.8 bits (137), Expect = 2e-11
Identities = 29/80 (36%), Positives = 43/80 (53%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL + L F Q+G + V+ D T + RGFGF+ + D A
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 78 RPHNIDGRVVETKRAVPRDE 97
+ H I+G VE K+AVP++E
Sbjct: 61 KFHPINGHRVEVKKAVPKEE 80
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 74.6 bits (184), Expect = 3e-18
Identities = 30/76 (39%), Positives = 52/76 (68%), Gaps = 1/76 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+ GL RTT++ L+A F ++G + +V++MKDP T SRGFGF+T+ + D A+ +
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62
Query: 78 -RPHNIDGRVVETKRA 92
++GRV++ ++A
Sbjct: 63 LNGKELEGRVIKVEKA 78
Score = 52.6 bits (127), Expect = 6e-10
Identities = 21/50 (42%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K+FV GL E +L FS+FG +E V ++ + ETG RGF F+ F
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFES 52
>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 = 73.1 bits (179), Expect = 1e-17
Identities = 30/75 (40%), Positives = 51/75 (68%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL + T+ + L+ +F ++GE+ D + DP T RSRGFGFI + +A V+ +
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 78 RPHNIDGRVVETKRA 92
+ H +DGR+++ K+A
Sbjct: 61 KEHRLDGRLIDPKKA 75
Score = 51.5 bits (123), Expect = 2e-09
Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
KMFVGGL D + DL++YF++FG + + + TG RGF FI F D V+K++
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 168 K 168
K
Sbjct: 61 K 61
>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 = 72.0 bits (177), Expect = 3e-17
Identities = 27/73 (36%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNI 82
GL ++TT++ L+ +F +GE++ V V KDP T +S+GFGF+ +++ + +S R H I
Sbjct: 6 GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQR-HMI 64
Query: 83 DGRVVETKRAVPR 95
DGR + K +
Sbjct: 65 DGRWCDVKIPNSK 77
Score = 48.9 bits (117), Expect = 2e-08
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRR 176
E DL++YFS FG + V + + +TG +GF F+ F DY+ K VLS+ ++ R
Sbjct: 10 KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVK-VLSQRHMIDGRW 68
Query: 177 VE 178
+
Sbjct: 69 CD 70
>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 = 71.6 bits (175), Expect = 4e-17
Identities = 30/75 (40%), Positives = 51/75 (68%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL + T+ + L + ++GE++D + DP+T RSRGFGF+ + +A VD +
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 78 RPHNIDGRVVETKRA 92
+ H +DG++++ KRA
Sbjct: 61 KEHKLDGKLIDPKRA 75
Score = 49.2 bits (117), Expect = 1e-08
Identities = 26/58 (44%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
KMF+GGL D + DL EY S+FG + + T+ TG RGF F+ F D VDK++
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVL 58
>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 = 71.2 bits (174), Expect = 6e-17
Identities = 33/62 (53%), Positives = 50/62 (80%), Gaps = 1/62 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
KK+FVGG+K D EE LR+YF ++G IE++ ++ ++++G KRGFAF+ F+D+D VDKIV+
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 167 SK 168
K
Sbjct: 61 QK 62
Score = 57.3 bits (138), Expect = 2e-11
Identities = 26/79 (32%), Positives = 49/79 (62%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+K+F+GG+ T + L+ +FE++G+I + VM+D + + RGF F+T+ + VD +
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 77 NRPHNIDGRVVETKRAVPR 95
+ H I+G E K+A+ +
Sbjct: 61 QKYHTINGHNCEVKKALSK 79
>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 = 70.3 bits (172), Expect = 1e-16
Identities = 33/76 (43%), Positives = 51/76 (67%), Gaps = 1/76 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-S 76
K+FIGGL + T ++SL+ F ++G+I +VVV+KD T+RSRGFGF+T+ DAM +
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 77 NRPHNIDGRVVETKRA 92
++DGR + +A
Sbjct: 62 MNGKSVDGRQIRVDQA 77
Score = 49.1 bits (117), Expect = 1e-08
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+F+GGL D E L + FS++G I V +V ++ET RGF F+ F + D
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPD 53
>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 = 69.7 bits (171), Expect = 2e-16
Identities = 28/75 (37%), Positives = 46/75 (61%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL TT+E ++ +F ++G IV++ + D T + RGF FIT+ + V +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 78 RPHNIDGRVVETKRA 92
+ H I G+ VE K+A
Sbjct: 61 QFHVIGGKKVEVKKA 75
Score = 65.9 bits (161), Expect = 6e-15
Identities = 27/71 (38%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGL + E+ +REYF +FG I + + +K+T +RGF FI F+ + V KI+ +
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 168 KITLLLDRRVE 178
+ ++ ++VE
Sbjct: 61 QFHVIGGKKVE 71
>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 = 69.4 bits (170), Expect = 2e-16
Identities = 28/74 (37%), Positives = 47/74 (63%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL TT++ ++ +F Q+G++ D ++M D T R RGFGF+T+ +VD
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 78 RPHNIDGRVVETKR 91
H I+ ++VE K+
Sbjct: 61 HFHEINNKMVECKK 74
Score = 58.2 bits (141), Expect = 6e-12
Identities = 30/71 (42%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGL + EDD+++YFSQFG +E ++ +K+T RGF F+ F DVVDK+
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 168 KITLLLDRRVE 178
+ ++ VE
Sbjct: 61 HFHEINNKMVE 71
>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 = 66.1 bits (162), Expect = 6e-15
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+++G L Y T+E L+ F Q+GE+ V+ D T RSRGFGF+ A+ + A+
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 78 -RPHNIDGRVVETKRAVP 94
+ GR + A P
Sbjct: 61 LNGTDFGGRTLTVNEARP 78
Score = 60.7 bits (148), Expect = 6e-13
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++VG L + E+DL++ F QFG + S ++T++ETG RGF F+E + + +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAI 58
>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 = 70.7 bits (173), Expect = 9e-15
Identities = 49/163 (30%), Positives = 79/163 (48%), Gaps = 10/163 (6%)
Query: 4 RYDDSKCTEPE-SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
R TE E R VF+ L + + L FF + G++ DV +KD ++RS+G +
Sbjct: 76 RNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAY 135
Query: 63 ITYSEAKMVDDAMS-------NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL 115
+ + + + V A++ RP + E RA + +P K++VG L
Sbjct: 136 VEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAA-KAATHQPGDIPNFLKLYVGNL 194
Query: 116 K-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ E +LR+ F FG IE V + + ETG +GF FI+F+D
Sbjct: 195 HFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHD 237
Score = 56.1 bits (135), Expect = 1e-09
Identities = 22/52 (42%), Positives = 36/52 (69%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEA 68
K+++G L + T++ L+ FE +G+I DV + +DP T RS+GFGFI + +A
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDA 238
Score = 41.8 bits (98), Expect = 9e-05
Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 3/105 (2%)
Query: 76 SNRPHNIDGRVVETKRAVPRDEIGKPEANAT--VKKMFVGGLKDQ-EEDDLREYFSQFGT 132
+ R +P A + +FV L + E DL E+FS+ G
Sbjct: 56 NRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGK 115
Query: 133 IESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
+ V + ++ + +G A++EF D + V K + +LL R +
Sbjct: 116 VRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPI 160
>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 = 68.7 bits (168), Expect = 5e-14
Identities = 44/155 (28%), Positives = 70/155 (45%), Gaps = 20/155 (12%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+++ LD ++ L+ F ++GEI VMKD + RSRGF F+ + + + A+
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239
Query: 79 -----PHNIDGRVVETKRAVPRDE-----IGKPE-------ANATVKKMFVGGLKDQ-EE 120
+G+ + RA R E K E A ++V L D +
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+ LRE FS+ G I S ++ + E G RGF F+ F
Sbjct: 300 EKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCF 333
Score = 63.7 bits (155), Expect = 2e-12
Identities = 44/161 (27%), Positives = 72/161 (44%), Gaps = 16/161 (9%)
Query: 15 SLRK-----VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAK 69
SLR+ +F+ LD +++L F ++G I+ V D +SRG+GF+ + + +
Sbjct: 82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEE 140
Query: 70 MVDDAMSNRPHNIDG-RVVETKRAVPR-DEIGKPEANAT---VKKMFVGGLKDQEEDDLR 124
A+ + + V R + + + P T VK + ED LR
Sbjct: 141 SAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNL----DPSVNEDKLR 196
Query: 125 EYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
E F++FG I S V +G RGFAF+ F ++ K V
Sbjct: 197 ELFAKFGEITSA-AVMKDGSGRSRGFAFVNFEKHEDAAKAV 236
Score = 57.9 bits (140), Expect = 3e-10
Identities = 38/151 (25%), Positives = 73/151 (48%), Gaps = 11/151 (7%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
+++G LD T+ L F+ +G ++ V V +D +T+RS G+G++ + +A+ + M
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 76 SNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIE 134
+ + + G+ + + RD + + FV L K + L + FS+FG I
Sbjct: 63 NFKR--LGGKPIRIMWSQ-RDPSLRRSGVGNI---FVKNLDKSVDNKALFDTFSKFGNIL 116
Query: 135 SVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
S + T+ E G RG+ F+ F + +
Sbjct: 117 SCKVATD-ENGKSRGYGFVHFEKEESAKAAI 146
Score = 49.4 bits (118), Expect = 2e-07
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++ LD TDE L+ F + GEI VM D SRGFGF+ +S + + A++
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVT 344
>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 = 62.0 bits (150), Expect = 2e-13
Identities = 29/76 (38%), Positives = 48/76 (63%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+K+F+GGL T E ++ +FEQ+G++ D ++M D T R RGFGF+T+ +V+
Sbjct: 4 KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63
Query: 77 NRPHNIDGRVVETKRA 92
H I+ ++VE K+A
Sbjct: 64 IHFHEINNKMVECKKA 79
Score = 48.5 bits (115), Expect = 2e-08
Identities = 25/58 (43%), Positives = 39/58 (67%), Gaps = 1/58 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 164
KK+FVGGL + +D+++YF QFG +E ++ +K T RGF F+ F + DVV+K+
Sbjct: 4 KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61
>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 = 61.5 bits (150), Expect = 3e-13
Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+G L TT+E L+ F ++G I + +++D T RS+GF F+ + + + + A+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 79 P-HNIDGRVVE 88
+ GR +
Sbjct: 60 NGKELGGRELR 70
Score = 60.3 bits (147), Expect = 8e-13
Identities = 27/56 (48%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
FVG L D E+DL++ FS+FG IES+ +V + ETG +GFAF+EF D + +K +
Sbjct: 2 FVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKAL 56
>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 = 61.6 bits (149), Expect = 3e-13
Identities = 29/74 (39%), Positives = 47/74 (63%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL TT E ++ +FEQ+G++ D ++M D T R RGFGF+T+ +V+
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 78 RPHNIDGRVVETKR 91
H I+ ++VE K+
Sbjct: 61 HFHEINNKMVECKK 74
Score = 48.1 bits (114), Expect = 4e-08
Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 164
K+FVGGL + +D+++YF QFG ++ ++ +K T RGF F+ F D+V+K+
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 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 = 60.3 bits (147), Expect = 1e-12
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 23 GLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYSE----AKMVDDAMS 76
GLD TT+E + I DV +++D +T SRGF F+ + + +D +
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68
Query: 77 NRPHNIDGRVV 87
P IDGRVV
Sbjct: 69 LDPFVIDGRVV 79
Score = 41.4 bits (98), Expect = 1e-05
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 120 EDDLREYFSQFG--TIESVNMVTNKETGAKRGFAFIEFND 157
E+D+ + S I+ V ++ +K TG RGFAF+EF
Sbjct: 16 EEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPS 55
>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 = 59.6 bits (145), Expect = 1e-12
Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+G L TT+E L+ F ++GEI V +++D +S+GF F+ + + + A+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59
Query: 79 PH-NIDGRVVE 88
+DGR ++
Sbjct: 60 NGKELDGRKLK 70
Score = 54.6 bits (132), Expect = 1e-10
Identities = 28/56 (50%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
FVG L D E+DLRE FS+FG IESV +V +K G +GFAF+EF + +K +
Sbjct: 2 FVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKAL 56
>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 = 58.8 bits (143), Expect = 4e-12
Identities = 22/59 (37%), Positives = 37/59 (62%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++IGGL Y T+ + F Q+GEIVD+ +++D T +S+GF F+ Y + + A+ N
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDN 70
Score = 51.9 bits (125), Expect = 2e-09
Identities = 20/48 (41%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++GGL + E D+ FSQ+G I +N+V +K+TG +GFAF+ + D
Sbjct: 13 YIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYED 60
>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 = 58.0 bits (141), Expect = 5e-12
Identities = 21/58 (36%), Positives = 37/58 (63%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++G L + T++ L+ FE +GEI V + +DP T RS+G+GFI +++A+ A+
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59
Score = 46.5 bits (111), Expect = 1e-07
Identities = 19/38 (50%), Positives = 24/38 (63%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
EDDLR F FG IE V + + ETG +G+ FI+F D
Sbjct: 12 EDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFAD 49
>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 = 57.8 bits (140), Expect = 8e-12
Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 5/73 (6%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDDA 74
+F+G L + DE L+A FE++G +V V+ D T RSRGFG++ + +AK +A
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 75 MSNRPHNIDGRVV 87
M + +DGR +
Sbjct: 61 MDGK--ELDGRPI 71
Score = 43.1 bits (102), Expect = 2e-06
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 109 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
+FVG L +D+ L+ F +FGT+ ++T++ETG RGF +++F + K + +
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 168 KITLLLDRR 176
LD R
Sbjct: 61 MDGKELDGR 69
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 59.3 bits (143), Expect = 9e-12
Identities = 30/75 (40%), Positives = 45/75 (60%), Gaps = 8/75 (10%)
Query: 15 SLR----KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
SLR K+FIGGL + T D SL+ F +G++VD V+ D T RSRGFGF+ +++
Sbjct: 29 SLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFND--- 85
Query: 71 VDDAMSNRPHNIDGR 85
+ A + +DG+
Sbjct: 86 -EGAATAAISEMDGK 99
Score = 49.7 bits (118), Expect = 4e-08
Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 109 KMFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+F+GGL +D LR+ F+ FG + ++ ++ETG RGF F+ FND
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEG 87
>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 = 57.7 bits (139), Expect = 1e-11
Identities = 28/79 (35%), Positives = 47/79 (59%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+ ++K+F+GGL+ T+E ++ +F ++GEI + + DP T + RGF FIT+ E V
Sbjct: 2 DPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKK 61
Query: 74 AMSNRPHNIDGRVVETKRA 92
+ + HN+ G E K A
Sbjct: 62 VLEKKFHNVSGSKCEIKVA 80
Score = 54.6 bits (131), Expect = 1e-10
Identities = 28/63 (44%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 107 VKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
VKK+FVGGL + E+ +REYF +FG IE++ + + +T +RGF FI F + D V K++
Sbjct: 4 VKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVL 63
Query: 166 LSK 168
K
Sbjct: 64 EKK 66
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 61.5 bits (148), Expect = 1e-11
Identities = 35/165 (21%), Positives = 71/165 (43%), Gaps = 20/165 (12%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E +F+G L Y T+E L+ F+++G + V +++D T +SRGF F+ + +
Sbjct: 111 SKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESA 170
Query: 72 DDAMSNRPH-NIDGRVVETKRAVPRDE------------------IGKPEANATVKKMFV 112
+ A+ ++GR + ++A P + GK ++V
Sbjct: 171 EKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYV 230
Query: 113 GGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
G L + E++L + F G I ++ +K+ + +F+
Sbjct: 231 GNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNE 275
Score = 53.8 bits (128), Expect = 5e-09
Identities = 31/101 (30%), Positives = 46/101 (45%), Gaps = 7/101 (6%)
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKK------MFVGGL-KDQEEDDLR 124
++ DG TK + K +FVG L D E+DLR
Sbjct: 74 EENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLR 133
Query: 125 EYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
E F +FG ++ V +V ++ETG RGFAF+EF + +K +
Sbjct: 134 ELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAI 174
>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 = 56.9 bits (138), Expect = 1e-11
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
RKVF+G L T+E L+ +F Q+GE+ DV + K R F F+T+++ ++
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCG 55
Query: 77 NRPHNIDGRVVETKRA 92
H I G V A
Sbjct: 56 -EDHIIKGVSVHVSNA 70
Score = 45.0 bits (107), Expect = 5e-07
Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 6/58 (10%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 164
+K+FVG L +D E+DLR+YFSQFG + V + R FAF+ F D +V +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSL 53
>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 = 56.5 bits (137), Expect = 2e-11
Identities = 25/66 (37%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 21 IGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRP- 79
+ L YRTT + L+ FE++GE+ DV + +D T+ SRGF F+ + + + +DAM
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 80 HNIDGR 85
+DGR
Sbjct: 63 KELDGR 68
Score = 36.9 bits (86), Expect = 5e-04
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
DDLR F ++G + V + ++ T RGFAF+ F D
Sbjct: 12 PDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYD 49
>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 = 56.8 bits (138), Expect = 2e-11
Identities = 22/46 (47%), Positives = 33/46 (71%), Gaps = 1/46 (2%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
E +LR+YFSQFGT+ + + +K+TG +G+AF+EF + V KIV
Sbjct: 13 EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEF-ESPEVAKIV 57
Score = 41.0 bits (97), Expect = 1e-05
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE---AKMVDDAM 75
V+IG L + + L+ +F Q+G + + + + T +S+G+ F+ + AK+V + M
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 76 SN 77
+N
Sbjct: 62 NN 63
>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 = 56.2 bits (136), Expect = 3e-11
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDDAM 75
+F+G L E+L+A F +GEI D V+KD T +S+G+GF+++ +A+ +M
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 76 SNRPHNIDGRVVET 89
+ + + GR + T
Sbjct: 62 NGQ--WLGGRAIRT 73
Score = 38.9 bits (91), Expect = 8e-05
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 110 MFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+FVG L + + LR F+ FG I +V + +TG +G+ F+ F
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSF 48
>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 = 55.8 bits (135), Expect = 4e-11
Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+ L + TT+E L+ FE +GEI +V + D TKRS+GF F+++ + A S
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 78 RPHNI-DGRVV 87
+I GR++
Sbjct: 61 LDGSIFQGRLL 71
Score = 46.9 bits (112), Expect = 8e-08
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
E++LRE F FG I V++ +KET +GFAF+ F
Sbjct: 13 EEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSF 48
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 55.6 bits (135), Expect = 5e-11
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-SN 77
+++ L T+E L+ FF +G++ V ++++ R RGF F+ ++ + + A+
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58
Query: 78 RPHNIDGRVVE 88
+DGR +
Sbjct: 59 NGLVLDGRTLR 69
Score = 42.9 bits (102), Expect = 3e-06
Identities = 22/54 (40%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 111 FVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+V L E+DLRE+FS +G +E V +V NK+ RGFAF+EF + +
Sbjct: 2 YVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEA 53
>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 = 55.6 bits (135), Expect = 5e-11
Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 1/48 (2%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
K+FVG L K E+D+R F ++G IE V ++ +K+TG +G AF++F
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKF 48
Score = 53.7 bits (130), Expect = 2e-10
Identities = 19/60 (31%), Positives = 36/60 (60%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+G L T+E ++A FE++G I +V +++D T +S+G F+ +S + A+
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
>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 = 55.3 bits (134), Expect = 6e-11
Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
FVG + D E+ L E FS+ G + S +VT+++TG +G+ F EF D +
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIE 51
Score = 49.2 bits (118), Expect = 1e-08
Identities = 17/59 (28%), Positives = 31/59 (52%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
VF+G + Y T+E L F + G +V ++ D T + +G+GF + + + A+ N
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN 59
>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 = 54.9 bits (133), Expect = 8e-11
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+++GGL ++ L A F +G+I D+ + D T++ RGF F+ + E + A+ N
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59
Score = 49.1 bits (118), Expect = 1e-08
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++VGGL ++ +E L F FG I+ + + + ET RGFAF+EF +
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEE 49
>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 = 53.9 bits (129), Expect = 2e-10
Identities = 24/61 (39%), Positives = 40/61 (65%), Gaps = 1/61 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGL D E+ ++EYF FG IE++ + + +T +RGF F+ + D + V K++ S
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 168 K 168
+
Sbjct: 61 R 61
Score = 53.5 bits (128), Expect = 4e-10
Identities = 28/75 (37%), Positives = 43/75 (57%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
KVF+GGL TT+E ++ +F +GEI ++ + D T RGF F+TY++ + V + +
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 78 RPHNIDGRVVETKRA 92
R H I E K A
Sbjct: 61 RYHQIGSGKCEIKVA 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 = 53.5 bits (128), Expect = 4e-10
Identities = 27/61 (44%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGL D E+ +REYF FG +ES+ + + +T +RGF FI F + + V KI+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 168 K 168
K
Sbjct: 61 K 61
Score = 48.5 bits (115), Expect = 2e-08
Identities = 26/75 (34%), Positives = 41/75 (54%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL T +E ++ +F +GE+ + + D T + RGF FIT+ E + V M
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 78 RPHNIDGRVVETKRA 92
+ HN+ E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia
(DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE.
