RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1314
(275 letters)
>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 = 105 bits (263), Expect = 5e-29
Identities = 34/74 (45%), Positives = 53/74 (71%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGGL+ E +E+ +R+YF ++G+I E + P DK N ++GFCFI+FD + +++L
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 162 PKQVICGKEVDVKR 175
VI GK+V+VK+
Sbjct: 61 QFHVIGGKKVEVKK 74
Score = 80.5 bits (199), Expect = 1e-19
Identities = 29/74 (39%), Positives = 46/74 (62%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL T E++I +YF ++G + I + D T + RGF F+TF +++ V +L
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 78 GDHYIGNKKIDPKR 91
H IG KK++ K+
Sbjct: 61 QFHVIGGKKVEVKK 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 = 104 bits (262), Expect = 7e-29
Identities = 37/72 (51%), Positives = 49/72 (68%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LF+GGL +T E+ + +YFS+YGEV I DP TG+SRGF FVTF +VD +LAA
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 79 DHYIGNKKIDPK 90
H + ++IDPK
Sbjct: 61 PHVLDGREIDPK 72
Score = 68.4 bits (168), Expect = 3e-15
Identities = 25/72 (34%), Positives = 45/72 (62%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+F+GGL+ + +E+ +R+YFS+YG + + D +GF F++F D + ++VLA
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 163 KQVICGKEVDVK 174
V+ G+E+D K
Sbjct: 61 PHVLDGREIDPK 72
>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 = 81.2 bits (200), Expect = 7e-20
Identities = 33/74 (44%), Positives = 52/74 (70%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL +T +K++ DYF+++GEV +IK DP+TG+SRGF F+ F +V+ +L
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 78 GDHYIGNKKIDPKR 91
+H + + IDPK+
Sbjct: 61 KEHRLDGRLIDPKK 74
Score = 57.7 bits (139), Expect = 3e-11
Identities = 26/74 (35%), Positives = 47/74 (63%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVGGL+ + S++D++DYF+++G +T+ D + +GF FI F D + E+VL
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 162 PKQVICGKEVDVKR 175
+ + G+ +D K+
Sbjct: 61 KEHRLDGRLIDPKK 74
>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 = 80.6 bits (199), Expect = 1e-19
Identities = 33/72 (45%), Positives = 48/72 (66%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+F+GGL T + + +YFS++GE++ + DP T +SRGF FVTF+ +VD +LA G
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 79 DHYIGNKKIDPK 90
H + KKIDPK
Sbjct: 61 PHELDGKKIDPK 72
Score = 61.3 bits (149), Expect = 1e-12
Identities = 24/72 (33%), Positives = 43/72 (59%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+F+GGL+ + + + +R+YFS++G I E D + +GF F++F D ++VLA
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 163 KQVICGKEVDVK 174
+ GK++D K
Sbjct: 61 PHELDGKKIDPK 72
>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 = 80.5 bits (199), Expect = 1e-19
Identities = 32/78 (41%), Positives = 48/78 (61%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLF+GGL T + + +YFSQ+GE+ + DP+T +SRGF FVTF + VD + A
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 78 GDHYIGNKKIDPKRVTKR 95
H + ++++PKR R
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
Score = 54.3 bits (131), Expect = 5e-10
Identities = 23/74 (31%), Positives = 43/74 (58%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+F+GGL+ E ++ +++YFSQ+G IT+ D + +GF F++F + + +
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 162 PKQVICGKEVDVKR 175
+ G+EV+ KR
Sbjct: 61 RPHKVDGREVEPKR 74
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 79.9 bits (198), Expect = 2e-19
Identities = 26/72 (36%), Positives = 45/72 (62%), Gaps = 1/72 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
LFVG L +T E+E+ + FS++G+VES+ + D TG+S+GFAFV F +++ + L A
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 78 GD-HYIGNKKID 88
+ + + +
Sbjct: 61 LNGKELDGRPLK 72
Score = 73.0 bits (180), Expect = 7e-17
Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-A 160
+FVG L + +E+++R+ FS++G + + DK KGF F+ F+ + AE+ L A
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 161 NPKQVICGKEVDV 173
+ + G+ + V
Sbjct: 61 LNGKELDGRPLKV 73
>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 = 80.0 bits (197), Expect = 2e-19
Identities = 35/74 (47%), Positives = 50/74 (67%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+F+GGL +T +K++ +Y S++GEV +IK DP TG+SRGF FV F +VD +L
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 78 GDHYIGNKKIDPKR 91
+H + K IDPKR
Sbjct: 61 KEHKLDGKLIDPKR 74
Score = 51.5 bits (123), Expect = 6e-09
Identities = 24/76 (31%), Positives = 43/76 (56%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+F+GGL+ + S++D+ +Y S++G + + D +GF F+ F D ++VL
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 162 PKQVICGKEVDVKRVK 177
+ + GK +D KR K
Sbjct: 61 KEHKLDGKLIDPKRAK 76
>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 = 79.9 bits (197), Expect = 2e-19
Identities = 34/73 (46%), Positives = 50/73 (68%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+FVGGL +T +K++ +YFS++GEV +IK DP TG+SRGF FV F +V+ +L
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 79 DHYIGNKKIDPKR 91
+H + + IDPKR
Sbjct: 61 EHKLDGRVIDPKR 73
Score = 51.8 bits (124), Expect = 4e-09
Identities = 23/73 (31%), Positives = 43/73 (58%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FVGGL+ + +++D+++YFS++G + + D +GF F+ F D E+VL
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 163 KQVICGKEVDVKR 175
+ + G+ +D KR
Sbjct: 61 EHKLDGRVIDPKR 73
>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 = 79.7 bits (197), Expect = 2e-19
Identities = 33/74 (44%), Positives = 50/74 (67%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL + E+E +YFSQ+G+V + D TG+SRGF FVTF ++ AV+ + +A
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 78 GDHYIGNKKIDPKR 91
G +G K+++ KR
Sbjct: 61 GMLELGGKQVEVKR 74
Score = 75.5 bits (186), Expect = 1e-17
Identities = 28/74 (37%), Positives = 48/74 (64%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGGL +++E++ ++YFSQ+G + + Q D +GF F++FD ++ E+V +
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 162 PKQVICGKEVDVKR 175
+ GK+V+VKR
Sbjct: 61 GMLELGGKQVEVKR 74
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to
the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p,
also termed cleavage factor IB (CFIB), is a
sequence-specific trans-acting factor that is essential
for mRNA 3'-end formation in yeast Saccharomyces
cerevisiae. It can be UV cross-linked to RNA and
specifically recognizes the (UA)6 RNA element required
for both, the cleavage and poly(A) addition, steps.
Moreover, Hrp1p can shuttle between the nucleus and the
cytoplasm, and play an additional role in the export of
mRNAs to the cytoplasm. Hrp1p also interacts with
Rna15p and Rna14p, two components of CF1A. In addition,
Hrp1p functions as a factor directly involved in
modulating the activity of the nonsense-mediated mRNA
decay (NMD) pathway. It binds specifically to a
downstream sequence element (DSE)-containing RNA and
interacts with Upf1p, a component of the surveillance
complex, further triggering the NMD pathway. Hrp1p
contains two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an
arginine-glycine-rich region harboring repeats of the
sequence RGGF/Y. .
Length = 76
Score = 78.8 bits (194), Expect = 5e-19
Identities = 31/77 (40%), Positives = 49/77 (63%), Gaps = 1/77 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+F+GGL+ T + + +YF Q+GEV ++ D TG+SRGF F+TF K+V++++
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKK- 59
Query: 79 DHYIGNKKIDPKRVTKR 95
+H + K IDPKR R
Sbjct: 60 EHILDGKIIDPKRAIPR 76
Score = 55.3 bits (133), Expect = 3e-10
Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+F+GGL E ++ +R+YF Q+G +T+ D + +GF F++F +V+
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKK- 59
Query: 163 KQVICGKEVDVKR 175
+ ++ GK +D KR
Sbjct: 60 EHILDGKIIDPKR 72
>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 = 78.5 bits (194), Expect = 5e-19
Identities = 34/73 (46%), Positives = 46/73 (63%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLFVGGL + E+++ +YFSQYG VES+ I D TG+ RGFAFVTF VD ++
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 78 GDHYIGNKKIDPK 90
H I +++ K
Sbjct: 61 KYHTINGHRVEVK 73
Score = 74.6 bits (184), Expect = 2e-17
Identities = 29/73 (39%), Positives = 48/73 (65%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVGGL +++E+D+R+YFSQYG++ + DK K+GF F++FDD + ++++
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 162 PKQVICGKEVDVK 174
I G V+VK
Sbjct: 61 KYHTINGHRVEVK 73
>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 = 77.9 bits (192), Expect = 1e-18
Identities = 37/78 (47%), Positives = 44/78 (56%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLFVGGL T ++ + YFSQYGEV I D T +SRGF FV F V +LA
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 78 GDHYIGNKKIDPKRVTKR 95
G H + + IDPK T R
Sbjct: 61 GPHTLDGRTIDPKPCTPR 78
Score = 59.8 bits (145), Expect = 6e-12
Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVGGL+ E +++ +R YFSQYG + + DK+ N +GF F+ F D N VLA
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 162 PKQVICGKEVDVKRVKFNPETM 183
+ G+ +D K P M
Sbjct: 61 GPHTLDGRTIDPKPC--TPRGM 80
>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 = 77.0 bits (189), Expect = 2e-18
Identities = 34/73 (46%), Positives = 51/73 (69%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+F+GGL +T +K++ DYFS++GEV ++K DP TG+SRGF FV F ++VD ++
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 79 DHYIGNKKIDPKR 91
+H + K IDPKR
Sbjct: 61 EHKLNGKVIDPKR 73
Score = 51.9 bits (124), Expect = 5e-09
Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+F+GGL+ + +++D++DYFS++G + + D +GF F+ F + ++V+
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 163 KQVICGKEVDVKR 175
+ + GK +D KR
Sbjct: 61 EHKLNGKVIDPKR 73
>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 = 75.5 bits (186), Expect = 9e-18
Identities = 33/74 (44%), Positives = 49/74 (66%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGGL ++E D+R YFSQ+G++TE +D K +GF FI+F+ ++ +QV+
Sbjct: 4 KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63
Query: 162 PKQVICGKEVDVKR 175
I GK+V+VKR
Sbjct: 64 HFHDINGKKVEVKR 77
Score = 70.9 bits (174), Expect = 5e-16
Identities = 29/75 (38%), Positives = 45/75 (60%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+K+FVGGL N E ++ YFSQ+G V + + D + RGF F+TF ++ +VD ++
Sbjct: 3 KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62
Query: 77 AGDHYIGNKKIDPKR 91
H I KK++ KR
Sbjct: 63 EHFHDINGKKVEVKR 77
>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 = 75.4 bits (185), Expect = 1e-17
Identities = 34/73 (46%), Positives = 47/73 (64%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+F+GGL T ++ + +YF Q+GEV+ + DP T +SRGF FVTF Q VD +LA
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 GDHYIGNKKIDPK 90
H + +K IDPK
Sbjct: 62 SRHELDSKTIDPK 74
Score = 56.6 bits (136), Expect = 9e-11
Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
CK+F+GGL+ + +++ +R+YF Q+G + E D +GF F++F DQ ++VLA
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 161 NPKQVICGKEVDVK 174
+ + K +D K
Sbjct: 61 QSRHELDSKTIDPK 74
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 73.4 bits (181), Expect = 6e-17
Identities = 28/56 (50%), Positives = 36/56 (64%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
KLFV GL T EKE+ FS++G VE + + DP TG+SRGF FVTF + + D
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADA 58
Score = 47.6 bits (114), Expect = 1e-07
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FV GL+T +E+++ FS++G + E D +GF F++F+ A+ + +
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62
Query: 162 -PKQVICGKEVDVKRVK 177
+ + G+ + V++ K
Sbjct: 63 LNGKELEGRVIKVEKAK 79
>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 = 73.0 bits (180), Expect = 7e-17
Identities = 28/70 (40%), Positives = 45/70 (64%), Gaps = 2/70 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LFVG L +T E+++ D FS++G +ESI I D TG+S+GFAFV F ++ + L A
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 79 D-HYIGNKKI 87
+ +G +++
Sbjct: 60 NGKELGGREL 69
Score = 66.1 bits (162), Expect = 2e-14
Identities = 23/70 (32%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
+FVG L + +E+D++D FS++G I + D++ KGF F+ F+D+ AE+ L
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGR-SKGFAFVEFEDEEDAEKALEAL 59
Query: 162 PKQVICGKEV 171
+ + G+E+
Sbjct: 60 NGKELGGREL 69
>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 = 71.7 bits (176), Expect = 2e-16
Identities = 29/74 (39%), Positives = 45/74 (60%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGGL+ +E DV+ YFSQ+G + + FDK N +GF F++F+ ++V ++V
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 162 PKQVICGKEVDVKR 175
I K V+ K+
Sbjct: 61 HFHEINNKMVECKK 74
Score = 70.2 bits (172), Expect = 7e-16
Identities = 32/74 (43%), Positives = 45/74 (60%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL NT E ++ YFSQ+G+VE + D T + RGF FVTF ++ VD +
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 78 GDHYIGNKKIDPKR 91
H I NK ++ K+
Sbjct: 61 HFHEINNKMVECKK 74
>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 = 70.5 bits (172), Expect = 7e-16
Identities = 33/73 (45%), Positives = 45/73 (61%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+F+GGL T + DYFS++GE+ + DP T +SRGF FVTF +VD +LA
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 78 GDHYIGNKKIDPK 90
H + +K IDPK
Sbjct: 61 PHHELDSKTIDPK 73
Score = 54.7 bits (131), Expect = 4e-10
Identities = 27/73 (36%), Positives = 42/73 (57%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+F+GGL+ + S +RDYFS++G I E D + +GF F++F D ++VLA
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 162 PKQVICGKEVDVK 174
P + K +D K
Sbjct: 61 PHHELDSKTIDPK 73
>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 = 69.7 bits (171), Expect = 1e-15
Identities = 30/76 (39%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT---TQKAVDDL 74
L V GL T E+++ DYFS +GE+ + +K DP TGQS+GF FV F Q V
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV--- 57
Query: 75 LAAGDHYIGNKKIDPK 90
+ H I + D K
Sbjct: 58 -LSQRHMIDGRWCDVK 72
Score = 52.0 bits (125), Expect = 4e-09
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+ V GL + +EQD++DYFS +G + Q D KGF F+ F D +VL+
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60
Query: 162 PKQVICGKEVDVK 174
+ +I G+ DVK
Sbjct: 61 -RHMIDGRWCDVK 72
>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 = 69.8 bits (170), Expect = 2e-15
Identities = 32/79 (40%), Positives = 48/79 (60%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T E+ + +Y+ Q+G++ + DP + +SRGF FVTF+ VD +A
Sbjct: 3 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62
Query: 77 AGDHYIGNKKIDPKRVTKR 95
A H I + ++PKR R
Sbjct: 63 ARPHTIDGRVVEPKRAVAR 81
Score = 51.6 bits (123), Expect = 7e-09
Identities = 24/74 (32%), Positives = 43/74 (58%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+F+GGL+ E +E+ +R+Y+ Q+G +T+ D + +GF F++F N + +A
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63
Query: 162 PKQVICGKEVDVKR 175
I G+ V+ KR
Sbjct: 64 RPHTIDGRVVEPKR 77
>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 = 68.9 bits (168), Expect = 3e-15
Identities = 32/73 (43%), Positives = 48/73 (65%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL +T E++I +YF +GE+E+I + D T + RGF FVT+T ++ V LL +
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 78 GDHYIGNKKIDPK 90
H IG+ K + K
Sbjct: 61 RYHQIGSGKCEIK 73
Score = 63.1 bits (153), Expect = 3e-13
Identities = 22/73 (30%), Positives = 45/73 (61%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVGGL+ + +E+ +++YF +G I + P D N ++GFCF+++ D+ +++L +
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 162 PKQVICGKEVDVK 174
I + ++K
Sbjct: 61 RYHQIGSGKCEIK 73
>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 = 68.4 bits (168), Expect = 4e-15
Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 4/61 (6%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
L+VG L N E+++ D F Q+GEV S + D TG+SRGF FV T A++
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 74 L 74
L
Sbjct: 61 L 61
Score = 44.5 bits (106), Expect = 2e-06
Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 4/78 (5%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++VG L ++E+D++D F Q+G +T + D+ +GF F+ + A +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 162 PKQVICGKEVDVKRVKFN 179
+ G + + + N
Sbjct: 61 ----LNGTDFGGRTLTVN 74
>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 = 67.7 bits (166), Expect = 7e-15
Identities = 26/70 (37%), Positives = 44/70 (62%), Gaps = 2/70 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LFVG L +T E+++ + FS++GE+ES+ I D G+S+GFAFV F + + + L A
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59
Query: 79 DHY-IGNKKI 87
+ + +K+
Sbjct: 60 NGKELDGRKL 69
Score = 64.2 bits (157), Expect = 1e-13
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-AN 161
+FVG L + +E+D+R+ FS++G I + DK KGF F+ F+ AE+ L A
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59
Query: 162 PKQVICGKEVDVK 174
+ + G+++ V
Sbjct: 60 NGKELDGRKLKVS 72
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the RRM
of SLIRP, a widely expressed small steroid receptor RNA
activator (SRA) binding protein, which binds to STR7, a
functional substructure of SRA. SLIRP is localized
predominantly to the mitochondria and plays a key role
in modulating several nuclear receptor (NR) pathways. It
functions as a co-repressor to repress SRA-mediated
nuclear receptor coactivation. It modulates SHARP- and
SKIP-mediated co-regulation of NR activity. SLIRP
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is required for SLIRP's corepression activities. .