This subfamily corresponds to the RRM domain of two
Deleted in AZoospermia (DAZ) autosomal homologs, DAZL
(DAZ-like) and BOULE. BOULE is the founder member of
the family and DAZL arose from BOULE in an ancestor of
vertebrates. The DAZ gene subsequently originated from
a duplication transposition of the DAZL gene.
Invertebrates contain a single DAZ homolog, BOULE,
while vertebrates, other than catarrhine primates,
possess both BOULE and DAZL genes. The catarrhine
primates possess BOULE, DAZL, and DAZ genes. The family
members encode closely related RNA-binding proteins
that are required for fertility in numerous organisms.
These proteins contain an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a varying number of
copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 53.0 bits (128), Expect = 5e-10
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+GG+ TT+E L+ FF ++G + DV ++ D S+G+GF+T+ + + ++
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGV-SKGYGFVTFETQEDAEKILAM 62
Query: 78 RPHNIDGRVVETKRAV 93
N G+ + A+
Sbjct: 63 GNLNFRGKKLNIGPAI 78
Score = 49.6 bits (119), Expect = 1e-08
Identities = 20/70 (28%), Positives = 44/70 (62%), Gaps = 2/70 (2%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
++FVGG+ D E++LR++FS+FG+++ V ++T++ G +G+ F+ F + +KI+
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAM 62
Query: 168 KITLLLDRRV 177
+++
Sbjct: 63 GNLNFRGKKL 72
>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 82
Score = 53.0 bits (128), Expect = 5e-10
Identities = 18/47 (38%), Positives = 29/47 (61%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
D E++L+E FSQFG ++ +V +K TG +G AF++F + K
Sbjct: 11 DATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQK 57
Score = 51.1 bits (123), Expect = 3e-09
Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 6/82 (7%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD--A 74
R VFI L + T+E L+ F Q+GE+ ++KD +T S+G F+ + +
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 75 MSNRPHN----IDGRVVETKRA 92
++ + +DGR + A
Sbjct: 61 AADNAEDSGLSLDGRRLIVTLA 82
>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 = 57.0 bits (137), Expect = 5e-10
Identities = 35/165 (21%), Positives = 74/165 (44%), Gaps = 23/165 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
+V++G + + +++++ F+ +G I + + DP T + +GF F+ Y A++ +
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 75 MS-----------NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDD 122
M+ RP N+ +A P ++ + EA +++V + D E D
Sbjct: 169 MNGQMLGGRNIKVGRPSNM-------PQAQPIIDMVQEEAKK-FNRIYVASVHPDLSETD 220
Query: 123 LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
++ F FG I + +G+ FIE+N+ + + S
Sbjct: 221 IKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS 265
Score = 47.8 bits (113), Expect = 8e-07
Identities = 19/98 (19%), Positives = 51/98 (52%), Gaps = 2/98 (2%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E + ++++ + ++ +++ FE +GEIV + + P + +G+GFI Y+ +
Sbjct: 200 EAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQ 259
Query: 72 DDAMSN-RPHNIDGRVVETKRAV-PRDEIGKPEANATV 107
+A+++ ++ G+ + + V P D + +P + +
Sbjct: 260 SEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAI 297
Score = 43.5 bits (102), Expect = 2e-05
Identities = 21/55 (38%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 102 EANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+A A + +++VG + + ED +R F FG I+S+NM + TG +GFAF+E+
Sbjct: 102 QALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEY 156
>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 = 53.0 bits (128), Expect = 6e-10
Identities = 22/49 (44%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
K +FV L D E LR F ++G I+ + +V +K+TG RG+AFIEF
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEF 50
Score = 49.6 bits (119), Expect = 1e-08
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+ +F+ L+Y TT+ L+ FE++G I + +++D T + RG+ FI + + + A
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61
Query: 77 NRPHNIDGRVVETKRAV 93
DG+ ++ +R +
Sbjct: 62 ----YADGKKIDGRRVL 74
>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 = 52.2 bits (126), Expect = 9e-10
Identities = 23/56 (41%), Positives = 36/56 (64%), Gaps = 3/56 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
+F+ L Y TTDE L+ FF + G I V+KD +K+ RGFG++T++ + +DA
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFA---LEEDA 54
Score = 37.6 bits (88), Expect = 3e-04
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
FV L D ++ L E+FS+ G I+ +V +K + RGF ++ F
Sbjct: 3 FVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF 48
>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 = 52.2 bits (126), Expect = 9e-10
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDDAM 75
V++ L DE L+ F ++G+I VMKD K S+GFGF+ + A+ + +
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGK-SKGFGFVNFENHEAAQKAVEEL 62
Query: 76 SNRPHNIDGRVVETKRA 92
+ + ++G+ + RA
Sbjct: 63 NGK--EVNGKKLYVGRA 77
Score = 35.6 bits (83), Expect = 0.002
Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
D +++ L+E F ++G I S ++ + + G +GF F+ F +++ K V
Sbjct: 12 DMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAV 59
>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 = 55.7 bits (134), Expect = 1e-09
Identities = 36/140 (25%), Positives = 74/140 (52%), Gaps = 10/140 (7%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNIDGRVVE 88
T E +++ F GEI +++D +T +S G+GF+ Y + + A++ +++G ++
Sbjct: 16 TQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN----SLNGLRLQ 71
Query: 89 TKRAVPRDEIGKPEANATVK--KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETG 145
K + +P ++ ++K ++V GL K + +L FS FG I + ++++ TG
Sbjct: 72 NKTI--KVSYARP-SSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTG 128
Query: 146 AKRGFAFIEFNDYDVVDKIV 165
+G FI F+ D D+ +
Sbjct: 129 LSKGVGFIRFDKRDEADRAI 148
Score = 43.4 bits (102), Expect = 2e-05
Identities = 18/73 (24%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFIT---YSEAKMVDDAM 75
+F+ L T + L F +G + +V +++D T + +G+GF++ Y EA M ++
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 76 SNRPHNIDGRVVE 88
+ + + RV++
Sbjct: 332 NG--YTLGNRVLQ 342
Score = 38.0 bits (88), Expect = 0.001
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FV L D +E L + F FG +++V ++ + T +G+ F+ +YD
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYD 322
Score = 37.2 bits (86), Expect = 0.002
Identities = 16/57 (28%), Positives = 31/57 (54%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL T L++ F +G+I+ ++ D +T S+G GFI + + D A+
Sbjct: 92 LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAI 148
>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 = 51.9 bits (125), Expect = 1e-09
Identities = 19/57 (33%), Positives = 34/57 (59%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+F+G +DY TT E LQ F+ G I + ++ D T + +GF +I + + V++A+
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL 58
Score = 46.5 bits (111), Expect = 1e-07
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
FVG + ++L+E+F GTI + ++ +K TG +GFA+IEF D V+
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVEN 56
>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 = 51.8 bits (125), Expect = 2e-09
Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 162
K+F+GGL ED ++E FG +++ N+V + TG +G+AF E+ D V D
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTD 56
Score = 39.1 bits (92), Expect = 8e-05
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
K+FIGGL +++ ++ E +G++ ++KD T S+G+ F Y + + D A
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQA 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 = 51.8 bits (124), Expect = 2e-09
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
+F+ L + T E L FF I VV+ DP T SRG+GF+T++ M++DA
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFA---MLEDA 54
Score = 40.6 bits (95), Expect = 3e-05
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
++DL ++FS I+ +VT+ ETG RG+ F+ F +
Sbjct: 10 SVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLE 52
>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 = 51.2 bits (123), Expect = 3e-09
Identities = 27/60 (45%), Positives = 36/60 (60%), Gaps = 5/60 (8%)
Query: 109 KMFVGGL-KDQEEDD----LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+FV G EDD L E+FS G I V++ T++ETGA +GFA+IEF D V+K
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60
Score = 30.1 bits (68), Expect = 0.17
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 18 KVFIGGLDYRTTDE----SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+F+ G D ++ SL F GEI V + D T S+GF +I + V+
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60
Query: 74 AM 75
A+
Sbjct: 61 AL 62
>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 = 50.4 bits (121), Expect = 5e-09
Identities = 25/69 (36%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
+FVG L D +DL +F G SV ++T+K+TG +G AF+EF+ + + K +
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 169 ITLLLDRRV 177
TLL R++
Sbjct: 63 HTLLKGRKI 71
Score = 48.9 bits (117), Expect = 2e-08
Identities = 21/67 (31%), Positives = 34/67 (50%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+G L Y TT E L A F+ G V ++ D T +S+G F+ + A+ + A+
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 79 PHNIDGR 85
+ GR
Sbjct: 63 HTLLKGR 69
>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 = 50.4 bits (121), Expect = 5e-09
Identities = 24/54 (44%), Positives = 35/54 (64%), Gaps = 5/54 (9%)
Query: 109 KMFVGGLK---DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+FVG L +E L+EYFSQFG ++S N+ +KETG +G+ F+ F+ D
Sbjct: 1 KLFVGNLPWTVGSKE--LKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRD 52
Score = 43.8 bits (104), Expect = 1e-06
Identities = 19/70 (27%), Positives = 41/70 (58%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+G L + + L+ +F Q+G++ V D T S+G+GF+++S +++A+
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 78 RPHNIDGRVV 87
+ H ++G +
Sbjct: 61 QKHILEGNKL 70
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the RRM
of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). This family
also includes yeast eIF3-p33, a homolog of vertebrate
eIF-3G, plays an important role in the initiation phase
of protein synthesis in yeast. It binds both, mRNA and
rRNA, fragments due to an RRM near its C-terminus. .
Length = 77
Score = 50.2 bits (121), Expect = 5e-09
Identities = 22/41 (53%), Positives = 27/41 (65%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
D +EDDLRE F FG I V + +KETG RGFAF+ F+
Sbjct: 10 DADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHT 50
Score = 43.7 bits (104), Expect = 2e-06
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 28 TTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
++ L+ F +G I V + KD T +SRGF F+T+
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFH 49
>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 = 50.1 bits (120), Expect = 5e-09
Identities = 21/48 (43%), Positives = 33/48 (68%)
Query: 109 KMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
++FV K E+DLRE F +FG IE V++V +K TG +GF +++F+
Sbjct: 3 RLFVVIPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFH 50
Score = 39.7 bits (93), Expect = 5e-05
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
T+E L+ F+++G+I V ++KD T S+GFG++ + + A+ N
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALEN 61
>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 = 49.6 bits (119), Expect = 1e-08
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +F+G LD R T+E L F Q G + V + KDP + + F F+T+ V A+
Sbjct: 2 RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQ 60
Score = 38.5 bits (90), Expect = 1e-04
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 162
+FVG L + E+ L E F Q G +E V + + G + FAF+ F V
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVP 56
>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 = 49.1 bits (118), Expect = 1e-08
Identities = 14/41 (34%), Positives = 27/41 (65%)
Query: 119 EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+D L+E FS +GT++ V++ ++E RG+A++EF +
Sbjct: 11 NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPE 51
Score = 39.1 bits (92), Expect = 8e-05
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+ +G L + L+ F +G + DV + D RG+ ++ + + + A+ +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 79 PH-NIDGRVV 87
IDG+ V
Sbjct: 61 DGGQIDGQEV 70
>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 = 49.2 bits (118), Expect = 1e-08
Identities = 18/75 (24%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSR---GFGFITYSEAKMVDD 73
R++++ LD++ ++ L+ F ++GE+ + + K K+ R GF F+T+ +A ++
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60
Query: 74 AMSNRPHNIDGRVVE 88
A+ + GR +
Sbjct: 61 ALQLNGTELGGRKIS 75
Score = 43.4 bits (103), Expect = 2e-06
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKR---GFAFIEFNDYDVVDKIVLSKITLLLDRR 176
EDDLR FS+FG +ES+ + ++ R GFAF+ F D + + T L R+
Sbjct: 14 EDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQLNGTELGGRK 73
Query: 177 VE 178
+
Sbjct: 74 IS 75
>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 = 49.5 bits (118), Expect = 2e-08
Identities = 25/103 (24%), Positives = 44/103 (42%), Gaps = 24/103 (23%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+ L Y T+ESL F ++G + + + D T R++G GF+ + + + + N
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63
Query: 79 P------------------------HNIDGRVVETKRAVPRDE 97
P + ++GRV+ AV RDE
Sbjct: 64 PAAGSTSLLSGSSLTADIGDDVMPEYVLEGRVLSVTPAVVRDE 106
Score = 34.1 bits (78), Expect = 0.010
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
D E+ L +FS+FG++ V +K TG +G F+ F D
Sbjct: 12 DATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKD 52
>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 = 48.7 bits (117), Expect = 2e-08
Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKI 169
FVG L D EE++LR++F G +E+V +V +++TG +GF ++ F D V +
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62
Query: 170 TLLLDRRV 177
L R++
Sbjct: 63 IKLKGRKI 70
Score = 48.7 bits (117), Expect = 2e-08
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
VF+G L + +E L+ FE G++ V +++D T +GFG++ + V A+
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK 59
>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 = 48.1 bits (115), Expect = 3e-08
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 111 FVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 160
+VGG+ ED++R YFS G IE ++++T +TG RG AFI F +
Sbjct: 2 YVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEA 52
Score = 38.1 bits (89), Expect = 2e-04
Identities = 18/47 (38%), Positives = 32/47 (68%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
V++GG+ Y +T++ ++++F GEI ++ +M P T R RG FIT+
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITF 47
>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 = 48.2 bits (115), Expect = 3e-08
Identities = 25/68 (36%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKI 169
++G L D EDD+RE+F I SV + T+KETG +GF ++F D + +D +
Sbjct: 3 YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLDG 61
Query: 170 TLLLDRRV 177
T+L R +
Sbjct: 62 TVLCGRPI 69
Score = 32.4 bits (74), Expect = 0.020
Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
V+IG L + T++ ++ FF+ EI V + D T +GFG + +++ + +D A+
Sbjct: 2 VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL 57
>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 = 48.5 bits (116), Expect = 3e-08
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 109 KMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++F+ K EDDLRE F+ FG I+ + +V +K+T +G A+++F
Sbjct: 5 RLFIVCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKF 51
Score = 39.2 bits (92), Expect = 8e-05
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 28 TTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNIDGRVV 87
T++ L+ F +GEI D+ V+KD TK S+G ++ +++A AM ++G+ +
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM----EEMNGKCL 69
Query: 88 E 88
Sbjct: 70 G 70
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 77
Score = 48.1 bits (115), Expect = 4e-08
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+G L + + L+ FF++ GE+VDV + +D RS+GFG + ++ + A+
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEKS 60
Query: 79 PHNIDGRVVETKRAVPR 95
+ GR + A R
Sbjct: 61 GEELLGREIRVDLATER 77
Score = 40.8 bits (96), Expect = 2e-05
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
+FVG L E+DDL E+F + G + V + + + G +GF +EF + K +
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60
Query: 169 ITLLLDRRV 177
LL R +
Sbjct: 61 GEELLGREI 69
>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 = 47.6 bits (114), Expect = 5e-08
Identities = 14/59 (23%), Positives = 34/59 (57%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++++ + +++ +++ FE +G+I + DP T + +G+GFI Y + DA++
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Score = 41.9 bits (99), Expect = 8e-06
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
EDD++ F FG I+S ++ + ETG +G+ FIE+
Sbjct: 14 EDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYE 50
>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 = 47.8 bits (114), Expect = 5e-08
Identities = 18/48 (37%), Positives = 31/48 (64%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
++FI L Y T+E L+ F ++G + +V + D +TK+ +GF F+TY
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
Score = 40.1 bits (94), Expect = 3e-05
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
E+DL + FS++G + V++ +K T +GFAF+ +
Sbjct: 16 EEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
>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 = 47.5 bits (113), Expect = 5e-08
Identities = 19/52 (36%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 160
+++G L E +L++YFSQFGT+++V + +K+TG + + FI+F + +V
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEV 53
Score = 40.9 bits (96), Expect = 2e-05
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE---AKMVDDAM 75
++IG L + ++ L+ +F Q+G + +V V + T S+ +GFI + A + +M
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 76 SNRPHNIDGRVVETK 90
+N + + G+V++
Sbjct: 62 NN--YLLMGKVLQVH 74
>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 = 48.0 bits (115), Expect = 5e-08
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND-------YD 159
+FVG L E+ LRE FS++G I + +V + TG +G+AF+E+ Y
Sbjct: 4 LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63
Query: 160 VVDKIVLSKITLLLDRRVE 178
K+V+ + +D E
Sbjct: 64 DAHKLVIDGSEIFVDFERE 82
Score = 44.9 bits (107), Expect = 8e-07
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 7/68 (10%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D T +F+G L +TT+E+L+ F ++G+I + +++D +T S+G+ F+ Y
Sbjct: 1 DPYLT-------LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYE 53
Query: 67 EAKMVDDA 74
+ A
Sbjct: 54 HERDALRA 61
>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 = 47.6 bits (114), Expect = 6e-08
Identities = 22/46 (47%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
FVGGL E DL E FS+FGT+ V ++ K+ G RGFA+I+
Sbjct: 3 FVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDL 48
Score = 32.1 bits (74), Expect = 0.026
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFIT 64
+F+GGL T+ L+ F ++G + DV ++K RGF +I
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYID 47
>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 = 47.2 bits (113), Expect = 7e-08
Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 5/56 (8%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
VF GL TT+ L+ F ++G I V V+ D T RSRGFGF+ + V+DA
Sbjct: 4 VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES---VEDA 54
Score = 46.1 bits (110), Expect = 2e-07
Identities = 19/39 (48%), Positives = 26/39 (66%)
Query: 119 EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
E DLRE FS++G IE V +V +++TG RGF F+ F
Sbjct: 12 TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES 50
>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 = 47.0 bits (112), Expect = 8e-08
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
+F+G L + ++S+ F ++GEI V + DP + R +GFG++ +S A+ DA+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 76 SNRPHNIDGRVV 87
++ GR V
Sbjct: 61 GGT--DLLGRPV 70
Score = 42.4 bits (100), Expect = 5e-06
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+FVG L D +ED + E F ++G I SV + T+ ++G +GF ++EF+ + +
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 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 = 47.0 bits (112), Expect = 1e-07
Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
K+FV GL +++L + F + G ++SV +VTN+ +G +G A++E+ + + VL
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVL 61
Score = 34.7 bits (80), Expect = 0.003
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRS---RGFGFITY------SEA 68
K+F+ GL + T E L+ F++ G + V + +T RS +G ++ Y S+A
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRL----VTNRSGKPKGLAYVEYENESSASQA 59
Query: 69 KMVDDAMSNRPHNI 82
+ D + I
Sbjct: 60 VLKMDGTEIKEKTI 73
>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 = 46.1 bits (110), Expect = 2e-07
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
VF+GGLD T++ L++ F +GEIV V K P K G GF+ + + A+
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYV---KIPPGK---GCGFVQFVHRAAAEAAIQ 55
Score = 35.0 bits (81), Expect = 0.002
Identities = 17/34 (50%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 104 NATVKKMFVGGL-KDQEEDDLREYFSQFGTIESV 136
N TV FVGGL ED+LR F FG I V
Sbjct: 1 NTTV---FVGGLDPAVTEDELRSLFGPFGEIVYV 31
>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 = 46.1 bits (110), Expect = 2e-07
Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
VF+ LDY ++ L+ F + GEI DV ++K+ +S+G+ ++ + + V +A+
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEALKLD 60
Query: 79 PHNIDGR 85
I GR
Sbjct: 61 RELIKGR 67
Score = 40.7 bits (96), Expect = 2e-05
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 7/56 (12%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDR 175
ED+LR+ FS+ G I V +V N + G +G+A++EF + + V + L LDR
Sbjct: 13 EDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQE------ALKLDR 61
>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 = 46.1 bits (110), Expect = 2e-07
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 7/47 (14%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++VGGL ++ E DLR++F QFG I S+ +V ++ AF+ F
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTF 44
Score = 31.1 bits (71), Expect = 0.055
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
++GGL R T++ L+ F Q+GEI + V+ + F+T+
Sbjct: 5 YVGGLGERVTEKDLRDHFYQFGEIRSITVVP------RQQCAFVTF 44
>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 = 46.1 bits (110), Expect = 2e-07
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 11/72 (15%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
V++G L + T+E LQ F +G I +V V KD +G+ F+ + A A+
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56
Query: 76 SNRPHNIDGRVV 87
+ I+G+ V
Sbjct: 57 NGTS--INGQTV 66
Score = 36.4 bits (85), Expect = 7e-04
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 10/52 (19%)
Query: 105 ATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
TV +VG L E++L+ FS FG IE V + +K G+AF+ F
Sbjct: 1 TTV---YVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRF 43
>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 = 46.2 bits (110), Expect = 2e-07
Identities = 19/53 (35%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
++FV L +EDDL + FS+FG + V++ +K++G +GFA++ F D +
Sbjct: 3 GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPE 55
Score = 44.3 bits (105), Expect = 9e-07
Identities = 13/52 (25%), Positives = 31/52 (59%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAK 69
++F+ L Y ++ L+ F ++GE+ +V V D + +S+GF ++ + + +
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPE 55
>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 = 46.1 bits (110), Expect = 2e-07
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+FI L TD+ L F +G ++ V D T +S+ FGF++Y + A+
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIK-- 58
Query: 79 PHNIDGRVVETKR 91
++G V KR
Sbjct: 59 --AMNGFQVGGKR 69
Score = 38.0 bits (89), Expect = 2e-04
Identities = 11/41 (26%), Positives = 22/41 (53%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
+ + DL + F+ FG + S + +K TG + F F+ ++
Sbjct: 8 NEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYD 48
>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 = 49.2 bits (117), Expect = 2e-07
Identities = 42/131 (32%), Positives = 58/131 (44%), Gaps = 10/131 (7%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRP-HNIDGRVV 87
TD L A F G I +M+D T S G+ F+ + +A S R N++G V
Sbjct: 120 TDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGS-----EADSQRAIKNLNGITV 174
Query: 88 ETKR-AVPRDEIGKPEANATVKKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETG 145
KR V G T ++V L DD L F ++G I N++ +K TG
Sbjct: 175 RNKRLKVSYARPGGESIKDT--NLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTG 232
Query: 146 AKRGFAFIEFN 156
RG AF+ FN
Sbjct: 233 TPRGVAFVRFN 243
Score = 40.8 bits (95), Expect = 2e-04
Identities = 17/65 (26%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 14 ESLR--KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
ES++ +++ L TD+ L F ++G+IV +++D +T RG F+ +++ +
Sbjct: 189 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEA 248
Query: 72 DDAMS 76
+A+S
Sbjct: 249 QEAIS 253
>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 = 46.1 bits (110), Expect = 3e-07
Identities = 16/39 (41%), Positives = 25/39 (64%)
Query: 119 EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++DL FS+FG I+S ++ +K+TG +AFIEF
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFET 54
Score = 39.9 bits (94), Expect = 4e-05
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA---MS 76
F+ L+ TTDE L+ F ++G+I V++D T S + FI + + ++A M
Sbjct: 7 FVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMD 66
Query: 77 N 77
N
Sbjct: 67 N 67
>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 = 45.8 bits (109), Expect = 3e-07
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
V++ L + T+ L F ++G++V V ++KD T++S+G FI +
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILF 50
Score = 34.6 bits (80), Expect = 0.004
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+DL + FS++G + V +V +KET +G AFI F D +
Sbjct: 15 NNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDRE 54
>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 = 45.7 bits (109), Expect = 3e-07
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVV-VMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+FIG LD ++ L F +G I+ +M+DP T S+GF FI+Y + D A+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Score = 43.4 bits (103), Expect = 2e-06
Identities = 18/56 (32%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTI-ESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+F+G L + +E L + FS FG I ++ ++ + +TG +GFAFI ++ ++ D
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDA 59
>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 = 45.5 bits (108), Expect = 3e-07
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
+FVG L + ED+LR +F + G I V M+T +++G +GFAF++F + + + K
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60
Query: 169 ITLLLDRRVE 178
RVE
Sbjct: 61 HLNGRALRVE 70
Score = 43.6 bits (103), Expect = 2e-06
Identities = 20/70 (28%), Positives = 37/70 (52%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+G L + TT++ L+A F + G I V +M + + +GF F+ + E + +A+ +
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60
Query: 79 PHNIDGRVVE 88
N VE
Sbjct: 61 HLNGRALRVE 70
>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 = 45.6 bits (108), Expect = 3e-07
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+F+G L TD +L A F + D VM D + RSRG+GF+++ + ++A++
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAIN 59
Score = 34.4 bits (79), Expect = 0.004
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 110 MFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FVG L + D L FS F + ++ + ++G RG+ F+ F
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQ 52
>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 = 48.7 bits (116), Expect = 4e-07
Identities = 36/176 (20%), Positives = 70/176 (39%), Gaps = 30/176 (17%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIV------DVVVMKDPITKRSRGFGFITYSEAKM 70
R++++GG+ +E++ FF D + + + F F+ + +
Sbjct: 176 RRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEE 235
Query: 71 VDDAMS-------------NRPHN------IDGRVVETKRAVPRDEIGKPEANATV---- 107
AM+ RPH+ I V + + K + TV
Sbjct: 236 ATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSK 295
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 162
++++G L ED ++E FG +++ N++ + TG +G+AF E+ D V D
Sbjct: 296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTD 351
Score = 38.7 bits (90), Expect = 9e-04
Identities = 16/66 (24%), Positives = 35/66 (53%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
T +S +++IG L ++ ++ E +G++ ++KD T S+G+ F Y + +
Sbjct: 290 TVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSV 349
Query: 71 VDDAMS 76
D A++
Sbjct: 350 TDVAIA 355
>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 = 45.5 bits (108), Expect = 4e-07
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+G L + T++ L+ FF+++G +++V + R FGF+ + + + V ++N
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64
Query: 78 RPHNIDGRV---VETKR 91
+P G VE K+
Sbjct: 65 KPIYFRGDHRLNVEEKK 81
Score = 43.5 bits (103), Expect = 2e-06
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
++FVG L D ED+L+E+F +FG + V + + G F F+ F+D + V KI+ +
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64
Query: 168 KITLLLD 174
K
Sbjct: 65 KPIYFRG 71
>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 = 44.9 bits (107), Expect = 5e-07
Identities = 15/57 (26%), Positives = 33/57 (57%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
VF+ L + + L FF + G++ DV +++D ++RS+G ++ + + + V A+
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58
Score = 38.4 bits (90), Expect = 1e-04
Identities = 14/43 (32%), Positives = 26/43 (60%)
Query: 119 EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 161
E DL E+FS+ G + V ++ ++ + +G A++EF D + V
Sbjct: 12 RERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54
>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 = 44.5 bits (106), Expect = 7e-07
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++ + L T++ L+ FE GE+ DV VM+ +SR FGF+ + + A+
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVK 59
Score = 32.6 bits (75), Expect = 0.016
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
ED LRE+F G + V ++ ++ G R F F+ F
Sbjct: 14 EDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGF 48
>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 = 44.6 bits (106), Expect = 8e-07
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
D +++LR F G IES +V ++ TG G+ F+++ D
Sbjct: 11 DMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVD 51
Score = 43.1 bits (102), Expect = 3e-06
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 27 RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNIDGRV 86
T E L++ FE G I +++D IT +S G+GF+ Y + A++ ++G
Sbjct: 11 DMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN----TLNGFE 66
Query: 87 VETKR 91
+ KR
Sbjct: 67 IRNKR 71
>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 = 44.1 bits (105), Expect = 1e-06
Identities = 18/35 (51%), Positives = 24/35 (68%), Gaps = 1/35 (2%)
Query: 122 DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
+LRE FS FG ++SV + K G+ RGFAF+EF
Sbjct: 16 ELRELFSPFGQVKSVRL-PKKFDGSHRGFAFVEFV 49
Score = 30.7 bits (70), Expect = 0.091
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
K+ + + + T + L+ F +G++ V + K RGF F+ + + +AM
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQEAQNAME 59
>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 = 43.8 bits (104), Expect = 1e-06
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 11/84 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
KV++G L R T L+ FE++G + V V ++P GF F+ + + + +DA+
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAV-- 53
Query: 78 RPHNIDGRVVETKRAVPRDEIGKP 101
+DGR + R R E+ +
Sbjct: 54 --RALDGRRICGNRV--RVELSRG 73
Score = 39.1 bits (92), Expect = 7e-05
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
K++VG L + +L + F ++G + SV + N GFAF+EF D + V
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDAV 53
>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 = 44.0 bits (104), Expect = 1e-06
Identities = 18/48 (37%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+++VG + + ED +R+ FS FG I+S++M + T +GFAF+E+
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEY 49
Score = 34.3 bits (79), Expect = 0.004
Identities = 12/48 (25%), Positives = 29/48 (60%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+V++G + + +++++ F +G I + + DP+T + +GF F+ Y
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEY 49
>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 = 43.7 bits (103), Expect = 2e-06
Identities = 19/58 (32%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
K+F+G L+ + T++ ++ F +G + D+ +M+D + K+SRG F+ YS +M A+
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEMAQAAI 57
Score = 35.6 bits (82), Expect = 0.002
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+FVG L Q E ++ E FS +G +E + M+ + E RG AF++++ +
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKE 51
>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 = 43.7 bits (103), Expect = 2e-06
Identities = 22/63 (34%), Positives = 42/63 (66%), Gaps = 2/63 (3%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
+FVGG+ +E ++R +F+++G+++ V ++T++ TG +G+ F+ F D V KIV S+
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66
Query: 169 ITL 171
I
Sbjct: 67 INF 69
Score = 39.4 bits (92), Expect = 6e-05
Identities = 16/49 (32%), Positives = 34/49 (69%), Gaps = 1/49 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++ +
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYD 55
>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 = 43.7 bits (103), Expect = 2e-06
Identities = 17/57 (29%), Positives = 31/57 (54%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
VF+G L + +E L F + G I V +++DP T +GF ++ + + V+ A+
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL 58
Score = 42.9 bits (101), Expect = 3e-06
Identities = 21/58 (36%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
+FVG L + E+ L F + G IE V +V + +T +GFA+++F D + V+K +L
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALL 59
>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 = 43.0 bits (102), Expect = 2e-06
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
E DL++ FS FG + V + G K+GFAF++F
Sbjct: 13 EADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQF 47
Score = 42.2 bits (100), Expect = 5e-06
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++ + L ++ T+ L+ F +G + +V + + P + +GF F+ ++ + A+
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKG 59
Query: 78 -RPHNIDGRVV 87
I GR V
Sbjct: 60 VNGKKIKGRPV 70
>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 = 43.5 bits (103), Expect = 2e-06
Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
K+F+G + ++ L+ FEQ+G+I ++ V+KD T +G F+TY
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 54
Score = 42.8 bits (101), Expect = 5e-06
Identities = 20/52 (38%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+FVG + ++ EE DLR F QFG I + ++ +K TG +G AF+ + +
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARE 58
>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 = 43.2 bits (102), Expect = 2e-06
Identities = 22/49 (44%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+K+FVG L K Q EDD+R F FGTIE ++ + G +G AF++F
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKF 49
Score = 37.0 bits (86), Expect = 5e-04
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
RK+F+G L + T++ ++ FE +G I + +++ P S+G F+ +S EA+ +
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGP-DGNSKGCAFVKFSSHAEAQAAIN 60
Query: 74 AM 75
A+
Sbjct: 61 AL 62
>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 = 42.6 bits (101), Expect = 4e-06
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVV-----MKDPITKRSRGFGFITYSEAKMVDD 73
+F+ L+++TT+E+L+ FE+ G + V + K P S G+GF+ + +
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 74 AMSNRPHN-IDGRVVETKR 91
A+ +DG +E K
Sbjct: 63 ALKRLQGTVLDGHALELKL 81
Score = 32.6 bits (75), Expect = 0.023
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKR-----GFAFIEFNDYDVVDK 163
E+ L+++F + G + SV + K+ G+ F+EF + K
Sbjct: 14 EETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
>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 = 42.6 bits (101), Expect = 4e-06
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAK 69
PE+ ++F+G L TDE L F ++ V++D T +S+G+GF+++S+
Sbjct: 3 PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN 59
Score = 34.1 bits (79), Expect = 0.006
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++FVG L + ++ L FS++ + + +V +K TG +G+ F+ F+D
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSD 57
>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 = 42.7 bits (101), Expect = 4e-06
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+++ + T + L+ F ++G IVDV + D T+R RGF ++ + + + +DA+
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 79 PH-NIDGRVVE 88
GR +E
Sbjct: 63 DRTRFLGREIE 73
Score = 34.7 bits (80), Expect = 0.004
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY-DVVDKIVLSKITLLLDRRVE 178
DDLR F ++G I V + + T RGFA+++F D D D + T L R +E
Sbjct: 15 DDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIE 73
>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 = 42.5 bits (100), Expect = 5e-06
Identities = 21/58 (36%), Positives = 38/58 (65%), Gaps = 2/58 (3%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++FVGG+ E+DLR++FSQ+GT++ V +V ++ G +G+ F+ F + KI+
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKIL 60
Score = 42.1 bits (99), Expect = 7e-06
Identities = 17/48 (35%), Positives = 34/48 (70%), Gaps = 1/48 (2%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
++F+GG+D++T + L+ FF Q+G + +V ++ D S+G+GF+T+
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTF 50
>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 = 42.5 bits (100), Expect = 5e-06
Identities = 18/58 (31%), Positives = 33/58 (56%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
V++G +DY T E L+A F G + V ++ D + +GF +I +S+ + V A++
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALA 59
Score = 39.0 bits (91), Expect = 7e-05
Identities = 16/58 (27%), Positives = 34/58 (58%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRVE 178
++L +F G++ V ++ +K +G +GFA+IEF+D + V + +L R+++
Sbjct: 14 EELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALDESLFRGRQIK 71
>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 = 42.3 bits (100), Expect = 6e-06
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+ VG L + ++ RE S FG +E +V ++ TG +G+ F+E+
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEY 48
Score = 34.2 bits (79), Expect = 0.005
Identities = 12/47 (25%), Positives = 22/47 (46%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
+G L TDE + +G + ++ T S+G+GF+ Y+
Sbjct: 3 CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYA 49
>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 = 42.3 bits (100), Expect = 6e-06
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+F+G L T E L F + G+I++V ++K + F FI + + A+
Sbjct: 4 YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVE 61
Query: 77 NRPHNI 82
+ H++
Sbjct: 62 SENHSM 67
Score = 38.9 bits (91), Expect = 1e-04
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
FVG L D +++L E FS+ G I VN++ K FAFI+F
Sbjct: 7 FVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFER 52
>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 = 42.3 bits (99), Expect = 6e-06
Identities = 17/58 (29%), Positives = 33/58 (56%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
K+F+G + T++ ++ FE+ G +++V ++KD T +G F+ YS D A+