Length = 73
Score = 66.9 bits (164), Expect = 1e-14
Identities = 24/73 (32%), Positives = 43/73 (58%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVG L + +++++YFSQ+G + PFDK + KG+ F+SF ++ E L
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 162 PKQVICGKEVDVK 174
K ++ G ++ V+
Sbjct: 61 QKHILEGNKLQVQ 73
Score = 63.5 bits (155), Expect = 2e-13
Identities = 27/71 (38%), Positives = 45/71 (63%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLFVG L G KE+ +YFSQ+G+V+S ++ D TG S+G+ FV+F+++ +++ L
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 78 GDHYIGNKKID 88
H + K+
Sbjct: 61 QKHILEGNKLQ 71
>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 = 67.0 bits (163), Expect = 2e-14
Identities = 29/79 (36%), Positives = 48/79 (60%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T ++ + +F Q+G + + DP+T +SRGF FVT+++ + VD +
Sbjct: 3 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62
Query: 77 AGDHYIGNKKIDPKRVTKR 95
A H + + ++PKR R
Sbjct: 63 ARPHKVDGRVVEPKRAVSR 81
Score = 42.4 bits (99), Expect = 1e-05
Identities = 19/74 (25%), Positives = 41/74 (55%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+F+GGL+ E +++ +R +F Q+G++T+ D + +GF F+++ + +
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63
Query: 162 PKQVICGKEVDVKR 175
+ G+ V+ KR
Sbjct: 64 RPHKVDGRVVEPKR 77
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important
role in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 80
Score = 66.9 bits (163), Expect = 2e-14
Identities = 28/74 (37%), Positives = 45/74 (60%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+K+FVGGL+ E++I +YF ++GE+E+I + DP T + RGF F+TF + V +L
Sbjct: 5 KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64
Query: 77 AGDHYIGNKKIDPK 90
H + K + K
Sbjct: 65 KKFHNVSGSKCEIK 78
Score = 61.5 bits (149), Expect = 1e-12
Identities = 28/78 (35%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+P+K KIFVGGL E +E+ +R+YF ++G I + P D N ++GF FI+F +++ +
Sbjct: 2 DPVK-KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVK 60
Query: 157 QVLANPKQVICGKEVDVK 174
+VL + G + ++K
Sbjct: 61 KVLEKKFHNVSGSKCEIK 78
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 71.5 bits (174), Expect = 2e-14
Identities = 33/164 (20%), Positives = 67/164 (40%), Gaps = 26/164 (15%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+ + LFVG L + E+++ + F ++G V+ + + D TG+SRGFAFV F ++++ +
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171
Query: 73 D-LLAAGDHYIGNKKIDPKRVTKRVNPLK-------------------------CKIFVG 106
+ + + + ++ P ++VG
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231
Query: 107 GLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
L + +E+++ D F G I P K + K F+ +
Sbjct: 232 NLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNE 275
Score = 64.2 bits (155), Expect = 7e-12
Identities = 19/101 (18%), Positives = 48/101 (47%), Gaps = 3/101 (2%)
Query: 84 NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
+ + R + +FVG L +++E+D+R+ F ++G + + D+ +G
Sbjct: 101 SSESPKSRQKSKEE--NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRG 158
Query: 144 FCFISFDDQNVAEQVL-ANPKQVICGKEVDVKRVKFNPETM 183
F F+ F+ + AE+ + + + G+ + V++ + +
Sbjct: 159 FAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPR 199
>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 = 66.4 bits (163), Expect = 2e-14
Identities = 26/61 (42%), Positives = 39/61 (63%), Gaps = 4/61 (6%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
KLFVG L + E+++ F +YG +E ++I D TGQS+G AFV F++ QKA++
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 74 L 74
L
Sbjct: 61 L 61
Score = 52.9 bits (128), Expect = 2e-09
Identities = 20/50 (40%), Positives = 26/50 (52%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
K+FVG L +E+DVR F +YG+I E DK KG F+ F
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSS 50
>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 = 66.2 bits (161), Expect = 3e-14
Identities = 29/68 (42%), Positives = 42/68 (61%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+K+FVGG+ +T E + DYF QYG++E I I D +G+ RGFAFVTF +VD ++
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60
Query: 77 AGDHYIGN 84
H +
Sbjct: 61 QKYHTVNG 68
Score = 57.3 bits (138), Expect = 5e-11
Identities = 25/74 (33%), Positives = 42/74 (56%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGG+ + E +RDYF QYG I + D+ K+GF F++FDD + ++++
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61
Query: 162 PKQVICGKEVDVKR 175
+ G +V++
Sbjct: 62 KYHTVNGHNCEVRK 75
>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 = 66.2 bits (161), Expect = 3e-14
Identities = 29/75 (38%), Positives = 45/75 (60%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+K+FVGG+ +T E + DYF +YG++E+I + D +G+ RGFAFVTF VD ++
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 77 AGDHYIGNKKIDPKR 91
H I + K+
Sbjct: 61 QKYHTINGHNCEVKK 75
Score = 62.7 bits (152), Expect = 5e-13
Identities = 26/74 (35%), Positives = 42/74 (56%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGG+ + E +RDYF +YG I + D+ K+GF F++FDD + ++++
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61
Query: 162 PKQVICGKEVDVKR 175
I G +VK+
Sbjct: 62 KYHTINGHNCEVKK 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 = 66.1 bits (162), Expect = 3e-14
Identities = 28/71 (39%), Positives = 47/71 (66%), Gaps = 1/71 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
++FVGG+ +T E+E+ D+FS++G V+ + I D G S+G+ FVTF TQ+ + +LA
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62
Query: 78 GDHYIGNKKID 88
G+ KK++
Sbjct: 63 GNLNFRGKKLN 73
Score = 63.1 bits (154), Expect = 4e-13
Identities = 24/72 (33%), Positives = 50/72 (69%), Gaps = 1/72 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+IFVGG+ + +E+++RD+FS++GS+ + + D++ + KG+ F++F+ Q AE++LA
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKILAM 62
Query: 162 PKQVICGKEVDV 173
GK++++
Sbjct: 63 GNLNFRGKKLNI 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 = 65.5 bits (159), Expect = 5e-14
Identities = 28/79 (35%), Positives = 47/79 (59%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RKLF+GGL T + + ++F ++G + + DP T +SRGF FVT++ + VD ++
Sbjct: 3 RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62
Query: 77 AGDHYIGNKKIDPKRVTKR 95
A H + + ++PKR R
Sbjct: 63 ARPHKVDGRVVEPKRAVSR 81
Score = 41.2 bits (96), Expect = 3e-05
Identities = 22/75 (29%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD-DQNVAEQVLA 160
K+F+GGL+ E ++ +R++F ++G++T+ D +GF F+++ + V + A
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63
Query: 161 NPKQVICGKEVDVKR 175
P +V G+ V+ KR
Sbjct: 64 RPHKVD-GRVVEPKR 77
>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 = 65.4 bits (160), Expect = 5e-14
Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISI--KNDPHTGQSR-GFAFVTFTTQKAVDD 73
R+++V L E ++ FS++GEVESI I K D G+ GFAFVTF + ++
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60
Query: 74 LLAAGDHYIGNKKID 88
L +G +KI
Sbjct: 61 ALQLNGTELGGRKIS 75
Score = 42.6 bits (101), Expect = 8e-06
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 7/77 (9%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKK-----GFCFISFDDQNVAE 156
+I+V L ++ E D+R FS++G + + P K ++ K+ GF F++F D + AE
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIP--KKQDEKQGRLNNGFAFVTFKDASSAE 59
Query: 157 QVLANPKQVICGKEVDV 173
L + G+++ V
Sbjct: 60 NALQLNGTELGGRKISV 76
>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 = 64.2 bits (157), Expect = 1e-13
Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+FVG LT +++E+D+R YFSQ+G +T+ P + F F++F D VA+ +
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCG 55
Query: 161 NPKQVICGKEVDV 173
+I G V V
Sbjct: 56 E-DHIIKGVSVHV 67
Score = 57.7 bits (140), Expect = 3e-11
Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
RK+FVG L + E+++ YFSQ+GEV + I R FAFVTF + L
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCG 55
Query: 77 AGDHYIGNKKI 87
DH I +
Sbjct: 56 E-DHIIKGVSV 65
>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 = 63.9 bits (155), Expect = 2e-13
Identities = 29/79 (36%), Positives = 45/79 (56%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+KLFVGG+ +T E + DYF +YG++++I I D +G+ RGF FVTF VD ++
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60
Query: 77 AGDHYIGNKKIDPKRVTKR 95
H I + ++ R
Sbjct: 61 QKYHTINGHNAEVRKALSR 79
Score = 57.4 bits (138), Expect = 5e-11
Identities = 24/74 (32%), Positives = 42/74 (56%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVGG+ + E +RDYF +YG I + D+ K+GF F++FDD + ++++
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61
Query: 162 PKQVICGKEVDVKR 175
I G +V++
Sbjct: 62 KYHTINGHNAEVRK 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 = 63.5 bits (154), Expect = 2e-13
Identities = 30/73 (41%), Positives = 45/73 (61%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL +T E++I +YF +GEVESI + D T + RGF F+TF ++ V ++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 78 GDHYIGNKKIDPK 90
H +G K + K
Sbjct: 61 KYHNVGLSKCEIK 73
Score = 59.6 bits (144), Expect = 7e-12
Identities = 21/58 (36%), Positives = 38/58 (65%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
KIFVGGL+ + E+ +R+YF +G + + P D N ++GFCFI+F ++ ++++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 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 = 68.4 bits (167), Expect = 4e-13
Identities = 45/162 (27%), Positives = 73/162 (45%), Gaps = 13/162 (8%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
D+R +FV L E+++ ++FS+ G+V + D ++ +S+G A+V F ++
Sbjct: 84 EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVES 143
Query: 71 VDDLLAA-GDHYIG------------NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDV 117
V LA G +G N+ P K++VG L I+EQ++
Sbjct: 144 VIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQEL 203
Query: 118 RDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
R F +G I + Q D KGF FI F D A++ L
Sbjct: 204 RQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL 245
Score = 61.8 bits (150), Expect = 7e-11
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
A G N KL+VG LH N E+E+ F +G++E + + DP TG+S+GF F+
Sbjct: 176 ATHQPGDIPNF-LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQ 234
Query: 65 F 65
F
Sbjct: 235 F 235
Score = 35.6 bits (82), Expect = 0.020
Identities = 23/97 (23%), Positives = 44/97 (45%), Gaps = 3/97 (3%)
Query: 78 GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS 137
D G +P +R +FV L + E+D+ ++FS+ G + + Q D++
Sbjct: 70 DDRRSGRNTKEPLTEAERD---DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRN 126
Query: 138 KNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
KG ++ F D + LA Q++ G+ + V+
Sbjct: 127 SRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ 163
>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 = 61.9 bits (151), Expect = 9e-13
Identities = 26/74 (35%), Positives = 42/74 (56%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
KIFVGGL ++ +R YFSQ+G I E D+ +G+ F++F D+ AE+
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 161 NPKQVICGKEVDVK 174
+P +I G++ +V
Sbjct: 61 DPNPIIDGRKANVN 74
Score = 58.8 bits (143), Expect = 1e-11
Identities = 24/51 (47%), Positives = 33/51 (64%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
K+FVGGL +T + + YFSQ+GE+E + D TG+SRG+ FVTF
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKD 51
>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 = 1e-12
Identities = 29/75 (38%), Positives = 44/75 (58%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+K+FVGGL NT +++ YF Q+G+VE + D T + RGF FVTF + V+ +
Sbjct: 4 KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63
Query: 77 AGDHYIGNKKIDPKR 91
H I NK ++ K+
Sbjct: 64 IHFHEINNKMVECKK 78
Score = 59.3 bits (143), Expect = 9e-12
Identities = 28/74 (37%), Positives = 45/74 (60%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVGGL+ +DV+ YF Q+G + + FDK+ N +GF F++F++++V E+V
Sbjct: 5 KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEI 64
Query: 162 PKQVICGKEVDVKR 175
I K V+ K+
Sbjct: 65 HFHEINNKMVECKK 78
>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 = 61.2 bits (148), Expect = 2e-12
Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
KIFVGGL+ + +DV+ YF Q+G + + FDK+ N +GF F++F+ +++ E+V
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 161 -----NPKQVICGK 169
N K V C K
Sbjct: 61 HFHEINNKMVECKK 74
Score = 59.3 bits (143), Expect = 8e-12
Identities = 28/74 (37%), Positives = 44/74 (59%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+FVGGL NT +++ YF Q+G+V+ + D T + RGF FVTF ++ V+ +
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 78 GDHYIGNKKIDPKR 91
H I NK ++ K+
Sbjct: 61 HFHEINNKMVECKK 74
>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 = 61.1 bits (148), Expect = 2e-12
Identities = 28/74 (37%), Positives = 41/74 (55%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLFVGGL + GE ++ ++FSQ+G VE + D TG+ RGF FV F + D
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 78 GDHYIGNKKIDPKR 91
H I +++ K+
Sbjct: 61 KFHPINGHRVEVKK 74
Score = 56.8 bits (137), Expect = 7e-11
Identities = 25/74 (33%), Positives = 43/74 (58%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVGGL ++ E D+ ++FSQ+G + + + DK K+GF F+ F + + A++
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 162 PKQVICGKEVDVKR 175
I G V+VK+
Sbjct: 61 KFHPINGHRVEVKK 74
>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 = 59.8 bits (145), Expect = 6e-12
Identities = 28/76 (36%), Positives = 46/76 (60%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
KLFVGGL+ T + + +F++YG++ + DP+T +SRGF F+TF++ D+ +
Sbjct: 2 LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
Query: 76 AAGDHYIGNKKIDPKR 91
A H I +I+ KR
Sbjct: 62 EAQPHSIDGNQIELKR 77
Score = 58.3 bits (141), Expect = 2e-11
Identities = 26/77 (33%), Positives = 45/77 (58%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
CK+FVGGL + S+ +R +F++YG +TE D + +GF FI+F + A++ +
Sbjct: 3 CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62
Query: 161 NPKQVICGKEVDVKRVK 177
I G ++++KR K
Sbjct: 63 AQPHSIDGNQIELKRAK 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 = 59.5 bits (144), Expect = 7e-12
Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLF+GGL +T E+ + FS+YG++ + + D T +SRGF FVTF D + A
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 78 GDHYIGNKKIDPKRV 92
+ K +D +++
Sbjct: 62 ----MNGKSVDGRQI 72
Score = 46.4 bits (110), Expect = 4e-07
Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 4/76 (5%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+F+GGL+ + +EQ + FS+YG I+E D+ +GF F++F++ + A+ +
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAM-- 59
Query: 162 PKQVICGKEVDVKRVK 177
+ GK VD ++++
Sbjct: 60 --MAMNGKSVDGRQIR 73
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 59.1 bits (144), Expect = 9e-12
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA- 77
L+V L + E+++ ++FS YG+VE + + + + RGFAFV F + + + L
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58
Query: 78 GDHYIGNKKI 87
+ + +
Sbjct: 59 NGLVLDGRTL 68
Score = 58.7 bits (143), Expect = 1e-11
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-N 161
++V L ++E+D+R++FS YG + + ++K+ +GF F+ F AE L
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVR--LVRNKDRPRGFAFVEFASPEDAEAALKKL 58
Query: 162 PKQVICGKEV 171
V+ G+ +
Sbjct: 59 NGLVLDGRTL 68
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 4/76 (5%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+ LFV L+ +T E ++ F +YG ++ I + D TG+ RG+AF+ F ++ D+ A