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
Score = 37.6 bits (87), Expect = 3e-04
Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
K+FVG + + E ++R F + G + V ++ +K TG ++G F++++ D D+ +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
>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 = 42.5 bits (100), Expect = 6e-06
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETG--AKRGFAFIEF 155
KMFVG + + E DLRE F Q+G + +N++ ++ +G F+ F
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52
Score = 36.7 bits (85), Expect = 7e-04
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 18 KVFIGGLDYRTTDES-LQAFFEQWGEIVDVVVMKDPIT--KRSRGFGFITYSEAKMVDDA 74
K+F+G + R+ E L+ FEQ+G + + V++D +S+G F+T+ K +A
Sbjct: 3 KMFVGQIP-RSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 61
Query: 75 MSNRPHNI 82
N HN+
Sbjct: 62 -QNALHNM 68
>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 = 42.3 bits (99), Expect = 6e-06
Identities = 20/40 (50%), Positives = 27/40 (67%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
E DLRE FS++G + VN+V ++ TG RGFAF+ F D
Sbjct: 13 ERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERID 52
Score = 36.1 bits (83), Expect = 0.001
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN-RPHN 81
GL TT+ L+ F ++G + V V+ D T RSRGF F+ + +AM +
Sbjct: 6 GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGME 65
Query: 82 IDGRVVETKRAVPR 95
+DGR + ++ +
Sbjct: 66 LDGRRIRVDYSITK 79
>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 = 41.8 bits (99), Expect = 7e-06
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
V++G LD + T+E L F Q G +V+V + KD +T+ +G+GF+ +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEF 47
Score = 38.3 bits (90), Expect = 2e-04
Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 111 FVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDYDV 160
+VG L ++ E+ L E F Q G + +V++ ++ T A +G+ F+EF ++ D
Sbjct: 2 YVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDA 53
>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 = 41.7 bits (98), Expect = 9e-06
Identities = 17/49 (34%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+FVG + + E+ L++ FS+ G + S +V ++ETG +G+ F E+ D
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKD 49
Score = 40.2 bits (94), Expect = 3e-05
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN- 77
VF+G + Y T+E L+ F + G +V ++ D T + +G+GF Y + + AM N
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 78 RPHNIDGR 85
+ ++GR
Sbjct: 61 NGYELNGR 68
>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 = 41.5 bits (97), Expect = 1e-05
Identities = 17/58 (29%), Positives = 33/58 (56%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++ GL T + L+ F Q+G I+ +++D +T SRG GFI + + ++A+
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Score = 38.4 bits (89), Expect = 1e-04
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
++V GL K + +L + FSQ+G I + ++ ++ TG RG FI F+
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFD 50
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRP 79
++ LD DE L+ F +G I VM D RS+GFGF+ +S + A++
Sbjct: 5 YVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVT--- 60
Query: 80 HNIDGRVVETK 90
++GR++ K
Sbjct: 61 -EMNGRIIGGK 70
Score = 39.1 bits (92), Expect = 8e-05
Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 109 KMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++V L D +D+ LRE FS FGTI S ++T+ E G +GF F+ F
Sbjct: 3 NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCF 49
>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 = 41.6 bits (97), Expect = 1e-05
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+G L T E +++ F +G+I D V+KD T +S+G+GF+++
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 50
Score = 37.8 bits (87), Expect = 3e-04
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDYDVVDKIV 165
+FVG L + +D++ F+ FG I +V + TG +G+ F+ F N D + IV
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 14/62 (22%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 21 IGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI---TYSEAKMVDDAMSN 77
+G L+ + + + F + GE+ V ++++ T +S G+GF+ T+ A+ +++
Sbjct: 4 MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63
Query: 78 RP 79
+P
Sbjct: 64 KP 65
Score = 39.2 bits (92), Expect = 7e-05
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 112 VGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 164
+G L +E + F++ G + SV ++ NK+TG G+ F+EF ++ ++
Sbjct: 4 MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQA 57
>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 = 41.2 bits (96), Expect = 1e-05
Identities = 18/47 (38%), Positives = 30/47 (63%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
VF+G L T + ++A F +G I D V+KD T +S+G+GF+++
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50
Score = 34.7 bits (79), Expect = 0.004
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIE-FNDYDVVDKI 164
+FVG L + DD++ F+ FG I +V + TG +G+ F+ FN +D + I
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60
>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 = 40.6 bits (95), Expect = 2e-05
Identities = 16/63 (25%), Positives = 36/63 (57%), Gaps = 8/63 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+G L T++ +++ FEQ+G++++ ++K+ +GF+ + D+A+ N
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRN 53
Query: 78 RPH 80
H
Sbjct: 54 LHH 56
Score = 29.5 bits (66), Expect = 0.23
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 9/58 (15%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
K+FVG L + E ++R F Q+G + +++ N + F+ +D D+ +
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAI 51
>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 = 41.0 bits (96), Expect = 2e-05
Identities = 20/70 (28%), Positives = 39/70 (55%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
V++G +DY +T E L+A F G I V ++ D + +G+ +I ++ V+ A++
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61
Query: 79 PHNIDGRVVE 88
+ GRV++
Sbjct: 62 ESSFRGRVIK 71
Score = 37.9 bits (88), Expect = 2e-04
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++L +FS G I V ++ +K +G +G+A+IEF D V+ V
Sbjct: 14 EELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAV 58
>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 = 40.9 bits (96), Expect = 2e-05
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+D++R FS G IES ++ +K TG G+ F+ + D + +K +
Sbjct: 15 QDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60
Score = 35.1 bits (81), Expect = 0.002
Identities = 13/48 (27%), Positives = 29/48 (60%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
T + +++ F GEI +++D +T +S G+GF+ Y + + + A++
Sbjct: 14 TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61
>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 = 40.7 bits (96), Expect = 2e-05
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 19 VFIGGLDYRTTDESLQAFFEQ-WGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-- 75
+F+G L TD LQ F + + V+ DP+T RS+G+GF+ + + D A+
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Query: 76 ------SNRPHNI 82
S+RP +
Sbjct: 64 MNGVYCSSRPMRV 76
Score = 30.7 bits (70), Expect = 0.079
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 110 MFVGGLK-DQEEDDLREYFSQ-FGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FVG L D + L+E F + ++ +V + TG +G+ F+ F D D
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDED 55
>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 = 40.7 bits (95), Expect = 2e-05
Identities = 18/58 (31%), Positives = 35/58 (60%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+VF+G + ++ L FE+ G I D+ +M DP++ ++RG+ FIT+ + +A+
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60
Score = 33.4 bits (76), Expect = 0.011
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++FVG + +D ED+L F + G I + ++ + +G RG+AFI F + + V
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60
>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 = 40.2 bits (94), Expect = 3e-05
Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+K+FVG L K E+D+R F+ FG+IE V + G RG AF+ F
Sbjct: 2 RKLFVGMLSKKCNENDVRIMFAPFGSIEECT-VLRDQNGQSRGCAFVTF 49
Score = 36.3 bits (84), Expect = 0.001
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
RK+F+G L + + ++ F +G I + V++D +SRG F+T++
Sbjct: 2 RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFA 50
>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 = 40.4 bits (95), Expect = 3e-05
Identities = 17/40 (42%), Positives = 26/40 (65%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
K+ + L+ FS++GT+ V++ K TG +GFAFIEF
Sbjct: 9 KNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEF 48
Score = 31.9 bits (73), Expect = 0.032
Identities = 16/56 (28%), Positives = 27/56 (48%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
V++ L T E L+A F ++G +V V + + T +GF FI + + A
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57
>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 = 39.7 bits (93), Expect = 4e-05
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++ + + +R D L+ F Q+G I+DV ++ + + S+GFGF+T++ + D A
Sbjct: 1 KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN--ERGSKGFGFVTFANSADADRARE 58
Query: 77 N-RPHNIDGRVVETKRA 92
++GR +E A
Sbjct: 59 KLHGTVVEGRKIEVNNA 75
Score = 37.0 bits (86), Expect = 4e-04
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+ DLR+ F QFG I V ++ N E G+K GF F+ F + D+
Sbjct: 14 DPDLRQMFGQFGPILDVEIIFN-ERGSK-GFGFVTFANSADADR 55
>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 = 39.6 bits (93), Expect = 4e-05
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFIT---YSEAKM 70
+F+ L + L F +G + +V V++D T + +G+GF+T Y EA
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYS 58
Score = 37.7 bits (88), Expect = 3e-04
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FV L D +E L + FS FG + +V ++ + T +G+ F+ +Y+
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE 54
>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 = 4e-05
Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+ + T E L+ F ++G IVDV V D T+R RGF +I + + + +DA+ N
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 79 PHN-IDGRVVETKRA 92
+ GR +E + A
Sbjct: 63 NRKWVCGRQIEIQFA 77
Score = 29.2 bits (65), Expect = 0.39
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 110 MFVGGLKDQEE-DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+FV + D +DLR F ++G I V + + T RGFA+I+F D
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFED 51
>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 = 39.5 bits (93), Expect = 5e-05
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+G L TT E L+A FE++G + + V+K+ +GF+ E + +DA+
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKA 52
Query: 78 -RPHNIDGRVV 87
+ G+ +
Sbjct: 53 LNGYEFMGKRI 63
Score = 27.6 bits (62), Expect = 0.77
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTN 141
K+FVG L D ++LR F ++GT+ ++V N
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN 34
>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 = 39.8 bits (94), Expect = 5e-05
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
++G L T+ L F G ++ + V +D IT+RS G+ ++ +
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNF 48
Score = 36.0 bits (84), Expect = 0.001
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 9/53 (16%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESV----NMVTNKETGAKRGFAFIEFNDY 158
+VG L D E L E FS G + S+ +++T + G+A++ F +
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRS----LGYAYVNFQNP 51
>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 = 39.0 bits (91), Expect = 7e-05
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMK 50
K+F+G +D T+ E L+A FE +G ++ VM+
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMR 34
>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 = 39.2 bits (91), Expect = 8e-05
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
++FVG L D +E +L+E+F FG + + + T G F F+ F+D + V +I+ +
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILGA 66
Query: 168 K 168
K
Sbjct: 67 K 67
Score = 31.9 bits (72), Expect = 0.033
Identities = 22/91 (24%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 4 RYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
RY DS ++F+G L + + L+ FF +G +V++ + + + FGF+
Sbjct: 1 RYPDS--------HQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFV 52
Query: 64 TYSEAKMVDDAMSNRPHNIDGRV---VETKR 91
+ +++ V + +P G V VE K+
Sbjct: 53 VFDDSEPVQRILGAKPIMFRGEVRLNVEEKK 83
>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 = 39.0 bits (92), Expect = 9e-05
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 31 ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
SL A F Q+G ++D+V K T + RG F+ + +
Sbjct: 18 RSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKD 51
Score = 31.3 bits (72), Expect = 0.043
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
KD+ + L FSQFG + + +T RG AF+ F D
Sbjct: 13 KDELKRSLYALFSQFGPVLDIVA---SKTLKMRGQAFVVFKD 51
>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 = 38.8 bits (90), Expect = 9e-05
Identities = 17/58 (29%), Positives = 34/58 (58%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++F+G + ++ L FE+ G I D+ +M DP+T +RG+ F+T+ + +A+
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60
Score = 32.7 bits (74), Expect = 0.018
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++FVG + +D ED+L F + G I + ++ + TG RG+AF+ F
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTF 50
>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 = 39.2 bits (91), Expect = 9e-05
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 9/79 (11%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+F+ + T E L+ F ++G IVDV V D T+R RGF ++ + + + +DA+
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL--- 59
Query: 79 PHNID-----GRVVETKRA 92
HN+D GR +E + A
Sbjct: 60 -HNLDRKWICGRQIEIQFA 77
Score = 29.9 bits (67), Expect = 0.17
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+FV + D +DLR F ++G I V + + T RGFA+++F D
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFED 51
>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 = 39.2 bits (92), Expect = 1e-04
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 108 KKMFVGGL----KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+ +FV L +D LR+ FSQ G + G RGFAF+E+
Sbjct: 3 RCLFVDRLPKTFRDVSI--LRKLFSQVGKPTFCQLAIA-PNGQPRGFAFVEYATA 54
Score = 28.4 bits (64), Expect = 0.65
Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 17 RKVFIGGL--DYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
R +F+ L +R L+ F Q G+ + P + RGF F+ Y+ A+ ++A
Sbjct: 3 RCLFVDRLPKTFRDVSI-LRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEA 60
Query: 75 MSNRPHNIDGRVVE 88
++G ++
Sbjct: 61 QQ----ALNGHSLQ 70
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 7/66 (10%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRG--FGFITYSEAKMVDDA 74
R +++G + TT L+ F+ +GEI ++ + R G +GF+TY A A
Sbjct: 3 RVIYVGKIPIDTTRSELRQRFQPFGEIEEIT-----LHFRDDGDNYGFVTYRYACDAFRA 57
Query: 75 MSNRPH 80
+ +
Sbjct: 58 IEHGND 63
Score = 28.4 bits (64), Expect = 0.61
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++VG + D +LR+ F FG IE + + ++ G GF +
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEIT-LHFRDDGDNYGFVTYRYAC 52
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
P + VF+GGL T+E ++ FEQ GEI+ I + F I ++E VD
Sbjct: 3 PPGCKTVFVGGLPENATEEIIREVFEQCGEIIA-------IRMSKKNFCHIRFAEEFAVD 55
Query: 73 DAM 75
A+
Sbjct: 56 KAI 58
Score = 36.2 bits (84), Expect = 0.001
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 9/62 (14%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK-IV 165
K +FVGGL ++ E+ +RE F Q G I ++ M +K+ F I F + VDK I
Sbjct: 7 KTVFVGGLPENATEEIIREVFEQCGEIIAIRM-------SKKNFCHIRFAEEFAVDKAIY 59
Query: 166 LS 167
LS
Sbjct: 60 LS 61
>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 = 38.4 bits (90), Expect = 1e-04
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
++V GL K + +L FS +G I + ++ + TG RG FI F+
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRI 53
Score = 37.3 bits (87), Expect = 4e-04
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+++ GL T + L+A F +G I+ ++ D +T SRG GFI +
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF 49
>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 = 38.5 bits (89), Expect = 2e-04
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN-RPHN 81
GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ + +A
Sbjct: 16 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME 75
Query: 82 IDGRVVETKRAVPR 95
+DGR + ++ +
Sbjct: 76 LDGRRIRVDFSITK 89
Score = 37.7 bits (87), Expect = 4e-04
Identities = 17/38 (44%), Positives = 27/38 (71%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
E DLRE FS++G I V++V ++++ RGFAF+ F +
Sbjct: 23 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 15/50 (30%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 111 FVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
FV G+ ++ +E+D+ + F++FG I+++++ ++ TG +G+A IE+
Sbjct: 10 FVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKK 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 = 38.3 bits (89), Expect = 2e-04
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
+ ED+LR+ F +G I N++ +K TG RG AF+ ++
Sbjct: 10 RQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYD 50
Score = 36.8 bits (85), Expect = 7e-04
Identities = 16/58 (27%), Positives = 31/58 (53%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++ L + T++ L+ FE +G IV +++D T RG F+ Y + + A+S
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
>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 = 38.0 bits (89), Expect = 2e-04
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
V+I GL TTDE L+ + +G+I+ + D T + +G+GF+ + +
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEA 54
Score = 36.5 bits (85), Expect = 6e-04
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++DL + FG I S + +K+T +G+ F++F
Sbjct: 14 DEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDF 49
>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 = 37.8 bits (88), Expect = 2e-04
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 7/75 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +FIG L+ TT L+ FE++GEI+D+ + K + + FI Y++ V AM
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQG---GNPAYAFIQYADIASVVKAM- 58
Query: 77 NRPHNIDGRVVETKR 91
+DG + R
Sbjct: 59 ---RKMDGEYLGNNR 70
Score = 32.0 bits (73), Expect = 0.030
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ +F+G L K DLRE F +FG I +++ K+ G +AFI++ D
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYAD 50
>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 = 2e-04
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 10/80 (12%)
Query: 19 VFIGGLDYRTTDESLQA----FFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
VF+ L +D+ L+A F ++G +V V V++D R R + F+ ++ +A
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNA 61
Query: 75 MSNRPHN--IDGRVVETKRA 92
++ + +DGR + +RA
Sbjct: 62 LA-KGQGTILDGRHIRCERA 80
Score = 30.5 bits (69), Expect = 0.14
Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 9/74 (12%)
Query: 110 MFVGGLKDQEEDD-----LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDYDVVDK 163
+FV L + DD + E+FS++GT+ V + ++ +R +AF++F ND D +
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTL--VFVKVLRDW-RQRPYAFVQFTNDDDAKNA 61
Query: 164 IVLSKITLLLDRRV 177
+ + T+L R +
Sbjct: 62 LAKGQGTILDGRHI 75
>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 = 38.0 bits (89), Expect = 2e-04
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVM---KDPITKRSRGFGFITYSEAKMVDDAM 75
+++G L+ + T+E L F ++G + V +M + +R+R GF+ + + A+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 76 SNRPHNIDGRVVE 88
+DG+ V
Sbjct: 64 ----DELDGKDVM 72
>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 = 37.6 bits (88), Expect = 3e-04
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 10/83 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE---AKMVDD 73
R +F+ ++ DE L+A FEQ+G+I + K RGF ++Y + A+
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGDIRTLYT----ACK-HRGFIMVSYYDIRAARRAKR 56
Query: 74 AMSNRPHNIDGRVVETKRAVPRD 96
A+ + GR ++ ++P+D
Sbjct: 57 ALQGTE--LGGRKLDIHFSIPKD 77
Score = 35.3 bits (82), Expect = 0.002
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+FV + E+++LR F QFG I ++ RGF + + D
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDIRTLYTACK-----HRGFIMVSYYD 47
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 40.4 bits (94), Expect = 3e-04
Identities = 40/156 (25%), Positives = 79/156 (50%), Gaps = 26/156 (16%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
+P +VF+G + ++ L FE+ G I ++ +M D + ++RG+ F+T+ EA
Sbjct: 54 QPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEA 112
Query: 69 KMVDDAMSN---RPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLR 124
K ++N RP GR++ +V N ++FVGG+ K+++ +++
Sbjct: 113 KEAVKLLNNYEIRP----GRLLGVCISV---------DNC---RLFVGGIPKNKKREEIL 156
Query: 125 EYFSQF--GTIESVNMVTNKETGAKRGFAFIEFNDY 158
E FS+ G ++ + + + RGFAF+E+ +
Sbjct: 157 EEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESH 192
>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 = 37.4 bits (87), Expect = 3e-04
Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
+ G D++ F G + V M++ + AFI F + + + +
Sbjct: 3 YAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRT----VQPHAFITFENLEAAQLAIET 56
>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 = 37.7 bits (87), Expect = 3e-04
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
RK+FIG + + + ++ F +G+I + +++ P SRG F+T++ M A+
Sbjct: 2 RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 59
Score = 36.6 bits (84), Expect = 7e-04
Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
+K+F+G + K E+D+R FS FG IE ++ + G RG AF+ F
Sbjct: 2 RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTFT 50
>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 = 37.3 bits (87), Expect = 3e-04
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 3/48 (6%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
VGG+ EDDL+E+FS G + V + +++ A+ FAF+EF D
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR--FAFVEFAD 49
Score = 36.2 bits (84), Expect = 0.001
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R + +GG+D +++ L+ FF GE+ V + D S F F+ + D +
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEF-----ADAESA 53
Query: 77 NRPHNIDG 84
N+ G
Sbjct: 54 LSALNLSG 61
>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 = 37.7 bits (88), Expect = 3e-04
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 120 EDDLREYFSQFG-TIESVNMVTNKETGAKRGFAFIEFN 156
E+D+R G + V ++ K TGA RGFAF+EF
Sbjct: 16 EEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFM 53
Score = 27.3 bits (61), Expect = 1.4
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 45 DVVVMKDPITKRSRGFGFITYS 66
DV +M+ T SRGF F+ +
Sbjct: 32 DVRLMRRKTTGASRGFAFVEFM 53
>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 = 37.4 bits (87), Expect = 3e-04
Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+FV G K E+ L +YFS FG + +V M +K+ G +A +EF+ + VDK++
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIM--DKDKGV---YAIVEFDSKEGVDKVL 56
Score = 34.7 bits (80), Expect = 0.003
Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRG-FGFITYSEAKMVDD 73
+ R VF+ G T++E L +F +G +++V++ KD +G + + + + VD
Sbjct: 1 AERSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDK 54
Query: 74 AMSNRPHNIDGRVVETKRA 92
+S H ++G + +
Sbjct: 55 VLSEPQHTLNGHRLRVRPR 73
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 37.0 bits (86), Expect = 4e-04
Identities = 13/50 (26%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEA 68
+F+ LDY+ + L+ F+ G++V + +D +SRG G + +
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHP 49
Score = 30.4 bits (69), Expect = 0.095
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF-NDYDVVDKIVLSKITLLLDRR 176
L+E F G + ++ +KE G RG ++F + + V I + +L DR
Sbjct: 12 WKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRP 68
>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 = 37.3 bits (87), Expect = 4e-04
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEI--VDVVVMKD-PITKRSRGFGFITYSEAKMVDDA 74
+++IG LD R T+ L F ++G+I D + K P+ + RG+ F+T+ + + A
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Score = 33.8 bits (78), Expect = 0.007
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNK---ETGAKRGFAFIEF 155
++++G L E L + FS++G I+ + + +K G RG+ F+ F
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTF 51
>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 = 37.4 bits (86), Expect = 4e-04
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL T + L+ F Q+G I+ ++ D +T SRG GFI + + ++A+
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61
Score = 34.7 bits (79), Expect = 0.004
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
++V GL K + +L + FSQ+G I + ++ ++ TG RG FI F+
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 52
>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 = 37.5 bits (86), Expect = 4e-04
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL T + L+ F Q+G I+ ++ D +T SRG GFI + + ++A+
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64
Score = 34.8 bits (79), Expect = 0.005
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
++V GL K + +L + FSQ+G I + ++ ++ TG RG FI F+
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 55
>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 = 37.3 bits (87), Expect = 4e-04
Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFG-TIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
+++G L+ +E+ ++ F+ G T+ SV ++ NK TG G+ F+EF D ++ +
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60
Score = 30.8 bits (70), Expect = 0.10
Identities = 9/59 (15%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGE-IVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++G L+ + ++ F GE ++ V ++++ +T G+ F+ +++ + +
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLH 60
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 36.9 bits (86), Expect = 4e-04
Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 12/68 (17%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+V+IG L YR + ++ FF+ +G I ++ + GFGF+ + + + DDA+
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAV-- 50
Query: 78 RPHNIDGR 85
+ ++G+
Sbjct: 51 --YELNGK 56
Score = 35.8 bits (83), Expect = 0.001
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 9/51 (17%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
++++G L + E D+ +F +G I +N+ K GF F+EF D
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDP 43
>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 = 37.1 bits (85), Expect = 6e-04
Identities = 18/62 (29%), Positives = 31/62 (50%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
S ++I GL TTD+ L + +G+IV + D T + +G+GF+ + A
Sbjct: 6 SKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKA 65
Query: 75 MS 76
+S
Sbjct: 66 VS 67
Score = 27.9 bits (61), Expect = 1.2
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 110 MFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+++ GL D DL + +G I S + +K T +G+ F++F+ K V
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV 66
>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 = 36.6 bits (85), Expect = 6e-04
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 122 DLREYFSQFGTIESVNMVTN-KETGAKRGFAFIEF 155
+LRE FS FG +++V + TG+ RGF F++F
Sbjct: 16 ELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDF 50
Score = 32.8 bits (75), Expect = 0.019
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRS-RGFGFITYS---EAKMVDD 73
K+ + + + T + L+ F +GE+ V + K S RGFGF+ + +AK
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFK 61
Query: 74 AMSNRPH 80
A+ + H
Sbjct: 62 ALCHSTH 68
>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 = 36.5 bits (84), Expect = 6e-04
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +F+G L+ R +E L F Q G + V + KD K + FGF+ + ++ V A++
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGK-PKSFGFVCFKHSESVPYAIA 60
>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 = 36.6 bits (84), Expect = 6e-04
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+S + + L T E L++ F GEI +++D IT +S G+GF+ Y + K +
Sbjct: 2 DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61
Query: 74 AMSNRPHNIDGRVVETK 90
A++ ++G ++TK
Sbjct: 62 AIN----TLNGLRLQTK 74
Score = 31.6 bits (71), Expect = 0.041
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+++L+ F G IES +V +K TG G+ F+ + D +K +
Sbjct: 18 QEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63
>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 = 36.4 bits (85), Expect = 8e-04
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
E+ + E FS+ G I+ + M ++ T GF F+E+
Sbjct: 12 EEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYT 49
Score = 34.4 bits (80), Expect = 0.004
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN- 77
+++G L + TT+E + F + G+I +++ D TK GF F+ Y + ++A+
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 78 RPHNIDGRVVET 89
+D R++
Sbjct: 61 NGTKLDDRIIRV 72
>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 = 36.6 bits (84), Expect = 9e-04
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++ +++ + F G IES +V +K TG G+ F+ + D + DK +
Sbjct: 13 QNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62
Score = 35.1 bits (80), Expect = 0.003
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+S + + L T E ++ F GEI +++D IT +S G+GF+ Y + D
Sbjct: 1 DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60
Query: 74 AMSNRPHNIDGRVVETK 90
A++ ++G ++TK
Sbjct: 61 AIN----TLNGLKLQTK 73
>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 = 36.1 bits (83), Expect = 0.001
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 7/82 (8%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
P+S ++F+G L + L+ FF+Q+G +V++ + + FGF+ + +++ V
Sbjct: 1 PDS-HQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSG---GKLPNFGFVVFDDSEPVQ 56
Query: 73 DAMSNRPHNIDGRV---VETKR 91
+SNRP G V VE K+
Sbjct: 57 KILSNRPIMFRGDVRLNVEEKK 78
Score = 30.7 bits (69), Expect = 0.095
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++FVG L D ++ +L+E+F Q+G + + + G F F+ F+D + V KI+
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQKIL 59
>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 = 35.8 bits (82), Expect = 0.001
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFIT---YSEAKM 70
+F+ L + L F +G + +V V++D T + +GFGF+T Y EA M
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAM 58
Score = 30.4 bits (68), Expect = 0.11
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FV L + +E L + F FG + +V ++ + T +GF F+ +YD
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYD 54
>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 = 35.7 bits (82), Expect = 0.002
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
++V GL K + ++ + FSQ+G I + ++ ++ TG RG FI F+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFD 51
Score = 34.2 bits (78), Expect = 0.005
Identities = 15/57 (26%), Positives = 32/57 (56%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++ GL + + ++ F Q+G I+ ++ D +T SRG GFI + + ++A+
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60
>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 = 35.6 bits (82), Expect = 0.002
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
K+ + L + T + ++ F +G++ V V K + +RGF F+ +S AK +AM
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKK-FDQSARGFAFVEFSTAKEALNAM 58
Score = 31.3 bits (71), Expect = 0.051
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 122 DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
D+R FS +G ++SV V K + RGFAF+EF
Sbjct: 16 DVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEF 48
>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 = 35.2 bits (81), Expect = 0.002
Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 9/72 (12%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRG--FGFITYSEAKMVDDAMS 76
+++G LD R T++ L+ F+ G + +V ++ D K ++G +GF+ Y ++ + A+
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD---KNNKGVNYGFVEYHQSHDAEIAL- 56
Query: 77 NRPHNIDGRVVE 88
++GR +E
Sbjct: 57 ---QTLNGRQIE 65
Score = 29.0 bits (65), Expect = 0.30
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++VG L ED L++ F G +++V ++ +K + F+E++
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQ 48
>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 = 35.7 bits (82), Expect = 0.002
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 9/76 (11%)
Query: 6 DDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
DD + T R +FIG LD+ ++ L+ F+++G I++ VV+K P + + F+ +
Sbjct: 3 DDQRAT-----RNLFIGNLDHNVSEVELRRAFDKYG-IIEEVVIKRPARGQGGAYAFLKF 56
Query: 66 SEAKMVDD---AMSNR 78
M AMS R
Sbjct: 57 QNLDMAHRAKVAMSGR 72
Score = 29.9 bits (67), Expect = 0.18
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
+ +F+G L E +LR F ++G IE V ++ G +AF++F + D+ + +
Sbjct: 9 RNLFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKFQNLDMAHRAKV 67
Query: 167 SKITLLLDR 175
+ ++ R
Sbjct: 68 AMSGRVIGR 76
>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 = 35.5 bits (81), Expect = 0.002
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++I GL TTD+ L + +G+IV + D T + +G+GF+ + A++
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61
Score = 27.4 bits (60), Expect = 1.3
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 110 MFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+++ GL D DL + +G I S + +K T +G+ F++F+ K V
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60
>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 = 35.4 bits (81), Expect = 0.002
Identities = 17/55 (30%), Positives = 29/55 (52%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
R VF L R L+ FF G++ DV ++ D ++RS+G ++ + E + V
Sbjct: 2 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 56
Score = 32.3 bits (73), Expect = 0.025
Identities = 10/34 (29%), Positives = 22/34 (64%)
Query: 122 DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
DL ++FS G + V +++++ + +G A++EF
Sbjct: 17 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 50
>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 = 34.4 bits (80), Expect = 0.002
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 5/33 (15%)
Query: 123 LREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
L + FS FG +E + ++ K GFAF+EF
Sbjct: 1 LYKLFSPFGNVEKIKLLKK-----KPGFAFVEF 28
Score = 33.6 bits (78), Expect = 0.005
Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 6/56 (10%)
Query: 33 LQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN-RPHNIDGRVV 87
L F +G + + ++K GF F+ +S + + A+ GR +
Sbjct: 1 LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPL 51
>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 = 34.9 bits (80), Expect = 0.002
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +F+G LD + T+E + F Q G ++ V + KD K + F F+ + V AM+
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGK-PKQFAFVNFKHEVSVPYAMN 60
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 35.0 bits (81), Expect = 0.002
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 111 FVGGLKDQE-EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
FVG L + DL F +++SV +V +KET +GF ++EF D +
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVE 53
>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 = 34.9 bits (81), Expect = 0.003
Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG---FITYSEAKMVDDAM 75
+F+ L + T + L+ F + G ++ V D RS+GFG F + +A+ +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPEDAQRAIEMF 59
Query: 76 SNRPHNIDGRVVETK 90
+ ++++GR +E +
Sbjct: 60 NG--YDLEGRELEVR 72
>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 = 35.1 bits (80), Expect = 0.003
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNIDGRVVE 88
T E ++ F GEI +++D IT +S G+GF+ Y + K + A++ ++G ++
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN----TLNGLRLQ 70
Query: 89 TK 90
TK
Sbjct: 71 TK 72
Score = 32.4 bits (73), Expect = 0.024
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++ +++ R F G IES +V +K TG G+ F+ + D +K +
Sbjct: 12 QNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
>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 = 34.8 bits (80), Expect = 0.003
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFE-QWGEIVDVVVMKDPITKRSRGFGFITYSEAK 69
+F+G L + L + F+ ++ +M DP+T SRG+GF+ +S+
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDEN 55
Score = 32.9 bits (75), Expect = 0.015
Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 110 MFVGGLK-DQEEDDLREYF-SQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FVG L + E DL F S+F + +S ++T+ TG RG+ F+ F+D +
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDEN 55
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 34.4 bits (80), Expect = 0.003
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 123 LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
L E+FS+FGTI ++ + N E+ A ++F+ + K S + +R +
Sbjct: 19 LNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKAYRSPEAVFNNRFI 67
>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 = 35.0 bits (80), Expect = 0.003
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 120 EDDLREYFSQFG-TIESVNMVTNKETGAKRGFAFIEFN 156
E D+R + G V ++ NK +G RGFAF+EFN
Sbjct: 16 ETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFN 53
>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 = 34.5 bits (80), Expect = 0.003
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
VF+G + ++ L FE+ G I ++ +M D +RG+ F+TY+ + A+
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAV 59
Score = 26.0 bits (58), Expect = 4.3
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
FVG + +D ED+L F + G I + ++ + +G RG+AF+ +
Sbjct: 5 FVGKIPRDLFEDELVPLFEKAGPIYELRLMMDF-SGLNRGYAFVTY 49
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed
U2 snRNP B") a unique protein that comprises the U2
snRNP. It was initially identified as binding to
stem-loop IV (SLIV) at the 3' end of U2 snRNA.
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. In addition, the nuclear transport of U2B" is
independent of U2 snRNA binding. U2B" contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It also contains a nuclear localization signal (NLS) in
the central domain. However, nuclear import of U2B''
does not depend on this NLS. The N-terminal RRM is
sufficient to direct U2B" to the nucleus. .
Length = 91
Score = 35.0 bits (80), Expect = 0.004
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 32 SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
SL A F Q+G +VD+V +K T + RG F+ + E +A+
Sbjct: 21 SLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELSSATNAL 61
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subfamily corresponds to the
RRM2 of SREK1, also termed
serine/arginine-rich-splicing regulatory protein 86-kDa
(SRrp86), or splicing factor arginine/serine-rich 12
(SFRS12), or splicing regulatory protein 508 amino acid
(SRrp508). SREK1 belongs to a family of proteins
containing regions rich in serine-arginine dipeptides
(SR proteins family), which is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. It is a unique SR family member and it may play
a crucial role in determining tissue specific patterns
of alternative splicing. SREK1 can alter splice site
selection by both positively and negatively modulating
the activity of other SR proteins. For instance, SREK1
can activate SRp20 and repress SC35 in a dose-dependent
manner both in vitro and in vivo. In addition, SREK1
contains two (some contain only one) RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains)
separated by an unusual glutamic acid-lysine (EK) rich
region. The RRM and SR domains are highly conserved
among other members of the SR superfamily. However, the
EK domain is unique to SREK1. It plays a modulatory
role controlling SR domain function by involvement in
the inhibition of both constitutive and alternative
splicing and in the selection of splice-site. .