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER---DMKA 58
Query: 77 AGDHYIGNKKIDPKRV 92
A + G KKID +RV
Sbjct: 59 AYKYADG-KKIDGRRV 73
Score = 39.9 bits (94), Expect = 9e-05
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+FV L + +E +R F +YG I + DK +G+ FI F+ +
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER 54
>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 = 57.3 bits (139), Expect = 4e-11
Identities = 19/47 (40%), Positives = 31/47 (65%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+VG LH N E ++ F +GE+E + ++ DP TG+S+G+ F+ F
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQF 47
Score = 43.8 bits (104), Expect = 3e-06
Identities = 20/59 (33%), Positives = 28/59 (47%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++VG L I+E D+R F +G I Q D KG+ FI F D A++ L
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59
>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 = 56.8 bits (138), Expect = 7e-11
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
FVG L + E+E+ +F G+VE++ I D TG +GF +V F T+ +V L
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62
Query: 80 HYIGNKKIDPKRVT 93
+ +KI RV
Sbjct: 63 IKLKGRKI---RVK 73
Score = 40.2 bits (95), Expect = 6e-05
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FVG L +I E+++R +F G + + D+ + KGF ++ F ++ L
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61
Query: 163 KQVICGKEVDVK 174
+ G+++ VK
Sbjct: 62 GIKLKGRKIRVK 73
>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 = 56.9 bits (138), Expect = 7e-11
Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V GL T E+++ + FS+YG +E + + D TG+SRGF FV F + V+D A
Sbjct: 2 LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES---VEDAKEAK 58
Query: 79 D 79
+
Sbjct: 59 E 59
Score = 49.9 bits (120), Expect = 2e-08
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 4/73 (5%)
Query: 105 VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQ 164
V GL+ +E+D+R+ FS+YG I + Q +D+ +GF F+ F+ +V + A K+
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFE--SVEDAKEA--KE 59
Query: 165 VICGKEVDVKRVK 177
+ G E+D +R++
Sbjct: 60 RLNGMEIDGRRIR 72
>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 = 56.0 bits (135), Expect = 2e-10
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
ERKLFVG L + E ++ F+ +G +E ++ D GQSRG AFVTF +++
Sbjct: 1 ERKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQC 54
Score = 40.6 bits (95), Expect = 6e-05
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
K+FVG L+ + +E DVR F+ +GSI E D++ +G F++F + A
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQCA 55
>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 = 60.0 bits (145), Expect = 2e-10
Identities = 58/248 (23%), Positives = 96/248 (38%), Gaps = 18/248 (7%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V L + ++EI F+ GE+ES + D TGQS G+ FV + + D A
Sbjct: 6 LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPE---DAEKAV 62
Query: 79 DHYIG----NKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
+ G NK I + +K ++V GL +++ ++ FS +G I +
Sbjct: 63 NSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRIL 122
Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGA 193
D + KG FI FD ++ A++ + + VKF S S +
Sbjct: 123 SDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQ 182
Query: 194 GARVASAGTAYAAAPGRVVAYPSTYAG-----YAATDYGYTAGSYDAYATAYPGYDYSAM 248
V + T ++ T AG +AA + +AG + A A
Sbjct: 183 LEAVQNPQT-----TRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQ 237
Query: 249 GYAYPAAA 256
+A A+
Sbjct: 238 QHAAQRAS 245
Score = 42.2 bits (99), Expect = 1e-04
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 3/86 (3%)
Query: 1 MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF 60
+A A A G +FV L +T E + F +G V+++ I D T Q +G+
Sbjct: 256 LAAGAQIAASDGAG--YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGY 313
Query: 61 AFVTFTT-QKAVDDLLAAGDHYIGNK 85
FV+ T +A +L+ + +GN+
Sbjct: 314 GFVSMTNYDEAAMAILSLNGYTLGNR 339
Score = 27.6 bits (61), Expect = 7.0
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K + V L ++++++R F+ G I + DK G+ F+++ AE+
Sbjct: 3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60
Score = 27.6 bits (61), Expect = 8.7
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
IFV L+ + E + F +G++ + D + N KG+ F+S N E +A
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSM--TNYDEAAMA 327
>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 = 55.4 bits (134), Expect = 2e-10
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISI---KNDPHTGQSRGFAFVTFTTQKAVDD- 73
+L++G L E + FS+YG+++ K+ P GQ RG+ FVTF T++ +
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 74 LLAAGDHYIGNKKI 87
L + KK+
Sbjct: 61 LKSLNGKTALGKKL 74
Score = 45.3 bits (108), Expect = 9e-07
Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKK---GFCFISFDDQNVAEQV 158
++++G L + ++E + FS+YG I +F F KS +K G+CF++F+ + AE+
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 159 L--ANPKQV 165
L N K
Sbjct: 61 LKSLNGKTA 69
>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 = 60.2 bits (146), Expect = 3e-10
Identities = 45/164 (27%), Positives = 77/164 (46%), Gaps = 32/164 (19%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L+V L + E ++ + F+++GE+ S ++ D +G+SRGFAFV F KAV+++
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239
Query: 75 LAAGDHYIGNKKIDPK----RVTKRV---NPLKCK----------------IFVGGLTTE 111
IG K K R KR L+ K ++V L
Sbjct: 240 ---NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDT 296
Query: 112 ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
++++ +R+ FS+ G IT + D+ K + +GF F+ F + A
Sbjct: 297 VTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEA 339
Score = 54.8 bits (132), Expect = 2e-08
Identities = 44/173 (25%), Positives = 75/173 (43%), Gaps = 34/173 (19%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L+VG L + E ++ D F +G V S+ + D T +S G+ +V F ++A++
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE-- 60
Query: 75 LAAGDHYIGNKKI-------DP-KRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
+G K I DP R + N IFV L + + + D FS++G+
Sbjct: 61 -TMNFKRLGGKPIRIMWSQRDPSLRRSGVGN-----IFVKNLDKSVDNKALFDTFSKFGN 114
Query: 127 ITE---FQQPFDKSKNMKKGFCFISFDDQNVAEQ-------VLANPKQVICGK 169
I KS +G+ F+ F+ + A+ +L N K+V G+
Sbjct: 115 ILSCKVATDENGKS----RGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGR 163
Score = 40.9 bits (96), Expect = 4e-04
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
L+V L ++++ + FS+ GE+ S + D G SRGF FV F+ + + +
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAV 343
>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 = 54.5 bits (131), Expect = 5e-10
Identities = 27/61 (44%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDD 73
KLFVG L++ EKE+ + FS YG VE I + D QSRG AFV + Q A+
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKA 59
Query: 74 L 74
L
Sbjct: 60 L 60
Score = 34.4 bits (79), Expect = 0.009
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
K+FVG L + +E++V + FS YG + + D+ K +G F+ + + +A+ +
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIK 58
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 54.6 bits (132), Expect = 5e-10
Identities = 25/60 (41%), Positives = 38/60 (63%), Gaps = 4/60 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK----AVDDL 74
+++GGL E +I FSQYGE+ I++ D TG+S+GFAF+ + Q+ AVD+L
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71
Score = 53.0 bits (128), Expect = 2e-09
Identities = 21/50 (42%), Positives = 31/50 (62%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
I++GGL E++E D+ FSQYG I + DK KGF F++++DQ
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQ 61
>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 = 55.0 bits (133), Expect = 5e-10
Identities = 19/54 (35%), Positives = 32/54 (59%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
LFVG L T E+ + + FS+YG++ + + D TG S+G+AFV + ++
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDAL 59
Score = 36.5 bits (85), Expect = 0.002
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+FVG L+ + +E+ +R+ FS+YG I + D KG+ F+ ++ + A +
Sbjct: 3 YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62
Query: 160 -ANPKQVICGKE--VDVKR 175
K VI G E VD +R
Sbjct: 63 RDAHKLVIDGSEIFVDFER 81
>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 = 54.5 bits (132), Expect = 6e-10
Identities = 25/63 (39%), Positives = 37/63 (58%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R +F+ L + E+E+ + FSQ+GEV+ I D TG S+G AFV F T+++ L
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 77 AGD 79
A D
Sbjct: 61 AAD 63
Score = 36.4 bits (85), Expect = 0.001
Identities = 15/64 (23%), Positives = 31/64 (48%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+F+ L + +E+++++ FSQ+G + + DK KG F+ F + A++ L
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 161 NPKQ 164
Sbjct: 61 AADN 64
>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 = 53.8 bits (130), Expect = 9e-10
Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L+VGGL EK ++ F +G+++ I I D T + RGFAFV F +D AA
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEP---EDAAAAI 57
Query: 79 D 79
D
Sbjct: 58 D 58
Score = 49.5 bits (119), Expect = 2e-08
Identities = 18/59 (30%), Positives = 30/59 (50%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++VGGL E+ E+ + F +G I + Q P D +GF F+ F++ A + N
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59
>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 = 53.3 bits (128), Expect = 1e-09
Identities = 22/64 (34%), Positives = 43/64 (67%), Gaps = 1/64 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+IFVGG+ + +E D+R +FSQYG++ E + D++ + KG+ F++F+ Q A+++L
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRA-GVSKGYGFVTFETQEDAQKILQE 62
Query: 162 PKQV 165
++
Sbjct: 63 ANRL 66
Score = 52.1 bits (125), Expect = 4e-09
Identities = 25/62 (40%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
++FVGG+ T E ++ +FSQYG V+ + I ND G S+G+ FVTF TQ+ +L
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62
Query: 78 GD 79
+
Sbjct: 63 AN 64
>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 = 53.1 bits (128), Expect = 2e-09
Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
LF+G L EK + D FS +G +++ I DP TG S+GFAF+++ + +A D + A
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 78 -GDHYIGNKKI 87
Y+ N+ I
Sbjct: 64 MNGQYLCNRPI 74
Score = 40.7 bits (96), Expect = 4e-05
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLAN 161
+F+G L E+ E+ + D FS +G I + + KGF FIS+D ++ +
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 162 PK-QVICGKEVDV 173
Q +C + + V
Sbjct: 64 MNGQYLCNRPITV 76
>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 = 52.4 bits (126), Expect = 2e-09
Identities = 23/69 (33%), Positives = 36/69 (52%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LFVG L +T +++ +F G S+ + D TG+S+G AFV F T +A+ L
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 79 DHYIGNKKI 87
+ +KI
Sbjct: 63 HTLLKGRKI 71
Score = 44.3 bits (105), Expect = 2e-06
Identities = 15/57 (26%), Positives = 25/57 (43%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+FVG L + + +D+ +F G+ + DK KG F+ FD + L
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL 59
>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 = 5e-09
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
KIF+GGL +SE V++ +G + F D + + KG+ F + D +V +Q +A
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 161 -NPKQVICGKEVDVKR 175
N Q + K++ V+R
Sbjct: 62 LNGMQ-LGDKKLTVQR 76
Score = 48.8 bits (117), Expect = 6e-08
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+F+GGL E ++ + +G++++ ++ D TG S+G+AF + D +A
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 78 -GDHYIGNKKIDPKR 91
+G+KK+ +R
Sbjct: 62 LNGMQLGDKKLTVQR 76
>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 = 51.7 bits (124), Expect = 6e-09
Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 2/55 (3%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTTQKA 70
K+FVG + R+ EK++ + F QYG V I++ D QS+G FVTF T+KA
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKA 57
Score = 43.6 bits (103), Expect = 5e-06
Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN--MKKGFCFISF 149
K+FVG + SE+D+R+ F QYG++ + D+S+N KG CF++F
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52
>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 = 51.5 bits (124), Expect = 6e-09
Identities = 19/48 (39%), Positives = 30/48 (62%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+LFV L T E+E+ + F +GE+ + + D T +S+GFAFV+F
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSF 48
Score = 44.2 bits (105), Expect = 2e-06
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
++FV L +E+++R+ F +G I+E P DK KGF F+SF
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMF 50
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to
the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contain three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. On the other hand, both RRM1 and RRM2 of
CELF-4 can activate cardiac troponin T (cTNT) exon 5
inclusion. CELF-5, expressed in brain, is also known as
bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein
6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent
manner and can activate inclusion via multiple copies
of a single element, MSE2. CELF-6 also promotes
skipping of exon 11 of insulin receptor, a known target
of CELF activity that is expressed in kidney. In
additiona to three highly conserved RRMs, CELF-6 also
possesses numerous potential phosphorylation sites, a
potential nuclear localization signal (NLS) at the C
terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 51.6 bits (124), Expect = 7e-09
Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
D KLFVG + RN EK++ F Q+G++ +++ D +TG +G AF+T+
Sbjct: 4 DAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 54
Score = 40.8 bits (96), Expect = 5e-05
Identities = 19/55 (34%), Positives = 29/55 (52%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
K+FVG + + E+D+R F Q+G I E DK M KG F+++ + A
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61
>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 = 51.1 bits (123), Expect = 7e-09
Identities = 20/68 (29%), Positives = 37/68 (54%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
FVG + T +E+ ++F G + I+I D TGQ +GFA++ F + +V++ L +
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62
Query: 80 HYIGNKKI 87
++I
Sbjct: 63 SEFRGRQI 70
Score = 40.0 bits (94), Expect = 7e-05
Identities = 19/71 (26%), Positives = 35/71 (49%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
IFVG + + ++++++F G+I DK KGF +I F D++ E L
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61
Query: 163 KQVICGKEVDV 173
+ G+++ V
Sbjct: 62 ESEFRGRQIKV 72
>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 = 50.8 bits (122), Expect = 8e-09
Identities = 23/52 (44%), Positives = 34/52 (65%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
++VGG+ + E EI YFS GE+E + + P TG+ RG AF+TF T++A
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEA 52
Score = 42.3 bits (100), Expect = 9e-06
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQ-QPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
++VGG+ +E ++R YFS G I E F + +G FI+F + A++ LA
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRF-RGIAFITFKTEEAAKRALA 58