Length = 85
Score = 34.6 bits (80), Expect = 0.004
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
R +++G LD TT + L FF Q GE+ V + D T+ +R + F+ ++E V +A+
Sbjct: 5 RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE-TQPTR-YAFVEFAEQTSVINAL 61
Score = 28.8 bits (65), Expect = 0.42
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 111 FVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+VG L D L E+FSQ G ++ V M ET R +AF+EF + V
Sbjct: 8 YVGNLDPTTTADQLLEFFSQAGEVKYVRMAG-DETQPTR-YAFVEFAEQTSVIN 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 = 34.6 bits (79), Expect = 0.004
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 122 DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
DL E+FS G + V M++++ + +G A++EF D
Sbjct: 17 DLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVD 52
Score = 32.7 bits (74), Expect = 0.020
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
R VF L R L+ FF G++ DV ++ D ++RS+G ++ + + V
Sbjct: 2 RTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSV 56
>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 = 34.2 bits (79), Expect = 0.004
Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 11/60 (18%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND----YDVVDKI 164
+++G L K E+DL+ F ++G I+S++M+ RG A++ + + K+
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP------RGCAYVCMETRQDAHRALQKL 58
Score = 33.5 bits (77), Expect = 0.009
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 6/49 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
++IG L + T+E L+ FE++GEI + ++ RG ++
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCM 45
>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 = 34.2 bits (79), Expect = 0.004
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
++VG L ED L E FSQ G I+S ++ +AF+E+ D+
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDH 47
Score = 29.2 bits (66), Expect = 0.28
Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE---AKMVDDAM 75
+++G LD T++ L F Q G I ++++ + + F+ Y + A M
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQTM 57
Query: 76 SNR 78
+ R
Sbjct: 58 NGR 60
>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 = 34.2 bits (78), Expect = 0.005
Identities = 20/50 (40%), Positives = 35/50 (70%), Gaps = 4/50 (8%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
K +FV GL +D E+ L+E F G+I + +VT+++TG+ +GF F++F+
Sbjct: 1 KTLFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFS 47
Score = 32.3 bits (73), Expect = 0.024
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
+ +F+ GL TT+E+L+ F+ + ++ D T S+GFGF+ +S +AK +
Sbjct: 1 KTLFVKGLSEDTTEETLKESFDG---SIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57
Query: 74 AMSNRPHNIDGRVVETKRAVPR 95
AM + IDG V A P+
Sbjct: 58 AMED--GEIDGNKVTLDFAKPK 77
>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 = 34.2 bits (79), Expect = 0.005
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
++F+G L T+E + F ++GE+ +V + K+ +GFGFI
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFI 42
Score = 34.2 bits (79), Expect = 0.005
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 7/46 (15%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFI 153
++FVG L D E++ +E FS++G + V + NKE +GF FI
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFL--NKE----KGFGFI 42
>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 = 34.2 bits (78), Expect = 0.005
Identities = 16/59 (27%), Positives = 33/59 (55%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++I GL T + ++ F ++G I++ V+ D T SRG FI + + ++A+++
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61
Score = 34.2 bits (78), Expect = 0.006
Identities = 16/48 (33%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
+++ GL + + D+ + FS+FG I + ++ ++ TG RG AFI F+
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFD 50
>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 = 33.8 bits (77), Expect = 0.006
Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 8/58 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+V+IG L Y+ + ++ FF+ +G+I++V + G+GF+ + + + DDA+
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAV 50
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 33.9 bits (78), Expect = 0.006
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++ +D + T+E L A F G++VD V DP F FI +++ + A+S
Sbjct: 3 RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDP--NSVLRFAFIEFTDEEGARAALS 60
>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 = 33.8 bits (78), Expect = 0.006
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFIT-YSEAKMVDDAM 75
+++G L + TTDE L+ + G ++ + + +S+GF ++ SEA A
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEA-----AA 55
Query: 76 SNRPHNIDGRVVETKRAV 93
+ ++GR K+ V
Sbjct: 56 AAVKEKLEGREFNGKKCV 73
Score = 28.0 bits (63), Expect = 0.75
Identities = 11/38 (28%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 120 EDDLREYFSQFG--TIESVNMVTNKETGAKRGFAFIEF 155
++DL ++ G ++S+ +K G +GFA++EF
Sbjct: 12 DEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEF 49
>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 = 33.7 bits (77), Expect = 0.007
Identities = 15/58 (25%), Positives = 34/58 (58%), Gaps = 8/58 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+V+IG L Y ++ +Q FF +G+++++ + G+GF+ + +++ DDA+
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAV 50
Score = 25.3 bits (55), Expect = 6.6
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 9/58 (15%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++++G L E D++ +F +G + +++ K G+ F+EF D D V
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAV 50
>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 = 33.9 bits (77), Expect = 0.007
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++ +D+LR FS G +ES ++ +K G G+ F+ +
Sbjct: 11 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 50
Score = 32.8 bits (74), Expect = 0.017
Identities = 14/48 (29%), Positives = 27/48 (56%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
T + L++ F GE+ +++D + S G+GF+ Y AK + A++
Sbjct: 14 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61
>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 = 33.6 bits (76), Expect = 0.008
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
S ++I GL TTD+ L + +G+IV + D T + +G+GF+ + A
Sbjct: 3 SKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKA 62
Query: 75 MSN 77
+++
Sbjct: 63 VAS 65
Score = 28.3 bits (62), Expect = 0.84
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 110 MFVGGLKDQEED-DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
+++ GL D DL + +G I S + +K T +G+ F++F+ K V S
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVAS 65
>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 = 33.5 bits (77), Expect = 0.008
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA-- 74
R +F+G L+ T+E L+ FE++G + DV + K P + + F+ + M A
Sbjct: 3 RTLFVGNLEITITEEELRRAFERYGVVEDVDI-KRPPRGQGNAYAFVKFLNLDMAHRAKV 61
Query: 75 -MSNR 78
MS +
Sbjct: 62 AMSGQ 66
Score = 31.2 bits (71), Expect = 0.054
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+FVG L+ E++LR F ++G +E V+ + G +AF++F + D+ +
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVD-IKRPPRGQGNAYAFVKFLNLDMAHR 58
>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 = 33.8 bits (77), Expect = 0.008
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 9/57 (15%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIES--------VNMVTNKETGAKRGFAFIEFND 157
+FV GL +D + + +YF Q G I++ +N+ T++ETG +G A + F+D
Sbjct: 5 IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 61
>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 = 33.9 bits (77), Expect = 0.008
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFIT---YSEAKM 70
+FI L + L F +G + +V V++D T + +GFGF+T Y EA M
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAM 58
Score = 30.8 bits (69), Expect = 0.089
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+D +E L + F FG + +V ++ + T +GF F+ +Y+
Sbjct: 11 QDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYE 54
>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 = 33.4 bits (77), Expect = 0.009
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 28 TTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN-RPHNIDGRV 86
TT+E L+ F ++GE+ V +KD + F+ + E AM ++G
Sbjct: 13 TTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEMNGKELEGSP 64
Query: 87 VETKRAVP 94
+E A P
Sbjct: 65 IEVSLAKP 72
Score = 31.4 bits (72), Expect = 0.044
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 9/54 (16%)
Query: 107 VKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
VK ++V L E+ LRE FS++G +E V + + +AF+ F + D
Sbjct: 1 VKVLYVRNLPLSTTEEQLRELFSEYGEVERVKKI--------KDYAFVHFEERD 46
>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 = 33.4 bits (77), Expect = 0.009
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 11/53 (20%)
Query: 108 KKMFVGGLK-----DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+ ++VGG+K Q E+ LR +F ++G IE + ++ +K G AF+ +
Sbjct: 2 RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLPSK------GIAFVRY 48
Score = 33.4 bits (77), Expect = 0.010
Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 13/70 (18%)
Query: 17 RKVFIGGLDYRT----TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAK 69
R +++GG+ + +E L+ F +WG+I D+ V+ S+G F+ Y + A+
Sbjct: 2 RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLP------SKGIAFVRYKYRASAE 55
Query: 70 MVDDAMSNRP 79
+AM+++
Sbjct: 56 FAKEAMADQS 65
>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 = 33.4 bits (77), Expect = 0.009
Identities = 15/36 (41%), Positives = 25/36 (69%), Gaps = 5/36 (13%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
ED+LR+ FS++G + V +V++K K+G A +EF
Sbjct: 18 EDELRKIFSKYGDVSDV-VVSSK----KKGSAIVEF 48
>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 = 33.5 bits (76), Expect = 0.010
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAK 69
R +++ GL T L+ F ++G++V V+ + + +R +GF+T S ++
Sbjct: 2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSE 54
Score = 29.7 bits (66), Expect = 0.23
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 108 KKMFVGGLKDQEE-DDLREYFSQFGTIESVNMVTNKETGAKRGFAFI 153
+ ++V GL DL+ FS++G + +VTN + R + F+
Sbjct: 2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFV 48
>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 = 33.1 bits (76), Expect = 0.010
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
++V GL + DL++ FS++G + +VTN + R F F+ + K +
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60
Score = 30.8 bits (70), Expect = 0.078
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 21 IGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS--NR 78
+ GL T L+ F ++G++V ++ + + +R FGF+T + + + +R
Sbjct: 4 VSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHR 63
Query: 79 PHNIDGRVV 87
+ GRV+
Sbjct: 64 T-ELHGRVI 71
>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 = 33.5 bits (76), Expect = 0.010
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFIT---YSEAKM 70
+F+ L + + L F +G + +V V++D T + +GFGF+T Y EA M
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60
Score = 33.1 bits (75), Expect = 0.015
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FV L D +E L + F FG + +V ++ + T +GF F+ +YD
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYD 56
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup
corresponds to the RRM1 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Its
cellular function remains unknown currently, however,
PSPC1 forms a novel heterodimer with the nuclear
protein p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 71
Score = 33.0 bits (75), Expect = 0.011
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
++F+G L T+E + FE++GE +V + +D RGFGFI
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFI 42
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and
U3 small nucleolar RNAs (snoRNAs). MRD1 is essential
for the initial processing at the A0-A2 cleavage sites
in the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which may play an important structural role in
organizing specific rRNA processing events. .
Length = 84
Score = 33.3 bits (76), Expect = 0.011
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 10/82 (12%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKR-----SRGFGFI---TYSEAKM 70
+F+ L++ TT++ L F+ V V P KR S GFGF+ T +A+
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 71 VDDAMSNRPHNIDGRVVETKRA 92
AM +DG + K +
Sbjct: 63 ALKAMDGF--VLDGHTLVVKFS 82
>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 = 33.0 bits (76), Expect = 0.012
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
E+ L++ FS FG I +++M ++ F+ F + D+ +
Sbjct: 16 EEILKKAFSPFGNIINISM------EKEKNCGFVTFEKMESADRAI 55
Score = 27.2 bits (61), Expect = 1.6
Identities = 14/60 (23%), Positives = 32/60 (53%), Gaps = 10/60 (16%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNIDGRVVE 88
T+E L+ F +G I+++ + K+ + GF+T+ + + D A++ ++G V+
Sbjct: 15 TEEILKKAFSPFGNIINISMEKE------KNCGFVTFEKMESADRAIA----ELNGTTVQ 64
>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 = 32.9 bits (75), Expect = 0.013
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
++F+G L T+E ++ FE++G+ ++ + KD +GFGFI + + A
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIA 53
>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 = 33.5 bits (77), Expect = 0.013
Identities = 13/48 (27%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
ED ++ YFS FG I + + T G I++ Y K +
Sbjct: 16 EDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKY--YGSPGKPDRA 61
Score = 25.8 bits (57), Expect = 8.9
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
G T+++ ++ +F +GEI ++ DP T G I Y
Sbjct: 9 GFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYY 52
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 32.6 bits (75), Expect = 0.014
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
DD++E+F +FG + ++ M + + K G F+EF + K +
Sbjct: 14 DDIQEFFEKFGKVNNIRMRRDLDKKFK-GSVFVEFKTEEDAKKFL 57
Score = 28.7 bits (65), Expect = 0.41
Identities = 12/49 (24%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
V++ G T + +Q FFE++G++ ++ + +D K+ +G F+ +
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDL-DKKFKGSVFVEFKT 49
>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 = 32.7 bits (75), Expect = 0.014
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
K +ED LR+ F FGTI V + K+ G R F F+ + + K
Sbjct: 10 KGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQK 56
Score = 32.7 bits (75), Expect = 0.019
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++ L+ FE +G I DV + + R FGF+ Y + A+
Sbjct: 13 KEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTEEEAQKALK 59
>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 = 33.1 bits (75), Expect = 0.015
Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 30 DES-LQAFFEQWGEIVDVVVMKDPITKRSRGFGFIT---YSEAKM 70
DES L F +G + +V V++D T + +GFGF+T Y EA M
Sbjct: 16 DESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAM 60
Score = 32.4 bits (73), Expect = 0.025
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
D +E L + F FG + +V ++ + T +GF F+ +YD
Sbjct: 14 DADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYD 56
>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional.
Length = 243
Score = 34.4 bits (79), Expect = 0.016
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 119 EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
E D+ ++FS G IE V ++ + E A++ F D ++ VL ++D+RV
Sbjct: 18 TEKDVYDFFSHCGAIEHVEIIRSGEYACT---AYVTFKDAYALETAVLLSGATIVDQRV 73
>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 = 32.6 bits (74), Expect = 0.016
Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 12/74 (16%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+VFIG L+ ++ ++ FF+ +G I D+ + RGFGF+ + + + DDA+
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDAV-- 50
Query: 78 RPHNIDGRVVETKR 91
+ +DG+ + +R
Sbjct: 51 --YELDGKELCNER 62
Score = 28.4 bits (63), Expect = 0.46
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 9/50 (18%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++F+G L E D+ +F +G I +++ KRGF F+EF+D
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDD 42
>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 = 32.8 bits (75), Expect = 0.017
Identities = 22/51 (43%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 109 KMFVGGL-KDQEEDDLREYF-SQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K+ V L KD E +REYF SQ G I+ V + N E G G A I F
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYN-EGGKSTGIANITFKR 50
>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 = 32.8 bits (75), Expect = 0.017
Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++VG L + E+ + E+F ++G +ESV ++ + + AF++F D
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA-AFVDFVD 49
>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 = 32.4 bits (74), Expect = 0.022
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+ +++G + D E+ LR FSQ+G IESVN + K AF+ F
Sbjct: 4 RNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNC------AFVNF 46
Score = 28.9 bits (65), Expect = 0.37
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEI 43
R V+IG +D T+E L+ F Q+GEI
Sbjct: 4 RNVYIGNIDDSLTEEKLRNDFSQYGEI 30
>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 = 32.6 bits (75), Expect = 0.022
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 108 KKMFVGGLKDQEEDD-LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+FVG + + DD +R+ + G + S V + TG + F F EF D
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFED 51
Score = 32.2 bits (74), Expect = 0.032
Identities = 13/52 (25%), Positives = 28/52 (53%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEA 68
VF+G + +D+ ++ E+ G+++ +KDP T + + FGF + +
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDP 52
>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 = 32.2 bits (73), Expect = 0.023
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 31 ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+SL A F Q+G+I+D+V +K T + RG F+ + + +A+
Sbjct: 18 KSLYAIFSQFGQILDIVALK---TLKMRGQAFVVFKDISSATNAL 59
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 32.0 bits (73), Expect = 0.025
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+ +++G L + E++LRE +FG I+ + +V ++ AF+ F
Sbjct: 4 RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVK------EKNIAFVHF 46
Score = 29.7 bits (67), Expect = 0.21
Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFI 63
R V+IG L ++E L+ E++G I + ++K+ + F+
Sbjct: 4 RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFV 44
>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 = 32.0 bits (73), Expect = 0.028
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 124 REYFSQFGTIESVN---MVTNKETGAKRGFAFIEFN 156
E+ S F + V +V +K TG GF F+++
Sbjct: 15 EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQ 50
Score = 31.2 bits (71), Expect = 0.058
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
TDE ++ F G + + +++D T S GFGF+ Y A +DA
Sbjct: 13 TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSA---EDA 55
>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 = 31.8 bits (73), Expect = 0.029
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 26 YRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAK 69
T E + F + GEI DV +++ K SR FI Y +
Sbjct: 11 SLTEAELKEHFSKHGGEITDVKLLRTEDGK-SRRIAFIGYKTEE 53
Score = 31.5 bits (72), Expect = 0.048
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 119 EEDDLREYFSQF-GTIESVNMVTNKETGAKRGFAFIEFND 157
E +L+E+FS+ G I V ++ ++ G R AFI +
Sbjct: 13 TEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKT 51
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 31.8 bits (73), Expect = 0.030
Identities = 16/76 (21%), Positives = 38/76 (50%), Gaps = 13/76 (17%)
Query: 17 RKVFIGGLD-YRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+VF+G L+ + + E L+ F ++G+I+ + + K G+GF+ + + A+
Sbjct: 1 SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK--------GYGFVQFDNEEDARAAV 52
Query: 76 SNRPHNIDGRVVETKR 91
+ +GR + ++
Sbjct: 53 AGE----NGREIAGQK 64
Score = 30.7 bits (70), Expect = 0.071
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 10/49 (20%)
Query: 111 FVGGLKDQ--EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
FVG L ++DL E FS++G I +++ +G+ F++F++
Sbjct: 4 FVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDN 44
>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 = 31.7 bits (72), Expect = 0.033
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 25 DYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS-NRPHNID 83
D R T+E + +F Q+G ++DV + P ++ R FGF+T+ A+ V +S PH I
Sbjct: 8 DSRFTEEDVSEYFGQFGPVLDVRI---PYQQK-RMFGFVTFENAETVKRILSKGNPHFIC 63
Query: 84 GRVVETK 90
G V K
Sbjct: 64 GSRVRVK 70
Score = 31.7 bits (72), Expect = 0.036
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSK 168
E+D+ EYF QFG + V + KR F F+ F + + V K +LSK
Sbjct: 13 EEDVSEYFGQFGPVLDVRI----PYQQKRMFGFVTFENAETV-KRILSK 56
>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 = 31.4 bits (72), Expect = 0.041
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++ + L Y T+E L+ F + GE+ V + D + RS G + + + + + A+
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAI 58
Score = 26.0 bits (58), Expect = 3.3
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
E+DL E F + G ++ V + ++ +G G A + F
Sbjct: 14 EEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVF 48
>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 = 31.5 bits (71), Expect = 0.044
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+FI L TD L F +G ++ V D T S+ FGF++Y D+ S +
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSY------DNPDSAQ 60
Query: 79 P--HNIDGRVVETKR 91
++G + TKR
Sbjct: 61 AAIQAMNGFQIGTKR 75
Score = 29.2 bits (65), Expect = 0.29
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ DL + F FG + S + +K+T + F F+ +++ D
Sbjct: 18 DTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPD 57
>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 = 31.4 bits (71), Expect = 0.051
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+FI L D L F +G ++ V D T +S+ FGF+++
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSF 53
Score = 26.0 bits (57), Expect = 4.5
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 122 DLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+L + F FG + S + ++ T + F F+ F++
Sbjct: 20 ELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDN 55
>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 = 31.1 bits (70), Expect = 0.056
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++FIG L ++ L E+ G+I ++ +M D +RG+ F+T+S + +A+
Sbjct: 3 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAI 59
>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 = 31.4 bits (72), Expect = 0.066
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 115 LKDQEE-----DDLREYFSQFGTIESVNMVTNKETG---AKRGFAFIEFNDYD 159
L+D EE +D++E ++G + SV + + G G F+EF D +
Sbjct: 15 LEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVE 67
>gnl|CDD|240704 cd12258, RRM2_RBM26_like, RNA recognition motif 2 of vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM2 of RBM26, also
known as cutaneous T-cell lymphoma (CTCL) tumor antigen
se70-2, which represents a cutaneous lymphoma
(CL)-associated antigen. RBM26 contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
The RRMs may play some functional roles in RNA-binding
or protein-protein interactions.