>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 = 55.5 bits (133), Expect = 8e-09
Identities = 56/238 (23%), Positives = 97/238 (40%), Gaps = 31/238 (13%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA- 76
+++VG + E I F +G ++SI++ DP TG+ +GFAFV + +A LA
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAA--QLAL 166
Query: 77 --AGDHYIGNKKIDPKR-------------VTKRVNPLKCKIFVGGLTTEISEQDVRDYF 121
+G + I R V + +I+V + ++SE D++ F
Sbjct: 167 EQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFN-RIYVASVHPDLSETDIKSVF 225
Query: 122 SQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN-------PKQVICGKEVDVK 174
+G I + Q + KG+ FI +++ + +A+ + + GK V
Sbjct: 226 EAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP 285
Query: 175 RVKFNPETMGSVSGAVRGAGARV-----ASAGTAYAAAPGRVVAYPSTYAGYAATDYG 227
P T+ ++ A A A A+ A AA G P+T + TD G
Sbjct: 286 DALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGAAVLGPRAQSPATPSSSLPTDIG 343
Score = 37.4 bits (86), Expect = 0.006
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
+ C+++VG ++ E+ E +R F +G I +D + KGF F+ ++ A+
Sbjct: 106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLA 165
Query: 159 LANPK-QVICGKEVDVKRVKFNPETMG 184
L Q++ G+ + V R P M
Sbjct: 166 LEQMNGQMLGGRNIKVGR----PSNMP 188
>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 = 50.7 bits (122), Expect = 9e-09
Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 6/52 (11%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
L+VGGL EK++ D+F Q+GE+ SI++ + AFVTFTT++A
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREA 49
Score = 43.4 bits (103), Expect = 5e-06
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 14/79 (17%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNM--KKGFCFISFDDQNVAEQV 158
++VGGL ++E+D+RD+F Q+G I +S + ++ F++F + AE+
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEI--------RSITVVPRQQCAFVTFTTREAAEKA 53
Query: 159 ---LANPKQVICGKEVDVK 174
L N K +I G+ + +K
Sbjct: 54 AERLFN-KLIINGRRLKLK 71
>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 = 50.9 bits (122), Expect = 9e-09
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 9/83 (10%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D +LFVG L + E E+ ++F ++G V + I + G+ F FV F +AV +
Sbjct: 2 DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61
Query: 75 LAA------GDHYIGNKKIDPKR 91
LA GDH + ++ K+
Sbjct: 62 LANKPIYFRGDHRL---NVEEKK 81
Score = 48.2 bits (115), Expect = 1e-07
Identities = 17/60 (28%), Positives = 35/60 (58%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++FVG L +I+E +++++F ++G++ E + F F+ FDD +++LAN
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 9/73 (12%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ--V 158
++VG L ++E++++ FS +G+I E + KG+ F+ FD A V
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRV------FKDKGYAFVRFDTHEAAATAIV 54
Query: 159 LANPKQVICGKEV 171
N I G+ V
Sbjct: 55 AVN-GTSINGQTV 66
Score = 33.7 bits (78), Expect = 0.012
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
++VG L E+E+ FS +G +E + + D +G+AFV F T +A
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEA 48
>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 = 50.8 bits (122), Expect = 1e-08
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
++V L +N + + FS+YG V +S+ HTG +GFAF+ F T QKA L
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 75 LAAGDHYIGNKKIDPKRVT 93
+ PK V
Sbjct: 62 NNPPETATDKPGKFPKTVA 80
Score = 38.5 bits (90), Expect = 3e-04
Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 4/79 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
++V L + + ++ FS+YG++ P K KGF FI F+ A++
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 161 --NPKQVICGKEVDVKRVK 177
P+ K V
Sbjct: 62 NNPPETATDKPGKFPKTVA 80
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 6/58 (10%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+C++FVG L +I+E++ ++ FS+YG ++E N +KGF FI D + AE+
Sbjct: 1 RCRLFVGNLPNDITEEEFKELFSKYGEVSEV------FLNKEKGFGFIRLDTRTNAEK 52
Score = 40.7 bits (96), Expect = 4e-05
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 6/50 (12%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
+LFVG L + E+E + FS+YGEV + + + +GF F+ T
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDT 46
>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 = 50.2 bits (121), Expect = 2e-08
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L+VG LH + E + + FS G V SI + D T +S G+A+V F ++A+D L
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61
Query: 75 LAAGDHYIGNKKI 87
I K I
Sbjct: 62 ---NFDVIKGKPI 71
Score = 33.7 bits (78), Expect = 0.011
Identities = 13/56 (23%), Positives = 27/56 (48%)
Query: 104 FVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+VG L +++E + + FS G + + D G+ +++F + AE+ L
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERAL 58
>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 = 50.4 bits (120), Expect = 2e-08
Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
+RKLF+G + + E +I FS +G++E I P G SRG AFVTFTT+ +
Sbjct: 1 DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 59
Query: 76 AA 77
A
Sbjct: 60 KA 61
Score = 36.2 bits (83), Expect = 0.002
Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K+F+G ++ + +E D+R FS +G I E + + +G F++F + +A+ +
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEE-CRILRGPDGLSRGCAFVTFTTRAMAQTAI 59
>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 = 50.1 bits (120), Expect = 2e-08
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 7/77 (9%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRG-FAFVTFTTQKAVDDL 74
ER +FV G R T E+++ DYFS +G V ++ + D +G +A V F +++ VD +
Sbjct: 2 ERSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDKV 55
Query: 75 LAAGDHYIGNKKIDPKR 91
L+ H + ++ +
Sbjct: 56 LSEPQHTLNGHRLRVRP 72
Score = 42.8 bits (101), Expect = 7e-06
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV G SE+ + DYFS +G + DK K + + FD + ++VL+ P
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVI--MDKD---KGVYAIVEFDSKEGVDKVLSEP 59
Query: 163 KQVICGKEVDVKR 175
+ + G + V+
Sbjct: 60 QHTLNGHRLRVRP 72
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 49.9 bits (120), Expect = 2e-08
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+FVG + R+ E E+ F + G + + + D +G +RG+AFVT+T ++A +
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDF-SGLNRGYAFVTYTNKEAAQRAVKQL 62
Query: 79 DHYIGNK 85
+Y
Sbjct: 63 HNYEIRP 69
Score = 32.1 bits (74), Expect = 0.038
Identities = 14/62 (22%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
C++FVG + ++ E ++ F + G I E + D S +G+ F+++ ++ A++ +
Sbjct: 1 GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAV 59
Query: 160 AN 161
Sbjct: 60 KQ 61
>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 = 50.0 bits (119), Expect = 3e-08
Identities = 20/55 (36%), Positives = 31/55 (56%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
KLFVG + R E+E+ F ++G V ++I D TG +G FV ++T+ D
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEAD 55
Score = 42.6 bits (100), Expect = 9e-06
Identities = 18/58 (31%), Positives = 35/58 (60%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K+FVG + I+EQ+VR F ++G++ E DK ++G CF+ + ++ A++ +
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
>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 = 49.5 bits (119), Expect = 3e-08
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
LFVGGL + E ++ + FS++G V + I G RGFA++ T
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRT 50
Score = 41.8 bits (99), Expect = 2e-05
Identities = 14/48 (29%), Positives = 29/48 (60%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+FVGGL+ ++E D+ + FS++G++++ + K +GF +I
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49
>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 = 49.5 bits (119), Expect = 3e-08
Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 27 NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDLLAAG-DHY 81
+ E ++ + F +G + + + D TGQSRGFAFVTF T ++A++ L G D+
Sbjct: 10 DADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYDNL 69
Query: 82 I 82
I
Sbjct: 70 I 70
Score = 42.1 bits (100), Expect = 1e-05
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 108 LTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
L+ + E D+R+ F +G I+ DK +GF F++F + AE+ +
Sbjct: 7 LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59
>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 = 48.3 bits (116), Expect = 7e-08
Identities = 18/62 (29%), Positives = 30/62 (48%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L VG L RN + + + FS YG V+ + + D RG+A+V F + + + +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 79 DH 80
D
Sbjct: 61 DG 62
Score = 42.2 bits (100), Expect = 1e-05
Identities = 15/55 (27%), Positives = 33/55 (60%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+ VG LT +++ +++ FS YG++ + P D+ N+ +G+ ++ F+ AE+
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEK 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 = 48.4 bits (116), Expect = 7e-08
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF-TTQKAVDDLLAA 77
LF+ L ++++ F+ +G V S + D +TGQS+ F FV++ + A + A
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 78 GDHYIGNKKI 87
+G K++
Sbjct: 61 NGFQVGGKRL 70
Score = 40.3 bits (95), Expect = 4e-05
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+F+ L E ++QD+ F+ +G++ + DK+ K F F+S+D+ A
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESA----QAA 56
Query: 163 KQVICGKEVDVKRVK 177
+ + G +V KR+K
Sbjct: 57 IKAMNGFQVGGKRLK 71
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 50.4 bits (120), Expect = 7e-08
Identities = 25/111 (22%), Positives = 52/111 (46%), Gaps = 4/111 (3%)
Query: 99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
+ K+F+GGL+ + +RD F+ +G + + + D+ +GF F++F+D+ A
Sbjct: 33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAA 92
Query: 159 LANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPG 209
++ + GKE++ + ++ NP + G G + G Y
Sbjct: 93 ISE----MDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGD 139
Score = 48.5 bits (115), Expect = 3e-07
Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KLF+GGL T + + D F+ +G+V + D TG+SRGF FV F + A ++
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95
Query: 78 GDHYIGNKKIDPKRVTKRVNP 98
D K+++ + + RVNP
Sbjct: 96 MD----GKELNGRHI--RVNP 110
>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 = 52.6 bits (126), Expect = 7e-08
Identities = 38/203 (18%), Positives = 78/203 (38%), Gaps = 43/203 (21%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG---------QSRGFAFVTFTT 67
R+L+VGG+ E+ + D+F+ + + + G + + FAF+ F T
Sbjct: 176 RRLYVGGIPPEFVEEAVVDFFND---LMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRT 232
Query: 68 QK------AVDDLLAAG--------DHYIGNKKIDPKRVTKRVN---------------- 97
+ A+D ++ + YI +I P+ K +
Sbjct: 233 VEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVL 292
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K +I++G L + E +++ +G + F D + + KG+ F + D +V +
Sbjct: 293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDV 352
Query: 158 VLANPKQVICG-KEVDVKRVKFN 179
+A G ++ V+R
Sbjct: 353 AIAALNGKDTGDNKLHVQRACVG 375
Score = 43.0 bits (101), Expect = 1e-04
Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
+ ++++G L GE +I + +G++++ ++ D TG S+G+AF + D +
Sbjct: 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354
Query: 76 AAGDHY-IGNKKIDPKRVTKRVNP 98
AA + G+ K+ +R N
Sbjct: 355 AALNGKDTGDNKLHVQRACVGANQ 378
>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 = 48.3 bits (115), Expect = 7e-08
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
LFV L + ++++ D+FS ++ + DP TG+SRG+ FVTF
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFA 49
Score = 31.0 bits (70), Expect = 0.11
Identities = 16/65 (24%), Positives = 29/65 (44%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV L ++++D+ D+FS I D +G+ F++F A++ LA
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 163 KQVIC 167
K
Sbjct: 62 KNKKL 66
>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 = 48.1 bits (115), Expect = 8e-08
Identities = 23/61 (37%), Positives = 33/61 (54%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V L T ++ F +YGEV + I D +T +SRGFAFV F ++ +D + A
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Query: 79 D 79
D
Sbjct: 61 D 61
Score = 40.7 bits (96), Expect = 4e-05
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 105 VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
V LT + D+R F +YG + + P D+ +GF F+ F D+ AE
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAE 54
>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 = 48.5 bits (116), Expect = 8e-08
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 18 KLFVGGLHRNTGEKEIND----YFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
+FV G + GE +I +FS GE+ +SI D TG S+GFA++ F + V+
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60
Query: 74 LL 75
L
Sbjct: 61 AL 62
Score = 33.1 bits (76), Expect = 0.023
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 102 KIFVGGLTTEISEQDVRD----YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
IFV G + + E D+R +FS G IT P D+ KGF +I F + E+
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60
Query: 158 VL 159
L
Sbjct: 61 AL 62
>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 = 48.5 bits (116), Expect = 8e-08
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
IFVG L+ +++++++ + FS++G I E K N F FI F+ + A + + +
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVN--LIKRANHTNAFAFIKFEREQAAARAVESE 63
Query: 163 K-QVICGKEVDVKR 175
++ K + V+
Sbjct: 64 NHSMLKNKTMHVQY 77
Score = 47.7 bits (114), Expect = 1e-07
Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDPHTGQSRGFAFVTFTTQKAVDD 73
D+ +FVG L + ++E+N+ FS++G++ ++ IK HT FAF+ F ++A
Sbjct: 2 DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHT---NAFAFIKFEREQAAAR 58
Query: 74 LLAAGDHYIGNKKIDPKRVTKR 95
+ + +H + K V +
Sbjct: 59 AVESENHSMLKNK--TMHVQYK 78
>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 = 47.8 bits (114), Expect = 1e-07
Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ----KAVDDL 74
LFVG L + E I + F +YGE+ S+ + DP +G+ +GF +V F++Q A+D L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Score = 42.7 bits (101), Expect = 6e-06
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-AN 161
+FVG L+ + E + + F +YG I+ + P D KGF ++ F Q A+ L A
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 162 PKQVICGKEV 171
+ G+ V
Sbjct: 61 GGTDLLGRPV 70
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVG + + +E+ + + FS+ G + F+ D+ KG+ F F+D A + N
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN 59
Score = 45.7 bits (109), Expect = 7e-07
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDDL 74
FVG + + E+++ + FS+ G V S + D TG+ +G+ F F T A+ +L
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
>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 = 48.0 bits (114), Expect = 1e-07
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
+FV + + +D+R F +YG I + P D +GF ++ F+D AE L N
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 162 PKQVICGKEVDVK 174
++ ICG++++++
Sbjct: 63 DRKWICGRQIEIQ 75
Score = 31.9 bits (72), Expect = 0.065
Identities = 17/57 (29%), Positives = 31/57 (54%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
LFV + +T +++ F +YG + + + D +T + RGFA+V F + +D L
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL 59
>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 = 47.4 bits (113), Expect = 2e-07
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
IFVG L+ EI + +R F+ +G I++ + D KG+ F+SF + AE + +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 163 K-QVICGKEV 171
Q + G+ +
Sbjct: 62 NGQWLGGRAI 71
Score = 45.8 bits (109), Expect = 5e-07
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
+FVG L + + F+ +GE+ + D TG+S+G+ FV+F +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKK 51
>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 = 47.3 bits (113), Expect = 2e-07
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
L++G L E I F++ GEV S+ I + TG+S G+ FV F T +A
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEA 53
Score = 39.2 bits (92), Expect = 2e-04
Identities = 14/57 (24%), Positives = 26/57 (45%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+++G L + E + F++ G +T + +K G+ F+ F AEQ L
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQAL 58
>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 = 46.8 bits (112), Expect = 3e-07
Identities = 16/52 (30%), Positives = 32/52 (61%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
FV L E+++ ++FS+ G+V + I D ++ +S+G A+V F +++V
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54
Score = 34.1 bits (79), Expect = 0.008
Identities = 17/72 (23%), Positives = 38/72 (52%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV L+ ++ E+D+ ++FS+ G + + + D++ KG ++ F D+ L
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLT 61
Query: 163 KQVICGKEVDVK 174
Q + G+ + V+
Sbjct: 62 GQRLLGQPIMVQ 73
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 47.2 bits (113), Expect = 3e-07
Identities = 16/51 (31%), Positives = 35/51 (68%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
+FV G+H E++++D F+++GE++++ + D TG +G+A + + T+K
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKK 59
Score = 39.1 bits (92), Expect = 2e-04
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
IFV G+ E E+DV D F+++G I D+ KG+ I ++ + A+ +
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 162 PKQVICGKEVDV 173
+ + G+ + V
Sbjct: 69 NGKELLGQTISV 80
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 46.8 bits (112), Expect = 3e-07
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
++V L + ++++ + F +YG++ S + D G+S+GF FV F QKAV++L
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEEL 62
Score = 37.9 bits (89), Expect = 4e-04
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 11/77 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD---KSKNMKKGFCFISFDDQNVAEQVL 159
++V L ++ ++ +++ F +YG IT + D KS KGF F++F++ A++ +
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKS----KGFGFVNFENHEAAQKAV 59
Query: 160 ANPKQVICGKEVDVKRV 176
+ GKEV+ K++
Sbjct: 60 EE----LNGKEVNGKKL 72
>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 = 46.5 bits (111), Expect = 3e-07
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 7/63 (11%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISI-KNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
K++VG L ++E+ D F +YG + S+ + +N P GFAFV F + +D +
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP------GFAFVEFEDPRDAEDAVR 54
Query: 77 AGD 79
A D
Sbjct: 55 ALD 57
Score = 36.8 bits (86), Expect = 8e-04
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 14/77 (18%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE----FQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K++VG L +++++ D F +YG + P GF F+ F+D AE
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---------GFAFVEFEDPRDAED 51
Query: 158 -VLANPKQVICGKEVDV 173
V A + ICG V V
Sbjct: 52 AVRALDGRRICGNRVRV 68
>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 = 46.6 bits (111), Expect = 4e-07
Identities = 17/59 (28%), Positives = 27/59 (45%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
++FV L E D+ FS++G ++E DK KGF ++ F D A +
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62
Score = 46.2 bits (110), Expect = 5e-07
Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+LFV L + E ++ FS++GE+ + + D +G+S+GFA+V F
Sbjct: 4 RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF 51
>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 = 46.7 bits (111), Expect = 4e-07
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
+RKLFVG L + E ++ F +G +E +I P G S+G AFV F++
Sbjct: 1 DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSSH 52
Score = 34.3 bits (79), Expect = 0.007
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE 129
K+FVG L+ + +E DVR F +G+I E
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEE 30
>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 = 46.5 bits (110), Expect = 4e-07
Identities = 21/64 (32%), Positives = 39/64 (60%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
++FVG + R+ E E+ F + G + + + DP +GQ+RG+AF+TF ++A + +
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62
Query: 78 GDHY 81
D+Y
Sbjct: 63 CDNY 66
Score = 30.7 bits (69), Expect = 0.14
Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV--L 159
++FVG + ++ E ++ F + G I + + D +G+ FI+F + A++ L
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62
Query: 160 ANPKQVICGKEVDV 173
+ ++ GK + V
Sbjct: 63 CDNYEIRPGKHLGV 76
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 46.3 bits (110), Expect = 5e-07
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
C+++VG ++ E+ E +R FS +G I +D KGF F+ ++
Sbjct: 1 CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYE 50
Score = 42.4 bits (100), Expect = 1e-05
Identities = 19/53 (35%), Positives = 31/53 (58%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
+++VG + GE I FS +G ++SI + DP T + +GFAFV + +A
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEA 54
>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 = 5e-07
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV L + E ++R FS+ G IT+ + + K KG+ ++ F+++ ++ L
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEALKLD 60
Query: 163 KQVICGK 169
+++I G+
Sbjct: 61 RELIKGR 67
Score = 45.7 bits (109), Expect = 5e-07
Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+FV L + E E+ FS+ GE+ + + + + G+S+G+A+V F +++V + L
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEESVQEALK 58
>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 = 45.6 bits (108), Expect = 6e-07
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 8/60 (13%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
K+FVG L E +EQ++R F QYG + E ++ K + F+ DD+ A++ + N
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLEC--------DIIKNYGFVHMDDKTAADEAIRN 53
Score = 44.5 bits (105), Expect = 2e-06
Identities = 24/65 (36%), Positives = 30/65 (46%), Gaps = 10/65 (15%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
KLFVG L E+EI F QYG+V E IKN + FV + A D+ +
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN---------YGFVHMDDKTAADEAIR 52
Query: 77 AGDHY 81
HY
Sbjct: 53 NLHHY 57
>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 = 50.0 bits (119), Expect = 6e-07
Identities = 50/193 (25%), Positives = 89/193 (46%), Gaps = 31/193 (16%)
Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
PGR E +FVG + R+ E E+ F + G + + + D +GQ+RG+AFVTF ++
Sbjct: 55 PGRGCE--VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEE 111
Query: 71 VDDLLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSI 127
+ + ++Y +I P R V V+ C++FVGG+ +++ + FS+ +
Sbjct: 112 AKEAVKLLNNY----EIRPGRLLGVCISVD--NCRLFVGGIPKNKKREEILEEFSK---V 162
Query: 128 TE-------FQQPFDKSKNMKKGFCFISFDDQNVAEQV---LANPKQVICGKEVDVK--- 174
TE + DK KN +GF F+ ++ A L + + G + V
Sbjct: 163 TEGVVDVIVYHSAADKKKN--RGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAE 220
Query: 175 -RVKFNPETMGSV 186
+ + + M V
Sbjct: 221 PEEEVDEDVMAKV 233
Score = 34.2 bits (78), Expect = 0.071
Identities = 64/273 (23%), Positives = 100/273 (36%), Gaps = 52/273 (19%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGE--VESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
D +LFVGG+ +N +EI + FS+ E V+ I + ++RGFAFV + + +A
Sbjct: 137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAA 196
Query: 73 DL---LAAGD-----HYIGNKKIDPKRVTKRVNPLKCKI-FVGGLTTEISEQDVRDYFSQ 123
L G H I +P+ K KI +V L T +E+ + FS+
Sbjct: 197 MARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSE 256
Query: 124 YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN---------PKQVICGKEVDVK 174
+ ++ K ++ + F+ F+D+ A + + +V K VD K
Sbjct: 257 FKP-----GKVERVKKIRD-YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKK 310
Query: 175 ---RVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYA------------ 219
R G A R + +V + A Y YA
Sbjct: 311 SYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYED--YYYHPPYAPSLHFPRMPGPI 368
Query: 220 ---------GYAATDYGYTAGSYDAYATAYPGY 243
AA GY Y+AY Y GY
Sbjct: 369 RGRGRGGAPSRAAGGRGYPPYGYEAYYGDYYGY 401
>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 = 45.4 bits (107), Expect = 9e-07
Identities = 21/56 (37%), Positives = 35/56 (62%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
++FVG + R+ E E+ F + G + + + DP TG +RG+AFVTF T++A +
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQE 58
Score = 34.6 bits (79), Expect = 0.006
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV--L 159
+IFVG + ++ E ++ F + G I + + D + +G+ F++F + A++ L
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62
Query: 160 ANPKQVICGKEVDV 173
N ++ GK + V
Sbjct: 63 YNNHEIRPGKHIGV 76
>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 = 45.5 bits (108), Expect = 9e-07
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 98 PLKCK-IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
P CK +FVGGL +E+ +R+ F Q G I + KK FC I F ++ +
Sbjct: 3 PPGCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMS-------KKNFCHIRFAEEFAVD 55
Query: 157 QVLA 160
+ +
Sbjct: 56 KAIY 59
Score = 32.0 bits (73), Expect = 0.055
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESI--SIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
+ +FVGGL N E+ I + F Q GE+ +I S KN F + F + AVD
Sbjct: 7 KTVFVGGLPENATEEIIREVFEQCGEIIAIRMSKKN---------FCHIRFAEEFAVDKA 57
Query: 75 LA 76
+
Sbjct: 58 IY 59
>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 = 45.6 bits (109), Expect = 9e-07
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 23 GLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTF-TTQKA---VDDLLA 76
GL T E++I S ++ + + D TG SRGFAFV F + + A +D L
Sbjct: 9 GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68
Query: 77 AGDHYIGNKKI 87
I + +
Sbjct: 69 LDPFVIDGRVV 79
Score = 37.9 bits (89), Expect = 4e-04
Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 16/82 (19%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPF-------DKSKNMKKGFCFISFDDQNVA 155
+ + GL +E+D+ S S+ P DK +GF F+ F A
Sbjct: 5 LILRGLDLLTTEEDILQALSAIASV-----PIKDVRLIRDKLTGTSRGFAFVEFPSLEDA 59
Query: 156 EQVL----ANPKQVICGKEVDV 173
Q + VI G+ V V
Sbjct: 60 TQWMDALNNLDPFVIDGRVVRV 81
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 10/76 (13%)
Query: 101 CKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD-QNVAEQV 158
++FVG L T+ +S++D+ + FS+YG I ++ KG+ F+ FD+ ++ V
Sbjct: 1 SRVFVGNLNTDKVSKEDLEEIFSKYGKILGI--------SLHKGYGFVQFDNEEDARAAV 52
Query: 159 LANPKQVICGKEVDVK 174
+ I G+++D+
Sbjct: 53 AGENGREIAGQKLDIN 68
Score = 38.7 bits (91), Expect = 1e-04
Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 10/74 (13%)
Query: 17 RKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
++FVG L+ + ++++ + FS+YG++ IS+ H +G+ FV F ++ +
Sbjct: 1 SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISL----H----KGYGFVQFDNEEDARAAV 52
Query: 76 AAGD-HYIGNKKID 88
A + I +K+D
Sbjct: 53 AGENGREIAGQKLD 66
>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 = 45.3 bits (108), Expect = 1e-06
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISI--KNDPHTGQSRGFAFVTFTTQKAVDDLL 75
KL V + +KE+ + FS +G+V+S+ + K D G RGFAFV F T++ + +
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD---GSHRGFAFVEFVTKQEAQNAM 58
Query: 76 AA 77
A
Sbjct: 59 EA 60
Score = 34.1 bits (79), Expect = 0.007
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
K+ V + E +++++R+ FS +G + + P K +GF F+ F
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLP-KKFDGSHRGFAFVEF 48
>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 = 44.7 bits (106), Expect = 1e-06
Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
++F+ L +E+D+ FS+YG ++E P DK KGF F+++
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
Score = 41.6 bits (98), Expect = 2e-05
Identities = 16/48 (33%), Positives = 28/48 (58%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+LF+ L E+++ FS+YG + + + D T + +GFAFVT+
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
>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 = 44.6 bits (106), Expect = 2e-06
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
L++G L + E+++ + F +YGE++SI + RG A+V T++ L
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRALQ 56
Query: 77 AGDHYIGNKK 86
+ K
Sbjct: 57 KLRNVKLAGK 66
Score = 28.1 bits (63), Expect = 1.2
Identities = 8/27 (29%), Positives = 20/27 (74%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITE 129
+++G L+ +++E+D+++ F +YG I
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQS 31
>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 = 45.0 bits (106), Expect = 2e-06
Identities = 26/86 (30%), Positives = 49/86 (56%), Gaps = 5/86 (5%)
Query: 95 RVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
R NP C + V GL+ +E+D+R+ FS+YG I + +D+ +GF F+ F++ +
Sbjct: 3 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62
Query: 154 VAEQVLANPKQVICGKEVDVKRVKFN 179
A++ K+ G E+D +R++ +
Sbjct: 63 DAKEA----KERANGMELDGRRIRVD 84
Score = 40.0 bits (93), Expect = 9e-05
Identities = 21/47 (44%), Positives = 30/47 (63%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L V GL T E+++ + FS+YG + +SI D + +SRGFAFV F
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58
>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 = 44.4 bits (105), Expect = 2e-06
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKI 87
E+++++YF Q+G V + I Q R F FVTF + V +L+ G+ H+I ++
Sbjct: 13 EEDVSEYFGQFGPVLDVRIPY----QQKRMFGFVTFENAETVKRILSKGNPHFICGSRV 67
Score = 37.4 bits (87), Expect = 5e-04
Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 7/63 (11%)
Query: 114 EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA--NPKQVICGKEV 171
E+DV +YF Q+G + + + P+ + K+ F F++F++ +++L+ NP ICG V
Sbjct: 13 EEDVSEYFGQFGPVLDVRIPYQQ----KRMFGFVTFENAETVKRILSKGNP-HFICGSRV 67
Query: 172 DVK 174
VK
Sbjct: 68 RVK 70
>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 = 44.4 bits (105), Expect = 2e-06
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVD 72
+FVGG+ E EI +F++YG V+ + I D TG S+G+ FV+F QK V+
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIVE 64
Score = 41.0 bits (96), Expect = 4e-05
Identities = 20/59 (33%), Positives = 36/59 (61%), Gaps = 5/59 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAEQ 157
+FVGG+ + E ++R +F++YGS+ E + D++ + KG+ F+SF D Q + E
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRT-GVSKGYGFVSFYDDVDVQKIVES 65
>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 = 44.2 bits (104), Expect = 3e-06
Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 4/72 (5%)