Length = 72
Score = 30.7 bits (70), Expect = 0.066
Identities = 11/31 (35%), Positives = 22/31 (70%)
Query: 108 KKMFVGGLKDQEEDDLREYFSQFGTIESVNM 138
+++ V G ++++D+L +F+QFG IE V +
Sbjct: 6 RQLSVTGFTEEDKDELLAHFAQFGEIEDVEV 36
>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 = 30.8 bits (70), Expect = 0.067
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDP-ITKRSRGFGFITYSEAKMVDDAMSNR 78
++G L Y T+E ++ FF + V + ++P R RGFG+ + + + A+S
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLN 63
Query: 79 PHNIDGRVV 87
++ R +
Sbjct: 64 DESLKNRRI 72
Score = 27.7 bits (62), Expect = 1.1
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNM-VTNKETGAKRGFAFIEFNDYD 159
++G L D E+D++E+F + SV + + G RGF + EF D D
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRD 54
>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 = 31.2 bits (71), Expect = 0.072
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 106 TVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++K F+ G++D E +R+YF QFG +SV + N + F+ F
Sbjct: 1 SIKSFFLFGVEDDLPEYKIRDYFEQFGKSKSV--IVNH----RAKCGFVRF 45
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate
nucleolin. This subfamily corresponds to the RRM3 of
ubiquitously expressed protein nucleolin, also termed
protein C23, is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. .
Length = 72
Score = 30.6 bits (69), Expect = 0.087
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 21 IGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK-RSRGFGFITYSEAKMVDDAMSN-R 78
+ L Y +++SLQ FE+ ++ P R +G+ F+ + A+ +A+++
Sbjct: 6 VNNLSYSASEDSLQEVFEK------ATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCN 59
Query: 79 PHNIDGRVV 87
I+GR +
Sbjct: 60 NTEIEGRSI 68
>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 = 0.088
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
E D+ ++FS G IE V + + E ++ A++ F D + +L ++D+ V
Sbjct: 12 ERDIYDFFSFSGDIEYVEIQRSGE-QSQ--TAYVTFKDPQAQETALLLSGATIVDQSV 66
>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 = 30.6 bits (70), Expect = 0.094
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 7/51 (13%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
++VGGL +L F +FG I ++ R +A+IE+ +
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPG------RNYAYIEYESIE 45
>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 = 30.6 bits (69), Expect = 0.10
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R ++I L + L+ FE +GEI + V+ I R +GFITY ++ ++
Sbjct: 3 RVIYIRNLSSSMSSTELKKRFEVFGEIEECKVL---IKSRGEKYGFITYRHSEHAALSLG 59
Query: 77 N 77
Sbjct: 60 K 60
>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 = 30.4 bits (68), Expect = 0.11
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 7/45 (15%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFI 153
++VG + K + DL F +FG IES+NM+ RG A++
Sbjct: 5 LWVGQVDKKATQQDLTNLFEEFGQIESINMI------PPRGCAYV 43
>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 = 30.3 bits (69), Expect = 0.11
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
R +++ L ++ + E L F ++G I + + TK +RG F+ Y +AK D
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYGAIRQIRI---GNTKETRGTAFVVYEDIYDAKNACD 59
Query: 74 AMSNRPHNIDGR 85
+S N+ R
Sbjct: 60 HLSG--FNVANR 69
Score = 28.0 bits (63), Expect = 0.90
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND-YD 159
++L + F ++G I + + KET RG AF+ + D YD
Sbjct: 17 EELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYD 53
>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 = 30.3 bits (69), Expect = 0.12
Identities = 18/51 (35%), Positives = 32/51 (62%), Gaps = 2/51 (3%)
Query: 18 KVFIGGL-DYRTTDESLQAFFEQWGEIVDVVVMKDPITK-RSRGFGFITYS 66
++F+GG+ +T +E L+ F + +VDV+V + P K ++RGF F+ Y
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYE 53
Score = 26.5 bits (59), Expect = 2.9
Identities = 16/53 (30%), Positives = 32/53 (60%), Gaps = 3/53 (5%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGT-IESVNMVTNKETGAK-RGFAFIEFNDY 158
++FVGG+ K + ++++ E FS+ + V + + + K RGFAF+E+ +
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESH 55
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline-
and glutamine-rich splicing factor, or 100 kDa
DNA-pairing protein (POMp100), or 100 kDa subunit of
DNA-binding p52/p100 complex, a multifunctional protein
that mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the
formation of D-loops in superhelical duplex DNA, and is
involved in cell proliferation. PSF can also interact
with multiple factors. It is an RNA-binding component
of spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions,
such as DNA recombination and RNA synthesis,
processing, and transport. PSF contains two conserved
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which are responsible for interactions with RNA and for
the localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. .
Length = 71
Score = 30.3 bits (68), Expect = 0.12
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 14/70 (20%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY--------SEAK 69
++F+G L T++ + F ++GE +V + K +GFGFI ++A+
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFINK------GKGFGFIKLESRALAEIAKAE 56
Query: 70 MVDDAMSNRP 79
+ D M R
Sbjct: 57 LDDTPMRGRQ 66
>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 = 30.0 bits (68), Expect = 0.15
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 48 VMKDPITKRSRGFGFITYSEAKMV 71
+ +DP T +S+GF ++TYS
Sbjct: 31 LKRDPYTGKSKGFAYVTYSNPASA 54
>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 = 29.8 bits (68), Expect = 0.15
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K +F+ L ++ ++ L F+QF + V +V +RG AF+EF
Sbjct: 3 KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFET 47
>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 = 29.8 bits (67), Expect = 0.16
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 5/72 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +F+ L Y T + L+ FE +I + S+G +I + + A+
Sbjct: 4 RTLFVKNLPYNITVDELKEVFEDAVDI--RLPSGK--DGSSKGIAYIEFKTEAEAEKALE 59
Query: 77 NRP-HNIDGRVV 87
+ +DGR +
Sbjct: 60 EKQGAEVDGRSI 71
>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 = 30.0 bits (68), Expect = 0.17
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 110 MFVGGLKDQEEDD--LREYFSQ-FGTIESVNMVTNKETGAKRGFAFIEFND 157
+FVG L + DD L E+FS+ + + + +V + + G RG+ F+ F+D
Sbjct: 4 LFVGDL-TPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSD 52
Score = 25.7 bits (57), Expect = 5.1
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 19 VFIGGLDYRTTDESLQAFF-EQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
+F+G L D L FF +++ V+ D SRG+GF+ +S+
Sbjct: 4 LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSD 52
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 29.9 bits (67), Expect = 0.19
Identities = 17/38 (44%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
E++L E FG I VN N GA R AF+EF D
Sbjct: 16 EEELIELCKPFGKI--VNTKCN--VGANRNQAFVEFAD 49
>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 = 29.8 bits (68), Expect = 0.20
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++ D+R+ F Q+G I S+ + R F +++F
Sbjct: 11 SFDQSDIRDLFEQYGEILSIRF-PSLRFNKTRRFCYVQF 48
>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 = 29.3 bits (66), Expect = 0.23
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+++VG L D E D+ + F ++G I+++++ K FAF+EF D
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFED 47
Score = 25.4 bits (56), Expect = 6.7
Identities = 12/61 (19%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++++G L + ++ F ++G I + +K+ +R F F+ + + + +DA+
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKA-IDLKNR--RRGPPFAFVEFEDPRDAEDAVRG 57
Query: 78 R 78
R
Sbjct: 58 R 58
>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 = 29.6 bits (66), Expect = 0.23
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 120 EDDLREYFSQFGTIESVNM-VTNKETGAKRGFAFIEF 155
E+D+RE F + ++ + ++TG RGFAF+EF
Sbjct: 19 ENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEF 55
>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 = 29.0 bits (65), Expect = 0.31
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 7/42 (16%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 162
DDL + F +G I+ + +ET KR FIEF YDV
Sbjct: 16 DDLHQIFGAYGEIKEI-----RETPNKRHHKFIEF--YDVRS 50
>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 = 29.1 bits (65), Expect = 0.35
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 31 ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN-RPHNIDGRVVET 89
L+ F ++G++ + + + K GF F+T + K + A+ N IDGR V
Sbjct: 16 VKLKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALENTNGLEIDGRPVAV 74
Query: 90 KRAVPRD 96
AV ++
Sbjct: 75 DWAVQKN 81
>gnl|CDD|237341 PRK13302, PRK13302, putative L-aspartate dehydrogenase;
Provisional.
Length = 271
Score = 30.6 bits (69), Expect = 0.35
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDV 160
GTI SV M+T K +G F+ N+ D+
Sbjct: 138 GTIHSVKMITRKPPDGLKGAPFLVTNNIDI 167
>gnl|CDD|240868 cd12422, RRM2_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
RRM2 of 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, and
RRM3 of PTBPH1 and PTBPH2. 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. This 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. .
Length = 85
Score = 29.1 bits (66), Expect = 0.36
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
D L + FS +G +E + + K TG + A ++F+
Sbjct: 15 VDVLHQVFSPYGAVEKIL-IFEKNTGVQ---ALVQFDS 48
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), 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 and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large
number of non-snRNP proteins, including polypyrimidine
tract binding protein (PTB), polypyrimidine-tract
binding protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an
important role in virus replication. U1A contains two
RNA recognition motifs (RRMs); the N-terminal RRM
(RRM1) binds tightly and specifically to the U1 snRNA
SLII and its own 3'-UTR, while in contrast, the
C-terminal RRM (RRM2) does not appear to associate with
any RNA and may be free to bind other proteins. U1A
also contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 89
Score = 29.2 bits (65), Expect = 0.39
Identities = 13/45 (28%), Positives = 27/45 (60%), Gaps = 3/45 (6%)
Query: 31 ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+SL A F ++G+I+D++V + + + RG F+ + E +A+
Sbjct: 22 KSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNAL 63
>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 = 29.1 bits (65), Expect = 0.41
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRG--FGFITYSEAKMVDDA 74
R V+IG + R T L+ F +GEI + I RS G +GF+TY + A
Sbjct: 3 RVVYIGKIPSRMTRSELKDRFSVFGEIEECT-----IHFRSEGDNYGFVTYRYTEEAFAA 57
Query: 75 MSN 77
+ N
Sbjct: 58 IEN 60
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 30.6 bits (68), Expect = 0.50
Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 5/49 (10%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
++ VGGL + DDL + FS GT+++V V K R FA+I+F+
Sbjct: 12 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK----GRSFAYIDFS 56
>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 = 28.3 bits (64), Expect = 0.50
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 7/41 (17%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 160
+ +LR FSQFG ++ + +ET + F+EF YD+
Sbjct: 15 DQELRSLFSQFGEVKDI-----RETPLRPSQKFVEF--YDI 48
>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 = 28.9 bits (64), Expect = 0.52
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+FI L D+ L F +G +V V D T S+ FGF++Y
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 56
Score = 26.9 bits (59), Expect = 2.2
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ DL + F FG + S + +K+T + F F+ +++
Sbjct: 21 DQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 58
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in
epithelial splicing regulatory protein ESRP1, ESRP2,
Drosophila RNA-binding protein Fusilli and similar
proteins. This subfamily corresponds to the RRM2 of
ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of the fibroblast growth factor
receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and
CTNND1 (also termed p120-Catenin) transcripts. They are
highly conserved paralogs and specifically bind to
GU-rich binding site. ESRP1 and ESRP2 contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
The family also includes Drosophila fusilli (fus) gene
encoding RNA-binding protein Fusilli.Loss of fusilli
activity causes lethality during embryogenesis in
flies. Drosophila Fusilli can regulate endogenous FGFR2
splicing and functions as a splicing factor. It shows
high sequence homology to ESRPs and contains three RRMs
as well. It also has an N-terminal domain with unknown
function and a C-terminal domain particularly rich in
alanine, glutamine, and serine. .
Length = 80
Score = 28.4 bits (64), Expect = 0.52
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVD----VVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
GL Y T + AFF +V ++ + P R G F+ + + A+
Sbjct: 8 GLPYSATAADILAFFGGLCPVVGGPDGILFVTGP-DGRPTGDAFVLFETEEDAQRALGKH 66
Query: 79 PHNIDGRVVETKRA 92
N+ R +E R+
Sbjct: 67 KENLGSRYIELFRS 80
>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 = 28.2 bits (63), Expect = 0.53
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 8/39 (20%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
D E +RE FS +G ++ V M++N FAF+EF
Sbjct: 10 DTSESAIREIFSPYGAVKEVKMISN--------FAFVEF 40
>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 = 28.4 bits (63), Expect = 0.53
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 9/54 (16%)
Query: 107 VKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
VK +FV L + E+ L + F QFG +E V + + +AFI F++ D
Sbjct: 1 VKVLFVRNLANTVTEEILEKAFGQFGKLERVKKL--------KDYAFIHFDERD 46
>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 = 28.5 bits (63), Expect = 0.53
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
E +R+ FS FG I V + +K G++F+ FN ++ ++S
Sbjct: 14 EQLMRQTFSPFGQIMEVRVFPDK------GYSFVRFNSHESAAHAIVS 55
Score = 27.3 bits (60), Expect = 1.2
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-SN 77
V+ GG+ T++ ++ F +G+I++V V D +G+ F+ ++ + A+ S
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56
Query: 78 RPHNIDGRVVE 88
I+G VV+
Sbjct: 57 NGTTIEGHVVK 67
>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 = 28.4 bits (63), Expect = 0.55
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ Q E+ +R FG +E +V ++ TG +G+ F+E+ D
Sbjct: 13 QQQFEELVRP----FGNLERCFLVYSETTGHSKGYGFVEYMKKD 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 = 28.9 bits (65), Expect = 0.57
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEI 43
KVF+GG+ + T+ L F+ +G +
Sbjct: 4 KVFLGGVPWDITEAGLINTFKPFGSV 29
>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 = 28.3 bits (63), Expect = 0.58
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
+VF+G + ++ L FE+ G+I + +M + + +RG+ F+ Y+
Sbjct: 2 CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYT 50
>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 = 28.8 bits (64), Expect = 0.58
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
R +F+G LD T+ L+ F+++G I +V + K P ++ +GF+ + M A
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVDI-KRPGRGQTSTYGFLKFENLDMAHRA 64
Score = 28.0 bits (62), Expect = 0.89
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
+ +F+G L E DLR F +FG I V+ + G + F++F + D+ + L
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVD-IKRPGRGQTSTYGFLKFENLDMAHRAKL 66
Query: 167 S 167
+
Sbjct: 67 A 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 = 28.4 bits (63), Expect = 0.59
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
VF+ LDY+ + L+ F G +V +++D K SRG G +T+ + A+S
Sbjct: 3 VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGK-SRGIGTVTFEQPIEAVQAIS 59
>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 = 28.3 bits (63), Expect = 0.59
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD 51
K+F+G + T + L+ FE++G +V+ +KD
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD 35
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing
protein 1 (RDM1) and similar proteins. This subfamily
corresponds to the RRM of RDM1, also termed RAD52
homolog B, a novel factor involved in the cellular
response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 28.5 bits (64), Expect = 0.61
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 7/54 (12%)
Query: 108 KKMFVGGL---KDQEE--DDLREYFSQFGTIESVNMVTNKETGAKRGF-AFIEF 155
K ++V G+ +EE + L FSQFG + SV + N A GF AF++F
Sbjct: 1 KTLYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPN-AAVATPGFYAFVKF 53
>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 = 28.3 bits (63), Expect = 0.63
Identities = 14/57 (24%), Positives = 25/57 (43%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
++ E +G IE +V ++ TG +G+ F+E+ D K L + L
Sbjct: 14 EEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLGKQLGEST 70
>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 = 28.1 bits (62), Expect = 0.64
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-SN 77
V+ GG+ T++ ++ F +G+I+++ V + +G+ FI +S + A+ S
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSV 56
Query: 78 RPHNIDGRVVE 88
I+G VV+
Sbjct: 57 NGTTIEGHVVK 67
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function
in RNA packaging, stabilization of RNA secondary
structure, or other macromolecular interactions. GRSF-1
contains three potential RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 28.2 bits (63), Expect = 0.69
Identities = 17/70 (24%), Positives = 31/70 (44%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
V + GL Y T++ + FF + D VV+ R G ++ ++ +M + A+
Sbjct: 4 VRLRGLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKH 63
Query: 79 PHNIDGRVVE 88
I R +E
Sbjct: 64 REEIGNRYIE 73
>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 = 28.3 bits (64), Expect = 0.71
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
L + FS FG I S + T+ E G +G+ F+ F
Sbjct: 17 KALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHF 50
>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 = 28.4 bits (64), Expect = 0.72
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESV 136
FVG L ++ DL++ F QFG IESV
Sbjct: 4 FVGNLPLTTKKKDLKKLFKQFGPIESV 30
>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 = 27.8 bits (62), Expect = 0.82
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+++VG L D E DL + F ++G I + + K FAF+ F D
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFED 47
>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 = 28.1 bits (62), Expect = 0.83
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY-DVVDKI 164
K++VG L + + +L F +G + SV + N GFAF+EF D D D +
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAV 58
Score = 27.7 bits (61), Expect = 1.2
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
KV++G L L+ F +G + V V ++P GF F+ + + + DA+
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV-- 58
Query: 78 RPHNIDGRVV 87
+DGR +
Sbjct: 59 --RELDGRTL 66
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both, nuclear and
cytoplasmic, roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 28.1 bits (63), Expect = 0.86
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
E DL E S+FG I V M+ K A +EF D
Sbjct: 16 EADLVEALSEFGPISYVTMMPKKRQ------ALVEFED 47
>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 = 28.0 bits (62), Expect = 0.86
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
+VF+G + ++ L FE G I ++ +M D ++RG+ F+ Y+ EAK
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVRE 61
Query: 75 MSN---RPHNIDG 84
++N RP + G
Sbjct: 62 LNNYEIRPGRLLG 74
>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 = 28.4 bits (63), Expect = 0.91
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIV 44
RKVF+GGL + T+ + F ++G +
Sbjct: 1 RKVFVGGLPWDITEADILNSFRRFGSLQ 28
>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 = 27.7 bits (61), Expect = 0.92
Identities = 10/34 (29%), Positives = 23/34 (67%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD 51
K+ +G + T++ L+A FE++G +++ ++KD
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD 35
>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 = 27.9 bits (62), Expect = 0.92
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 9/57 (15%)
Query: 110 MFVGGLKDQEE-DDLREYFSQFGTIE--------SVNMVTNKETGAKRGFAFIEFND 157
++V GL D ++L ++F G ++ VN+ T+KETG +G A + + D
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYED 59
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 27.7 bits (62), Expect = 0.95
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIES--------VNMVTNKETGAKRGFAFIEFND 157
++ GL D ED L E F G I+ + + T+KET K G A + ++D
Sbjct: 2 YISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPK-GEATVTYDD 56
>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 = 28.2 bits (63), Expect = 0.96
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIV 44
RKVF+GGL ++ + A F ++G +V
Sbjct: 1 RKVFVGGLPPDIDEDEITASFRRFGPLV 28
>gnl|CDD|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and
CTD-associated factor 4 (SCAF4) and similar proteins.