Query: 21 VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH 80
V GL T E+++ + FS+YG + +++ D TG+SRGFAFV F + +DD A +H
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYF---ERIDDSKEAMEH 60
Query: 81 YIGNKKIDPKRV 92
G ++D +R+
Sbjct: 61 ANG-MELDGRRI 71
Score = 37.6 bits (87), Expect = 6e-04
Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 4/75 (5%)
Query: 105 VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQ 164
V GL+ +E+D+R+ FS+YG + +D+ +GF F+ F+ + +++ + +
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHAN- 62
Query: 165 VICGKEVDVKRVKFN 179
G E+D +R++ +
Sbjct: 63 ---GMELDGRRIRVD 74
>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 = 44.2 bits (105), Expect = 3e-06
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
+L V L E ++ FS +G V ++I P G+ +GFAFV FT+ +KA+
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKG 59
Query: 74 L 74
+
Sbjct: 60 V 60
Score = 34.9 bits (81), Expect = 0.005
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++ V L + +E D++ FS +G + E P KGF F+ F + AE+ +
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKK-KGFAFVQFTSKADAEKAIKG 59
Query: 162 PKQVICGKEVDVKRV 176
GK++ + V
Sbjct: 60 VN----GKKIKGRPV 70
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 44.1 bits (105), Expect = 3e-06
Identities = 19/52 (36%), Positives = 30/52 (57%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+IFVG L E++++ + FS+Y S + + DK KG+ F+SF D N
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN 59
Score = 44.1 bits (105), Expect = 3e-06
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 8/82 (9%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
ND R +FVG L ++ + FS+Y + + D TG+S+G+ FV+F +D
Sbjct: 5 NDFR-IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSF---SDPND 60
Query: 74 LLAA----GDHYIGNKKIDPKR 91
L A Y+GN+ I ++
Sbjct: 61 YLKAMKEMNGKYVGNRPIKLRK 82
>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 = 44.0 bits (104), Expect = 3e-06
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYF-SQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
E +FVG L E ++ F S++ +S I DP TG SRG+ FV F+ +
Sbjct: 1 EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDEN 55
Score = 34.4 bits (79), Expect = 0.007
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 103 IFVGGLTTEISEQDVRDYF-SQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
IFVG L+ E++E D+ F S++ S + D + +G+ F+ F D+N ++ L
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63
Query: 162 PKQVICG 168
+ V CG
Sbjct: 64 MQGVYCG 70
>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 = 43.9 bits (104), Expect = 4e-06
Identities = 12/41 (29%), Positives = 25/41 (60%)
Query: 26 RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
++ E ++ + F+ +GE++ I + D T +S+G A+V F
Sbjct: 12 KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFA 52
Score = 32.7 bits (75), Expect = 0.032
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 112 ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
++E D+R+ F+ +G I + DK KG ++ F
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFA 52
>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 = 43.5 bits (103), Expect = 4e-06
Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+R LFVG L E+ + + F Q G +E + I DP+ G+ + FAFVTF + +V
Sbjct: 1 DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVP 56
Score = 32.7 bits (75), Expect = 0.029
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
+FVG L ++E+ + + F Q G + + P D + K F F++F
Sbjct: 2 RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFKH 51
>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 = 43.5 bits (103), Expect = 4e-06
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
++++G L E+DV +F YG I E N+K GF F+ F+D A+
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREI--------NLKNGFGFVEFEDPRDAD 47
Score = 40.0 bits (94), Expect = 6e-05
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
++++G L E+++ +F YG + I++KN GF FV F + DD
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINLKN--------GFGFVEFEDPRDADD 48
>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 = 43.5 bits (103), Expect = 4e-06
Identities = 22/49 (44%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
R LFVG L E+E+ F +YG VE + IK P GQ +AFV F
Sbjct: 3 RTLFVGNLEITITEEELRRAFERYGVVEDVDIKR-PPRGQGNAYAFVKF 50
Score = 32.8 bits (75), Expect = 0.031
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVA 155
+FVG L I+E+++R F +YG + + ++P + + F+ F + ++A
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRP---PRGQGNAYAFVKFLNLDMA 56
>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 = 43.1 bits (102), Expect = 5e-06
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
L V L ++ ++E+ F G +ES I D TGQS G+ FV + + +
Sbjct: 1 TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60
Query: 77 AGDHY-IGNKKI 87
+ + I NK++
Sbjct: 61 TLNGFEIRNKRL 72
>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 = 42.9 bits (102), Expect = 6e-06
Identities = 18/56 (32%), Positives = 31/56 (55%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
+++G L E ++R YFSQ+G++T + K KG+ F+ F+ VA+ V
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIV 57
Score = 42.6 bits (101), Expect = 9e-06
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+++G L E E+ YFSQ+G V + + TG+S+G+AFV F
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEF 48
>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 = 43.0 bits (102), Expect = 6e-06
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
LFV L +T ++++ ++FS+ G ++ + D + + RGF +VTF + +D A
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALE---EDAKRA 57
Score = 32.6 bits (75), Expect = 0.031
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 9/59 (15%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPF---DKSKNMKKGFCFISF---DDQNVA 155
+FV L + +++ + ++FS+ G I ++ F DK +GF +++F +D A
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPI---KRCFVVKDKGSKKCRGFGYVTFALEEDAKRA 57
>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 = 43.6 bits (103), Expect = 6e-06
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 10/67 (14%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSR------GFAFVTFTTQKA 70
RK+FVGGL + E EI F ++G + + + PH +S+ G+AF+ F + +
Sbjct: 1 RKVFVGGLPPDIDEDEITASFRRFGPL----VVDWPHKAESKSYFPPKGYAFLLFQEESS 56
Query: 71 VDDLLAA 77
V L+ A
Sbjct: 57 VQALIDA 63
Score = 41.7 bits (98), Expect = 3e-05
Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEF--QQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K+FVGGL +I E ++ F ++G + + KS KG+ F+ F +++ + ++
Sbjct: 2 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 61
>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 = 42.9 bits (101), Expect = 7e-06
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
IFVG L+ E+++ + FS + S ++ + +D +G+ F+SF Q AE +
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAIN 59
Score = 40.2 bits (94), Expect = 7e-05
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
+FVG L + + FS + + D +G+SRG+ FV+F +Q
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQ 51
>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 = 42.7 bits (101), Expect = 8e-06
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPH--TGQSRGFAFVTFTTQKA 70
L+VG L T ++++ ++ G V+ SIK H G+S+GFA+V F ++ A
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAA 54
Score = 41.1 bits (97), Expect = 3e-05
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK-NMK-KGFCFISFDDQNVAEQVLA 160
++VG LT +++D+ ++ G + F + K N K KGF ++ F + A V
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 161 N-PKQVICGKEVDVK 174
+ GK+ V
Sbjct: 61 KLEGREFNGKKCVVT 75
>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 = 42.8 bits (101), Expect = 8e-06
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++VG L + E++I D F +YG +++I +KN + FAFV F + +D +
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRR---RGPPFAFVEFEDPRDAEDAVRG 57
Query: 78 GDHY 81
D Y
Sbjct: 58 RDGY 61
Score = 39.3 bits (92), Expect = 1e-04
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+I+VG L +I E+D+ D F +YG I K++ F F+ F+D AE
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAE 52
>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 = 42.8 bits (101), Expect = 8e-06
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 4/59 (6%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
LFVG L + ++ + F ++G V + D TG+SRGF +V F + +KA++
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIE 59
Score = 32.4 bits (74), Expect = 0.031
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVG L+ + ++ ++ F ++G++ + D+ +GF ++ F+ A++ +
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 162 PKQVICGKEVDVKRVKFN 179
GKE+D + + +
Sbjct: 61 MD----GKELDGRPINVD 74
>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 = 42.6 bits (101), Expect = 8e-06
Identities = 17/52 (32%), Positives = 32/52 (61%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
LFV L+ T ++++ FS++G+++S + D TG S +AF+ F T++
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKED 57
Score = 29.2 bits (66), Expect = 0.51
Identities = 14/55 (25%), Positives = 26/55 (47%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+FV L +++D+ FS++G I + DK + FI F+ + E+
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60
>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 = 42.6 bits (101), Expect = 9e-06
Identities = 16/60 (26%), Positives = 36/60 (60%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++V +H + E +I F +G+++S S+ DP TG+ +G+ F+ + ++ D +A+
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61
Score = 33.0 bits (76), Expect = 0.019
Identities = 15/59 (25%), Positives = 29/59 (49%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+I+V + ++SE D++ F +G I D KG+ FI +++ A+ +A
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
L VG L +++ + S +G VE + TG+S+G+ FV + ++
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASK 51
Score = 29.5 bits (67), Expect = 0.37
Identities = 12/55 (21%), Positives = 27/55 (49%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+ VG L E +++ R+ S +G++ + +S KG+ F+ + + A +
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALK 56
>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 = 42.6 bits (100), Expect = 1e-05
Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+FVG L E+ + F + G +E + I DP T +GFA+V F + AV+ L
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL--- 58
Query: 79 DHYIGNKKIDPKRVTKRVNPLKCK 102
+ N+K P + + + +CK
Sbjct: 59 ---LLNEKKFPPMLPRELRVSRCK 79
Score = 41.8 bits (98), Expect = 2e-05
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL--- 159
+FVG L E E+ + F + G I + D N+ KGF ++ F D+N E+ L
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61
Query: 160 ANPKQVICGKEVDVKRVK 177
+ +E+ V R K
Sbjct: 62 EKKFPPMLPRELRVSRCK 79
>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 = 42.2 bits (99), Expect = 1e-05
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+C++FVG L T+I+E+D + F +YG +P + N +GF FI + + +AE
Sbjct: 1 RCRLFVGNLPTDITEEDFKKLFEKYG------EPSEVFINRDRGFGFIRLESRTLAE 51
Score = 33.8 bits (77), Expect = 0.012
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
+LFVG L + E++ F +YGE + I D RGF F+ ++
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESR 47
>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 = 42.1 bits (99), Expect = 1e-05
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+++G L EKE+ YFSQ+G V+++ + TG S+ + F+ F
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQF 48
Score = 37.9 bits (88), Expect = 4e-04
Identities = 16/54 (29%), Positives = 28/54 (51%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
I++G L E++++ YFSQ+G++ + K K + FI F + VA
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAA 55
>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 = 42.0 bits (99), Expect = 1e-05
Identities = 14/37 (37%), Positives = 27/37 (72%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
E+++ + F ++G++E +SI D +TG+S+GF +V F
Sbjct: 14 EEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFH 50
Score = 30.1 bits (68), Expect = 0.22
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 111 EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+E+D+R+ F ++G I DK+ KGF ++ F + A L N
Sbjct: 11 SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALEN 61
>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 = 42.3 bits (99), Expect = 1e-05
Identities = 17/59 (28%), Positives = 36/59 (61%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+++ GL ++++DV D FS++G I + D++ + +G FI FD ++ AE+ + +
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61
Score = 40.4 bits (94), Expect = 7e-05
Identities = 18/58 (31%), Positives = 33/58 (56%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
L++ GL R +K++ D FS++G + + + D TG SRG AF+ F + ++ +
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT 60
>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 = 41.8 bits (98), Expect = 2e-05
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+V GL + +KE+ FSQYG + + I D TG SRG F+ F
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRF 49
Score = 36.1 bits (83), Expect = 0.002
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++V GL ++++++ FSQYG I + D+ + +G FI FD + AE+ +
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAI 59
>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 = 41.5 bits (98), Expect = 2e-05
Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 9/51 (17%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESI--SIKNDPHTGQSRGFAFVTF 65
R LFV ++ N ++E+ F Q+G++ ++ + K+ RGF V++
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKH-------RGFIMVSY 45
Score = 33.4 bits (77), Expect = 0.016
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
+FV + + + ++++R F Q+G I + K+ +GF +S+ D
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDIRTL---YTACKH--RGFIMVSYYD 47
>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 = 41.5 bits (97), Expect = 3e-05
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P C +F+ L E ++ D+ F +G++ + DK N+ K F F+S+D+ + A+
Sbjct: 2 PEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQA 61
Query: 158 VLANPKQVICGKEVDVKRVK 177
+ Q + G ++ KR+K
Sbjct: 62 AI----QAMNGFQIGTKRLK 77
Score = 27.7 bits (61), Expect = 1.8
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LF+ L + + ++ F +G V S + D T S+ F FV++ + + A
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66
Query: 79 DHY-IGNKKI 87
+ + IG K++
Sbjct: 67 NGFQIGTKRL 76
>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 = 41.1 bits (96), Expect = 3e-05
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+C++FVG L +I+E + + F++YG +P + N KGF FI + + +AE
Sbjct: 1 RCRLFVGNLPADITEDEFKKLFAKYG------EPGEVFINKGKGFGFIKLESRALAE 51
Score = 31.8 bits (72), Expect = 0.047
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
+LFVG L + E E F++YGE + I + +GF F+ ++
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFIN------KGKGFGFIKLESR 47
>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 = 41.3 bits (97), Expect = 3e-05
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L V L +N + EI FS GE+ES + D TGQS G+ FV + +KA++ L
Sbjct: 4 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63
Score = 28.5 bits (64), Expect = 0.83
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
K + V L +++ ++R FS G I + DK G+ F+++ D AE+