The CD corresponds to the RRM of SCAF4 (also termed
splicing factor, arginine/serine-rich 15 or SFR15, or
CTD-binding SR-like protein RA4) that belongs to a new
class of SCAFs (SR-like CTD-associated factors).
Although its biological function remains unclear, SCAF4
shows high sequence similarity to SCAF8 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) and may play a direct role
in coupling with both, transcription and pre-mRNA
processing, processes. SCAF4 and SCAF8 both 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 = 81
Score = 28.1 bits (62), Expect = 0.97
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFI 153
++VG L K + D+ +FG IES+NM+ RG A+I
Sbjct: 7 LWVGQLDKRTTQQDVTSLLEEFGPIESINMI------PPRGCAYI 45
>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 = 28.0 bits (63), Expect = 0.97
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 113 GGLK---DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
GGL +EE L F ++GT+E + M K + F+ ++
Sbjct: 9 GGLGNGVSREE--LLRVFEKYGTVEDLVMPPGKP------YCFVSYSS 48
>gnl|CDD|236239 PRK08322, PRK08322, acetolactate synthase; Reviewed.
Length = 547
Score = 29.4 bits (67), Expect = 0.98
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 29 TDESLQAFFEQWGEIVDVVVMKDPITKRSR 58
S Q F+ IVDVV M P+TK +R
Sbjct: 101 IKRSKQGSFQ----IVDVVAMMAPLTKWTR 126
>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 = 27.8 bits (61), Expect = 0.99
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 110 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
++VG L +D E + + FSQ G +S M+T E + + F+EF ++
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMIT--EHTSNDPYCFVEFYEH 49
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP
2H9), which represent a group of nuclear RNA binding
proteins that are involved in pre-mRNA processing.
GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of fibroblast growth factor receptor
2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. Fusilli shows
high sequence homology to ESRPs. It can regulate
endogenous FGFR2 splicing and functions as a splicing
factor. The biological roles of both, RBM12 and RBM12B,
remain unclear. RBM19 is a nucleolar protein conserved
in eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 27.5 bits (62), Expect = 0.99
Identities = 14/71 (19%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVD-VVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
V + GL + T+E ++ FF D + ++ D + + G ++ ++ + A+
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPT-GEAYVEFASPEDARRALRK 60
Query: 78 RPHNIDGRVVE 88
+ + GR +E
Sbjct: 61 HNNKMGGRYIE 71
>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 = 27.8 bits (61), Expect = 1.0
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGE-IVDVVVMKDPI-TKRSRGFGFITYSEAKMVDDA 74
++F+G + T E++ F + E +VDV++ P K++RGF F+ Y + K A
Sbjct: 4 RLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHKSAAQA 62
Score = 25.5 bits (55), Expect = 7.3
Identities = 14/53 (26%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQF--GTIESVNMVTNKETGAKRGFAFIEFNDY 158
++FVG + K++ ++++ E FS+ G ++ + + RGF F+E+ D+
Sbjct: 4 RLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDH 56
>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 = 28.0 bits (62), Expect = 1.1
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
R +++G + TT L+ FE +GEI + V + +GFITY
Sbjct: 3 RVIYVGKIRPDTTRTELRDRFEVFGEIEECTV---NLRDDGDSYGFITY 48
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 and RRM4 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
and is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 82
Score = 27.6 bits (61), Expect = 1.1
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 10/58 (17%)
Query: 111 FVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF----NDYDVVDKI 164
VG ++ E +LR+ ++G IES+ ++ ++ AFI F N + +
Sbjct: 12 DVGDERNLPEKELRKECEKYGEIESIRILR------EKACAFINFMNIPNAIAALQTL 63
Score = 26.0 bits (57), Expect = 5.1
Identities = 13/79 (16%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 17 RKVFIGGLDYRT-----TDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE---- 67
R V+IG + ++ L+ E++GEI + ++++ + FI +
Sbjct: 3 RNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILRE------KACAFINFMNIPNA 56
Query: 68 AKMVDDAMSNRPHNIDGRV 86
+ +P++ R+
Sbjct: 57 IAALQTLNGKKPYDTIVRI 75
>gnl|CDD|146805 pfam04358, DsrC, DsrC like protein. Family member dsvC has been
observed to co-purify with Desulfovibrio vulgaris
dissimilatory sulfite reductase, and many members of
this family are annotated as the third (gamma) subunit
of dissimilatory sulphite reductase. However, this
protein appears to be only loosely associated to the
sulfite reductase, which suggests that DsrC may not be
an integral part of the dissimilatory sulphite
reductase. Members of this family are found in organisms
such as E. coli and H. influenzae which do not contain
dissimilatory sulphite reductases but can synthesise
assimilatory sirohaem sulphite and nitrite reductases.
It is speculated that DsrC may be involved in the
assembly, folding or stabilisation of sirohaem proteins.
The strictly conserved cysteine in the C terminus
suggests that DsrC may have a catalytic function in the
metabolism of sulphur compounds.
Length = 109
Score = 27.9 bits (63), Expect = 1.4
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 123 LREYFSQFGTIESVNMVTNKETGAKRG 149
LR+Y+++FG ++ M+ K G K G
Sbjct: 50 LRDYYAEFGIAPAIRMLV-KALGKKLG 75
>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 = 26.8 bits (60), Expect = 1.6
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 105 ATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
TVK V L KD E+ +R++F G I V +V + G A IEF D
Sbjct: 1 LTVK---VKNLPKDTTENKIRQFFKDCGEIREVKIV--ESEGGL--VAVIEFETED 49
Score = 25.7 bits (57), Expect = 4.1
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDP 52
V + L TT+ ++ FF+ GEI +V +++
Sbjct: 3 VKVKNLPKDTTENKIRQFFKDCGEIREVKIVESE 36
>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 = 27.3 bits (61), Expect = 1.8
Identities = 10/36 (27%), Positives = 15/36 (41%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
+R +F FG IE + + TG G + F
Sbjct: 12 PKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTF 47
Score = 26.2 bits (58), Expect = 3.8
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
+ I GL TT + ++ F +GEI + + DP T +S G +T+
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTF 47
>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 = 26.7 bits (59), Expect = 2.0
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 9/51 (17%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ +F G + D + ++ F ++G ++ V+M K GFAF+ D
Sbjct: 1 RPVFCGNFEYDARQSEIERLFGKYGRVDRVDM--------KSGFAFVYMED 43
>gnl|CDD|236285 PRK08554, PRK08554, peptidase; Reviewed.
Length = 438
Score = 28.6 bits (64), Expect = 2.0
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 45 DVVVMKDPITKRSRGFGFI--TYSEAKMVDDAMSNRPHNIDGRVVETKRA 92
D + MK PI +R +GFG SE V + + I VVET+ A
Sbjct: 163 DGIGMK-PIIRRRKGFGVTIRVPSEKVKVKGKLREQTFEIRTPVVETRHA 211
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 28.1 bits (63), Expect = 2.0
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
E D++E+FS G IE V M + E A++ F D
Sbjct: 18 ERDIKEFFSFSGDIEYVEMQSENERSQ---IAYVTFKD 52
>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 = 26.7 bits (60), Expect = 2.1
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVM-KDPITK----RSRGFGFITYSEAKMV 71
R++++G L T+E L FF Q + +P+ + F F+ E + V
Sbjct: 2 RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFV---EFRTV 58
Query: 72 DDA 74
++A
Sbjct: 59 EEA 61
Score = 26.3 bits (59), Expect = 2.8
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQF-----GTIESVNMVTNKETGAKRGFAFIEF 155
++++VG L E++L ++F+Q N V + + ++ FAF+EF
Sbjct: 2 RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEF 55
>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 = 26.7 bits (59), Expect = 2.1
Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 4/67 (5%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
V++G L + ++ F ++G IVD+ +K P R G+ FI + +A+ +DA+ R
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDID-LKLPP--RPPGYAFIEFEDARDAEDAIRGR 58
Query: 79 P-HNIDG 84
++ DG
Sbjct: 59 DGYDFDG 65
Score = 26.3 bits (58), Expect = 2.8
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 110 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++VG L D E ++ + F ++G I +++ K G+AFIEF D
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFED 47
>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 = 26.8 bits (59), Expect = 2.1
Identities = 11/47 (23%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 110 MFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEF 155
++V G E+ L+E F Q +E++ + + +G + F++F
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKF 47
>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains. .
Length = 85
Score = 27.0 bits (59), Expect = 2.1
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGE-IVDVVVMKDPI-TKRSRGFGFITYSEAKMVDDA 74
++F+G + T E + F + E + DV++ P K++RGF F+ Y + K A
Sbjct: 4 RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHKTAAQA 62
>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 = 26.8 bits (59), Expect = 2.3
Identities = 7/23 (30%), Positives = 16/23 (69%)
Query: 133 IESVNMVTNKETGAKRGFAFIEF 155
+ ++ ++ +K+T RGFAF++
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQL 53
>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 = 26.8 bits (59), Expect = 2.4
Identities = 7/20 (35%), Positives = 15/20 (75%)
Query: 135 SVNMVTNKETGAKRGFAFIE 154
++ ++ +K+T RGFAF++
Sbjct: 33 NIRLIKDKQTQQNRGFAFVQ 52
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 26.4 bits (59), Expect = 2.5
Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 3/38 (7%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
EDD + FG M G + AF F++
Sbjct: 13 EDDKEDLLKHFGASSVRVM---SRRGKLKNTAFATFDN 47
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 26.5 bits (59), Expect = 2.7
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 119 EEDDLREYFSQFGTIESVNMVTNKETGA 146
+DL S +GT+++ V K A
Sbjct: 13 RWEDLDSLLSTYGTVKNCEQVPTKSETA 40
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its median
region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated in
protein shuttling and protein-protein interactions. .
Length = 77
Score = 26.5 bits (58), Expect = 3.2
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K++VG L + +L FS +G + +V + N GFAF+EF D
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFED 45
>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 = 26.3 bits (58), Expect = 3.4
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 10/52 (19%)
Query: 110 MFVGGLKDQ--EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FV G E+D+ + F FG + ++ ++ FAF+EF D +
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSE 45
>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 = 26.4 bits (59), Expect = 3.8
Identities = 15/36 (41%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 123 LREYFSQFGTIESVNM-VTNKETGAKRGFAFIEFND 157
LR+ FS+FG + V + + ETG +G+AF+EF
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFAT 59
>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 = 25.8 bits (57), Expect = 4.2
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 110 MFVGGL-KDQEEDDLREYFS-QFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+++G L D E DLR+ F + SV + K G+AF++ D DK
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVK-------KGGYAFVDCPDQSWADK 49
>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 = 26.0 bits (58), Expect = 4.4
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 9/61 (14%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV---LSKITLLLDRR 176
E DL S FG + +V ++ K A +E + + +V L+ L+ RR
Sbjct: 13 ESDLIALVSPFGKVTNVLLLRGK------NQALVEMDSVESAKSMVDYYLTVPALIRGRR 66
Query: 177 V 177
V
Sbjct: 67 V 67
>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 = 27.5 bits (61), Expect = 4.9
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
E DL E FG + V M+ K A +EF D
Sbjct: 16 EADLVEALIPFGPVSYVMMLPGKRQ------ALVEFED 47
>gnl|CDD|241225 cd12781, RRM1_hnRPLL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). This subgroup corresponds to the RRM1 of
hnRNP-LL, which plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 25.8 bits (56), Expect = 5.0
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
E DL E +FG I V M+ K A +EF + K V
Sbjct: 17 EADLVEALEKFGPICYVMMMPFKRQ------ALVEFEMVESAKKCV 56
>gnl|CDD|241183 cd12739, RRM2_ESRP1, RNA recognition motif 2 in epithelial
splicing regulatory protein 1 (ESRP1) and similar
proteins. This subgroup corresponds to the RRM2 of
ESRP1, also termed RNA-binding motif protein 35A
(RBM35A), which has been identified as an epithelial
cell type-specific regulator of fibroblast growth
factor receptor 2 (FGFR2) splicing. It is required for
expression of epithelial FGFR2-IIIb and the regulation
of CD44, CTNND1 (also termed p120-Catenin) and ENAH
(also termed hMena) splicing. It enhances
epithelial-specific exons of CD44 and ENAH, silences
mesenchymal exons of CTNND1, or both within FGFR2.
Additional research indicated that ESRP1 functions as a
tumor suppressor in colon cancer cells. It may be
involved in posttranscriptional regulation of various
genes by exerting a differential effect on protein
translation via 5' untranslated regions (UTRs) of
mRNAs. ESRP1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 109
Score = 26.2 bits (57), Expect = 5.3
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 23 GLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
GL + T E + AFF Q P+T G F+TY +++ DA
Sbjct: 23 GLPFTATAEEVLAFFGQ----------HCPVTGGKEGILFVTYPDSRPTGDA 64
>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 = 26.0 bits (58), Expect = 5.3
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 111 FVGGLKDQEEDD--LR--EYFSQFGTIESVNMVTNKET 144
+V GL + D+ L+ EYF Q+G I+ + V N+ T
Sbjct: 9 YVVGLPPRLADEEVLKKPEYFGQYGKIKKI--VINRNT 44
>gnl|CDD|178645 PLN03097, FHY3, Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional.
Length = 846
Score = 27.3 bits (60), Expect = 6.1
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQW 40
M+ Y+D K P +R F+ G+ ES+ AFF+++
Sbjct: 433 MQSLYEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKY 472
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family
of histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes
Set1A and Set1B that are ubiquitously expressed
vertebrates histone methyltransferases exhibiting high
homology to yeast Set1. Set1A and Set1B proteins
exhibit a largely non-overlapping subnuclear
distribution in euchromatic nuclear speckles, strongly
suggesting that they bind to a unique set of target
genes and thus make non-redundant contributions to the
epigenetic control of chromatin structure and gene
expression. With the exception of the catalytic
component, the subunit composition of the Set1A and
Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The
genomic targeting of these complexes is determined by
the identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast
to Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 25.7 bits (57), Expect = 6.2
Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG---FITYSEAKMVDD 73
R+V L+ + L+ +++GE+ +V + P T + G F + AK +
Sbjct: 3 REVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVE 62
Query: 74 AMSNRPH 80
++
Sbjct: 63 KLNQTSV 69
>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 = 25.3 bits (56), Expect = 7.0
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 120 EDDLREYFSQFGTIESVNMVTN 141
EDD+ E FS G ++ +V
Sbjct: 14 EDDIVELFSAIGALKRARLVRP 35
>gnl|CDD|233340 TIGR01279, DPOR_bchN, light-independent protochlorophyllide
reductase, N subunit. This enzyme describes the N
subunit of the dark form protochlorophyllide reductase,
a nitrogenase-like enzyme involved in
bacteriochlorophyll biosynthesis. This subunit shows
homology to the nitrogenase molybdenum-iron protein NifN
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Chlorophyll and bacteriochlorphyll].
Length = 407
Score = 26.7 bits (59), Expect = 8.3
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 101 PEANATVKK--MFVGGLKDQEEDDLREYFSQFG 131
PEA A+ ++ + VG + D D LR Q G
Sbjct: 146 PEAPASEQRALVLVGSVNDIVADQLRLELKQLG 178
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal Rrp7 domain. .
Length = 102
Score = 25.3 bits (56), Expect = 9.3
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 120 EDDLREYFSQFGTIESV 136
E+ L+ FS+ G +ESV
Sbjct: 14 EESLKRLFSRCGKVESV 30
>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 = 25.0 bits (55), Expect = 9.6
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 121 DDLREYFSQFGTIESVNMVTNKETG 145
+D++ F+QFG ++ V+ +TG
Sbjct: 16 EDIKAVFAQFGEVKYVDFTEGADTG 40
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
0.318 0.137 0.389
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,327,954
Number of extensions: 868014
Number of successful extensions: 1522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1409
Number of HSP's successfully gapped: 600
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.2 bits)