Sbjct: 1 KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEK 58
>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 = 41.1 bits (96), Expect = 3e-05
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+V GL + +KE+ FSQYG + + I D TG SRG F+ F
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRF 50
Score = 39.2 bits (91), Expect = 1e-04
Identities = 18/57 (31%), Positives = 32/57 (56%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++V GL +S++++ FSQYG I + D+ + +G FI FD + AE+ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 41.2 bits (96), Expect = 4e-05
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
+FV + +D+R F +YG I + P D +GF +I F+D AE L N
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 162 PKQVICGKEVDVK 174
++ +CG++++++
Sbjct: 63 NRKWVCGRQIEIQ 75
Score = 31.1 bits (70), Expect = 0.11
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
LFV + T +++ F +YG + + + D +T + RGFA++ F + +D L
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDAL 59
>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 = 43.9 bits (103), Expect = 4e-05
Identities = 38/160 (23%), Positives = 69/160 (43%), Gaps = 8/160 (5%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
N L V L ++ ++E+ F G + + I D TG S G+AFV F +
Sbjct: 103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADS 162
Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGS 126
Q+A+ +L + NK++ +K ++V L I++ + F +YG
Sbjct: 163 QRAIKNLNGIT---VRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQ 219
Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVI 166
I + DK +G F+ F+ + A++ ++ VI
Sbjct: 220 IVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVI 259
>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 = 40.5 bits (95), Expect = 4e-05
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+++G L +I+E DVR++F IT + DK KGF + F D+ + L
Sbjct: 2 VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60
Query: 163 KQVICGKEVDV 173
V+CG+ + +
Sbjct: 61 GTVLCGRPIRI 71
Score = 38.1 bits (89), Expect = 3e-04
Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
++G L + E ++ ++F E+ S+ + D TG+ +GF V F ++++D L
Sbjct: 3 YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLDG 61
Query: 80 HYIGNKKI 87
+ + I
Sbjct: 62 TVLCGRPI 69
>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 = 40.7 bits (96), Expect = 5e-05
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R ++VG L T ++ ++FSQ GEV+ + + D Q +AFV F Q +V + L
Sbjct: 5 RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE--TQPTRYAFVEFAEQTSVINALK 62
Query: 77 AGDHYIGNKKI 87
G + +
Sbjct: 63 LNGAMFGGRPL 73
Score = 32.3 bits (74), Expect = 0.049
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
I+VG L + + ++FSQ G + + D+++ + + F+ F +Q
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR--YAFVEFAEQT 55
>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 = 40.5 bits (95), Expect = 5e-05
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 31 KEINDYFSQYGEVESISI-KNDPHTGQSRGFAFVTFTT 67
KE+ + FS +GE++++ + K TG RGF FV F T
Sbjct: 15 KELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFIT 52
Score = 30.1 bits (68), Expect = 0.26
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS-KNMKKGFCFISF 149
KI V + E + +++R+ FS +G + + P + +GF F+ F
Sbjct: 1 SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDF 50
>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 = 40.7 bits (96), Expect = 5e-05
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+V GL + ++E+ FS YG + + I D TG SRG F+ F
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF 49
Score = 36.9 bits (86), Expect = 9e-04
Identities = 17/54 (31%), Positives = 28/54 (51%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
++V GL +++Q++ FS YG I + D + +G FI FD + AE
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAE 56
>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 = 40.6 bits (95), Expect = 5e-05
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P C +F+ L E + ++ F +G++ + D++ N K F F+SFD+ A+
Sbjct: 2 PEGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQA 61
Query: 158 VLANPKQVICGKEVDVKRVK 177
+ Q + G ++ +KR+K
Sbjct: 62 AI----QAMNGFQIGMKRLK 77
Score = 32.1 bits (73), Expect = 0.051
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
LF+ L + G+ E+ F +G V S + D T QS+ F FV+F
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSF 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 = 40.6 bits (95), Expect = 5e-05
Identities = 18/59 (30%), Positives = 32/59 (54%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVG + E +E+ ++D FS+ G + F+ +D+ KG+ F + DQ A + N
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRN 59
Score = 32.5 bits (74), Expect = 0.037
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
+FVG + E+++ D FS+ G V S + D TG+ +G+ F + Q
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQ 50
>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 = 40.1 bits (94), Expect = 5e-05
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQ-QPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVG L+ E +E ++R +F + G I + F+ S KGF F+ F++ A L
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKC-KGFAFVDFEEIEFATNALKG 59
Query: 162 P 162
Sbjct: 60 K 60
Score = 39.0 bits (91), Expect = 2e-04
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LFVG L T E E+ +F + G + + + +G+ +GFAFV F + + L G
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL-KG 59
Query: 79 DHYIGNK 85
H G
Sbjct: 60 KHLNGRA 66
>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 = 40.7 bits (95), Expect = 5e-05
Identities = 20/63 (31%), Positives = 30/63 (47%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D +LFVG L + E E+ ++F +G V + I G+ F FV F + V +
Sbjct: 4 DSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRI 63
Query: 75 LAA 77
L A
Sbjct: 64 LGA 66
Score = 37.6 bits (87), Expect = 6e-04
Identities = 16/62 (25%), Positives = 32/62 (51%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P ++FVG L +I E +++++F +G++ E + F F+ FDD ++
Sbjct: 3 PDSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62
Query: 158 VL 159
+L
Sbjct: 63 IL 64
>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 = 40.3 bits (94), Expect = 6e-05
Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P ++FVG L ++ + +++++F QYG++ E + S F F+ FDD ++
Sbjct: 1 PDSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQK 57
Query: 158 VLAN 161
+L+N
Sbjct: 58 ILSN 61
Score = 38.4 bits (89), Expect = 3e-04
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D +LFVG L + + E+ ++F QYG V + I + G+ F FV F + V +
Sbjct: 2 DSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSG---GKLPNFGFVVFDDSEPVQKI 58
Query: 75 LA 76
L+
Sbjct: 59 LS 60
>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 = 40.1 bits (94), Expect = 6e-05
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
++VG L + E+E+ D F +YG + I +K P + G+AF+ F + +D +
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPP---RPPGYAFIEFEDARDAEDAIRGR 58
Query: 79 DHY 81
D Y
Sbjct: 59 DGY 61
Score = 39.0 bits (91), Expect = 2e-04
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
++VG L +I E++V D F +YG I + K G+ FI F+D AE
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAE 52
>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 = 40.4 bits (95), Expect = 6e-05
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+ + GL T K+I +F +GE+E +K DP TGQS G VTF
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTF 47
>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 = 40.0 bits (94), Expect = 7e-05
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LFVG L + + ++ ++F + GEV + I D G+S+GF V F T++ L
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKALEKS 60
Query: 79 DHYIGNKKI 87
+ ++I
Sbjct: 61 GEELLGREI 69
Score = 31.5 bits (72), Expect = 0.087
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FVG L+ + D+ ++F + G + + + D KGF + F + A++ L
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60
Query: 163 KQVICGKEVDV 173
+ + G+E+ V
Sbjct: 61 GEELLGREIRV 71
>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 = 40.0 bits (94), Expect = 8e-05
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
+FV L + E + FS +G V ++ + D T + +G+ FVT T
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMT 51
Score = 28.1 bits (63), Expect = 1.1
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
IFV L + E + FS +G++T + D + N KG+ F++ N E A
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTM--TNYEEAYSA 59
>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 = 39.5 bits (93), Expect = 8e-05
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVD 72
+++ GL NT ++++ +G++ S D T + +G+ FV F KA++
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
Query: 73 DLLAAG 78
L G
Sbjct: 61 GLNGRG 66
Score = 30.3 bits (69), Expect = 0.19
Identities = 13/48 (27%), Positives = 24/48 (50%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
+++ GL +++D+ +G I + DK N KG+ F+ FD
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFD 50
>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 = 39.6 bits (93), Expect = 9e-05
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
++ V L I E +R F +G+IT+ Q + K +K F F+ + + A++ L
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRK-FGFVGYKTEEEAQKALK 59
Score = 33.4 bits (77), Expect = 0.014
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+L V L + E ++ F +G + + +K G+ R F FV + T+ ++ A
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTK-DGKFRKFGFVGYKTE---EEAQKA 57
Query: 78 GDH----YIGNKKI 87
H +I KI
Sbjct: 58 LKHFNNSFIDTSKI 71
>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 = 39.7 bits (92), Expect = 1e-04
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+V GL + +KE+ FSQYG + + I D TG SRG F+ F
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 51
Score = 35.9 bits (82), Expect = 0.002
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++V GL ++++++ FSQYG I + D+ + +G FI FD + AE+ +
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61
>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 = 39.7 bits (93), Expect = 1e-04
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT-QKAVDD 73
++ KLFV GL + ++E+ F ++G V+S+ + + +G+ +G A+V + A
Sbjct: 1 EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQA 59
Query: 74 LLAAGDHYIGNKKI 87
+L I K I
Sbjct: 60 VLKMDGTEIKEKTI 73
Score = 31.6 bits (72), Expect = 0.074
Identities = 13/60 (21%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K K+FV GL ++++++ F ++G + + ++S KG ++ +++++ A Q +
Sbjct: 2 KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAV 60
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 9/65 (13%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISI--KNDPHTGQ---SRGFAFVTF----TTQK 69
LFV L+ T E+ + +F + G V S++I K DP S G+ FV F QK
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 70 AVDDL 74
A+ L
Sbjct: 63 ALKRL 67
Score = 28.3 bits (64), Expect = 1.2
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKK-------GFCFISFDDQN 153
+FV L + +E+ ++ +F + G + K K+ K G+ F+ F +
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIA--KKKDPKGPGKLLSMGYGFVEFKSKE 58
Query: 154 VAEQVL 159
A++ L
Sbjct: 59 AAQKAL 64
>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 = 39.4 bits (91), Expect = 1e-04
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+V GL + +KE+ FSQYG + + I D TG SRG F+ F
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 54
Score = 35.9 bits (82), Expect = 0.003
Identities = 17/57 (29%), Positives = 32/57 (56%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++V GL ++++++ FSQYG I + D+ + +G FI FD + AE+ +
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 75
Score = 39.0 bits (91), Expect = 2e-04
Identities = 23/58 (39%), Positives = 31/58 (53%), Gaps = 9/58 (15%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISI--KNDPHTGQSRGFAFVTFT----TQKA 70
L+VG L N E+ I+++F +YG VES+ I K G + AFV F QKA
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA---AFVDFVDIKSAQKA 56
Score = 29.0 bits (65), Expect = 0.53
Identities = 7/25 (28%), Positives = 16/25 (64%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSI 127
++VG L + E+ + ++F +YG +
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRV 26
>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 = 39.3 bits (91), Expect = 2e-04
Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 12/63 (19%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE-------FQQPFDKSKNMKKGFCFISFDDQNV 154
++FVG + +++++ + FS+ +TE + QP DK KN +GFCF+ ++D
Sbjct: 4 RLFVGSIPKNKTKENILEEFSK---VTEGLVDVILYHQPDDKKKN--RGFCFLEYEDHKS 58
Query: 155 AEQ 157
A Q
Sbjct: 59 AAQ 61
>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 = 38.9 bits (91), Expect = 2e-04
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 9/84 (10%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R + VGG+ + E ++ ++FS GEV + + D S FAFV F ++ L
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQ--HSARFAFVEFADAESALSALN 58
Query: 77 AGDHYIGNKKIDPKRVTKRVNPLK 100
+G + RV+P K
Sbjct: 59 LSGTLLGGHPL-------RVSPSK 75
Score = 35.4 bits (82), Expect = 0.003
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
I VGG+ +SE D++++FS G +T + D+ + + F F+ F D
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR--FAFVEFAD 49
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 15/84 (17%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITE-------FQQPFDKSKNMKKGFCFISFDDQ 152
C++FVGG+ +++++ + FS+ +TE ++ P DK+KN +GF F+ ++
Sbjct: 1 NCRLFVGGIPKTKTKEEILEEFSK---VTEGVVDVIVYRSPDDKNKN--RGFAFVEYESH 55
Query: 153 NVAEQV---LANPKQVICGKEVDV 173
A L + ++ G EV V
Sbjct: 56 RAAAMARRKLVPGRILLWGHEVAV 79
Score = 37.6 bits (88), Expect = 6e-04
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQ-SRGFAFVTFTTQKA 70
+LFVGG+ + ++EI + FS+ E V + + P +RGFAFV + + +A
Sbjct: 3 RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRA 57
>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 = 39.3 bits (91), Expect = 2e-04
Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 4/84 (4%)
Query: 94 KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
++ P +F+ L E +QD+ F +G++ + DK N+ K F F+S+D+
Sbjct: 1 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 60
Query: 154 VAEQVLANPKQVICGKEVDVKRVK 177
A+ + Q + G ++ +KR+K
Sbjct: 61 SAQAAI----QAMNGFQIGMKRLK 80
Score = 27.3 bits (60), Expect = 3.0
Identities = 18/70 (25%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LF+ L + G++++ F +G V S + D T S+ F FV++ + + A
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69
Query: 79 DHY-IGNKKI 87
+ + IG K++
Sbjct: 70 NGFQIGMKRL 79
>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 = 38.9 bits (90), Expect = 2e-04
Identities = 18/59 (30%), Positives = 36/59 (61%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+FVG L+ EI+ +D++ F+ +G I++ + D + KG+ F+SF ++ AE + +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62
Score = 37.0 bits (85), Expect = 0.001
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ-KAVDDLLAA 77
+FVG L ++I F+ +G++ + D TG+S+G+ FV+F + A + ++
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 78 GDHYIGNKKIDPKRVTK 94
G ++G ++I T+
Sbjct: 64 GGQWLGGRQIRTNWATR 80
>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 = 38.6 bits (90), Expect = 2e-04
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+I+VG L +++ E+D+ D F +YG I + + K++ F F+ F+D AE
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAE 52
Score = 37.5 bits (87), Expect = 6e-04
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
+++VG L + EK++ D F +YG + I +KN FAFV F + +D
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNR---RGLVPFAFVRFEDPRDAED 53
>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 = 38.7 bits (91), Expect = 2e-04
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+ + GL + E++I D+FS + I I D G+ G A+V F + + L
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRALRK 60
Query: 78 GDHYIGNKKI 87
++ +G + I
Sbjct: 61 HNNKMGGRYI 70
Score = 31.0 bits (71), Expect = 0.11
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 8/75 (10%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYG----SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
+ + GL +E+D+RD+FS I + G ++ F A +
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRP----TGEAYVEFASPEDARRA 57
Query: 159 LANPKQVICGKEVDV 173
L + G+ ++V
Sbjct: 58 LRKHNNKMGGRYIEV 72
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 39.3 bits (92), Expect = 2e-04
Identities = 14/51 (27%), Positives = 23/51 (45%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
+I V G SE +++YFS +G I E + D + + G I +
Sbjct: 3 VEIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYG 53
Score = 38.9 bits (91), Expect = 3e-04
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 21 VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
V G +T E I +YFS +GE+ I NDP+T G + +
Sbjct: 7 VWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYY 52
>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein
Vip1 and similar proteins. This subfamily corresponds
to Vip1, an RNA-binding protein encoded by gene vip1
from fission yeast Schizosaccharomyces pombe. Its
biological role remains unclear. Vip1 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 68
Score = 38.3 bits (89), Expect = 3e-04
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 27 NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK 86
T EK+I+D+FS G++ ++ + ND + A +TF A L + +G K
Sbjct: 9 KTTEKQISDFFSFCGKISNLDLTNDGESQT----ATITFEKPSAAKTALLLDNALLGGKV 64
Query: 87 I 87
I
Sbjct: 65 I 65
>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 = 38.3 bits (89), Expect = 3e-04
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 10/80 (12%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
+ ++FVG L +I+E+++R F +YG E + KGF FI + + +AE
Sbjct: 1 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEI------FIHKDKGFGFIRLETRTLAEIAK 54
Query: 160 ANPKQVIC-GKEVDVKRVKF 178
A + GK++ RV+F
Sbjct: 55 AELDNMPLRGKQL---RVRF 71
Score = 36.4 bits (84), Expect = 0.001
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+LFVG L + E+E+ F +YG+ I I D +GF F+ T+ +
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAE 51
>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 = 38.4 bits (89), Expect = 3e-04
Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
R LF+G L N E E+ F +YG +E + IK P GQ +AF+ F
Sbjct: 9 RNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKR-PARGQGGAYAFLKF 56
Score = 28.0 bits (62), Expect = 1.8
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+F+G L +SE ++R F +YG I E ++P ++ + F+ F + ++A +
Sbjct: 11 LFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRP---ARGQGGAYAFLKFQNLDMAHR 64
>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 = 38.0 bits (88), Expect = 3e-04
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 12/75 (16%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++F+G L E+DV +F YG I + ++K+GF F+ FDD A+ +
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDI--------DLKRGFGFVEFDDPRDADDAVYE 52
Query: 162 PKQVICGKEVDVKRV 176
+ GKE+ +RV
Sbjct: 53 ----LDGKELCNERV 63
Score = 36.1 bits (83), Expect = 0.002
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 12/76 (15%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
++F+G L+ EK++ +F YG + I +K RGF FV F + DD +
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDLK--------RGFGFVEFDDPRDADDAV-- 50
Query: 78 GDHYIGNKKIDPKRVT 93
+ + K++ +RVT
Sbjct: 51 --YELDGKELCNERVT 64
>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 = 38.4 bits (90), Expect = 3e-04
Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 12/90 (13%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
R++ L+ N E + D +YGEVE + I P T + G A V F + K+ +
Sbjct: 2 PREVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCV 61
Query: 76 AAGDHY--------IGNKKIDPK-RVTKRV 96
+ I +DPK + KR+
Sbjct: 62 ---EKLNQTSVMGKIIKVFLDPKGEIRKRL 88
>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 = 38.0 bits (88), Expect = 4e-04
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
+R LFVG L E+ I + F Q G V + I D G+ + FAFV F + +V
Sbjct: 1 DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSV 55
Score = 31.8 bits (72), Expect = 0.060
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+FVG L +++E+ + + F Q G + + + P DK K+ F F++F
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQ-FAFVNF 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 = 4e-04
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R LF+G L + T ++ + F ++GE+ I IK +AF+ + +V +
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPA---YAFIQYADIASVVKAMR 59
Query: 77 AGD-HYIGNKKI 87
D Y+GN ++
Sbjct: 60 KMDGEYLGNNRV 71
Score = 27.8 bits (62), Expect = 1.4
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITE 129
+F+G L + D+R+ F ++G I +
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIID 31
>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 = 38.0 bits (89), Expect = 4e-04
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ----KAVDD 73
L+V L + ++ + + FS +G + S + D G+S+GF FV F++ KAV +
Sbjct: 3 NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVTE 61
Query: 74 L 74
+
Sbjct: 62 M 62
Score = 31.1 bits (71), Expect = 0.11
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 13/55 (23%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK------KGFCFISFD 150
++V L I ++ +R+ FS +G+IT +K M KGF F+ F
Sbjct: 3 NLYVKNLDDSIDDERLREEFSPFGTIT-------SAKVMTDEKGRSKGFGFVCFS 50
>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 = 37.6 bits (88), Expect = 4e-04
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 111 EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
E+SE D D +G + + + K F +FD++ A Q L
Sbjct: 10 ELSEDDKEDLLKHFG-ASSVR--VMSRRGKLKNTAFATFDNEQAASQAL 55
>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 = 37.7 bits (88), Expect = 5e-04
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 14/73 (19%)
Query: 34 NDY---FSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK 90
ND FS+YG+V ++I D T +S+G AF+ F ++ D + K ++ K
Sbjct: 16 NDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDRE---------DAHKCVKALNNK 66
Query: 91 RVTKRVNPLKCKI 103
+ R LKC I
Sbjct: 67 ELFGRT--LKCSI 77
Score = 29.6 bits (67), Expect = 0.41
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K ++V L ++ D+ FS+YG + + DK KG FI F D+ A + +
Sbjct: 1 KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60
Query: 160 A--NPKQVI 166
N K++
Sbjct: 61 KALNNKELF 69
>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 = 37.7 bits (88), Expect = 5e-04
Identities = 16/54 (29%), Positives = 26/54 (48%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
L+V GL T ++ FS+YG+V I + + +R F FVT + +
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAA 55
>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 = 38.4 bits (89), Expect = 6e-04
Identities = 25/109 (22%), Positives = 44/109 (40%), Gaps = 29/109 (26%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSIT------EFQQPFDKSK---------------- 138
K+FVGGL +I+E D+ + F ++GS+ ++ D
Sbjct: 1 RKVFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDSDPSLCNEKSDGSINGDKG 60
Query: 139 NMKKGFCFISFDDQ-NVAEQVLA------NPKQVICGKEVDVKRVKFNP 180
KG+ F+ F+ + +V +LA ++ D KRV+ P
Sbjct: 61 QHPKGYVFLLFEKERSVRSLLLACSEEEGGLFRITSSSSTDSKRVQIRP 109
Score = 36.9 bits (85), Expect = 0.002
Identities = 26/105 (24%), Positives = 41/105 (39%), Gaps = 29/105 (27%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYG--EVE--------------------SISIKNDPHT 54
RK+FVGGL + E +I + F ++G +V+ S N
Sbjct: 1 RKVFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDSDPSLCNEKSDGSINGDKG 60
Query: 55 GQSRGFAFVTFTTQKAVDDLLAAGDHYIG-------NKKIDPKRV 92
+G+ F+ F +++V LL A G + D KRV
Sbjct: 61 QHPKGYVFLLFEKERSVRSLLLACSEEEGGLFRITSSSSTDSKRV 105
>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 = 37.5 bits (87), Expect = 6e-04
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
++VG + + +E+ +FS G + ++I D +G +G+A++ F T+ +V+ +A
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61
Query: 79 DHYIGNK--KIDPKR 91
+ + K+ PKR
Sbjct: 62 ESSFRGRVIKVLPKR 76
Score = 29.8 bits (67), Expect = 0.27
Identities = 16/71 (22%), Positives = 32/71 (45%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
++VG + + +++ +FS G I DK KG+ +I F ++ E +A
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61
Query: 163 KQVICGKEVDV 173
+ G+ + V
Sbjct: 62 ESSFRGRVIKV 72
>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 = 37.7 bits (88), Expect = 6e-04
Identities = 18/62 (29%), Positives = 30/62 (48%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L+V + T ++ F +YG + + I D +T + RGFA+V F + +D L
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 79 DH 80
D
Sbjct: 63 DR 64
Score = 32.7 bits (75), Expect = 0.028
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
++V + D+R F +YG I + P D +GF ++ F+D AE L
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 162 PKQVICGKEVDV 173
+ G+E+++
Sbjct: 63 DRTRFLGREIEI 74
>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 = 37.3 bits (87), Expect = 6e-04
Identities = 16/55 (29%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
++LFV + ++ +++++ F +E +K DP+TG+S+GFA+VT++ +
Sbjct: 1 QRLFVV-VSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASA 54
>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 = 37.8 bits (87), Expect = 6e-04
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQ----YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
++FVG + +++ + + FS+ + + QP DK KN +GFCF+ ++D A Q
Sbjct: 4 RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKN--RGFCFLEYEDHKTAAQ 61
>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 = 37.2 bits (87), Expect = 6e-04
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
+FV L + +++ D F + G V +K D G+S+GF V F + +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPE 50
Score = 26.8 bits (60), Expect = 3.3
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 7/57 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSIT--EFQQPFD-KSKNMKKGFCFISFDDQNVAE 156
IFV L ++ QD++D F + G++ + + D +S KGF + F+ A+
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRS----KGFGTVLFESPEDAQ 53
>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 = 36.3 bits (85), Expect = 8e-04
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 33 INDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKI 87
+ FS +G VE I + GFAFV F+T++A + + + G + +
Sbjct: 1 LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPL 51
Score = 34.0 bits (79), Expect = 0.006
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 117 VRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN-PKQVICGKEVDVK 174
+ FS +G++ + + K GF F+ F + AE+ + + G+ + V
Sbjct: 1 LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54
>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 = 37.8 bits (88), Expect = 8e-04
Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP---FDKSKNMKKGFCFISFD-DQNVAE 156
CK+F+GG+ +I+E + + F +GS++ + P ++ KG+ ++ F+ +++V
Sbjct: 3 CKVFLGGVPWDITEAGLINTFKPFGSVS-VEWPGKDGKHPRHPPKGYVYLIFESEKSVKA 61
Query: 157 QVLANPKQVICGKE 170
+ A + G E
Sbjct: 62 LLQACTHDFLNGGE 75
Score = 27.8 bits (62), Expect = 2.2
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
K+F+GG+ + E + + F +G VE +G+ ++ F ++K+V LL
Sbjct: 4 KVFLGGVPWDITEAGLINTFKPFGSVSVEWPGKDGKHPRHPPKGYVYLIFESEKSVKALL 63
Query: 76 AAGDH 80
A H
Sbjct: 64 QACTH 68
>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 = 37.4 bits (86), Expect = 8e-04
Identities = 25/81 (30%), Positives = 33/81 (40%), Gaps = 21/81 (25%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L V L +N ++E F GE+ES + D TGQS G+ FV +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY------------- 51
Query: 79 DHYIGNKKIDPKRVTKRVNPL 99
IDPK K +N L
Sbjct: 52 --------IDPKDAEKAINTL 64
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 36.9 bits (85), Expect = 9e-04
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 11/78 (14%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-- 159
++++G L+ + E+DV +F YG I E ++K G+ F+ FDD A+ +
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEV--------DLKNGYGFVEFDDLRDADDAVYE 52
Query: 160 ANPKQVICGKEVDVKRVK 177
N K +CG+ V V+ +
Sbjct: 53 LNGKD-LCGERVIVEHAR 69
Score = 28.8 bits (64), Expect = 0.64
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
++++G L E+++ +F YG++ + +KN G+ FV F + DD
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDLKN--------GYGFVEFDDLRDADD 48
>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 = 37.6 bits (87), Expect = 0.001
Identities = 19/61 (31%), Positives = 29/61 (47%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV L + +E+ + +FS++GS+ DKS KG F+ F DQ L N
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63
Query: 163 K 163
Sbjct: 64 P 64
Score = 35.7 bits (82), Expect = 0.005
Identities = 18/58 (31%), Positives = 28/58 (48%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
LFV L + E+ + +FS++G V D TG+++G FV F Q + L
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 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 = 37.1 bits (85), Expect = 0.001
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K +++ GL ++QD+ YG I + DK+ N KG+ F+ FD A++ +
Sbjct: 4 KTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAV 63
Query: 160 ANPK 163
A+ K
Sbjct: 64 ASLK 67
Score = 32.5 bits (73), Expect = 0.036
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L++ GL T ++++ YG++ S D +T Q +G+ FV F + QKAV L
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66
Query: 75 LAAG 78
A G
Sbjct: 67 KANG 70
>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 = 36.5 bits (85), Expect = 0.001
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+FVGGL ++E ++R F +G I + P KG F+ F + AE +
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG------KGCGFVQFVHRAAAEAAIQ 55
Score = 34.2 bits (79), Expect = 0.007
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 6/48 (12%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
+FVGGL E E+ F +GE+ + I +G FV F
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP------GKGCGFVQFV 45
>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 = 37.0 bits (86), Expect = 0.001
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
+ F+ G+ + E +I DYF Q+G+ +S+ + + FV F T++A
Sbjct: 3 KSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAK------CGFVRFETREA 50
Score = 32.4 bits (74), Expect = 0.052
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 104 FVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK--NMKKGFCFISFDDQNVAEQVLA 160
F+ G+ ++ E +RDYF Q+G KS N + F+ F+ + AE+ A
Sbjct: 6 FLFGVEDDLPEYKIRDYFEQFGKS--------KSVIVNHRAKCGFVRFETREAAEKFAA 56
>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 = 37.0 bits (85), Expect = 0.001
Identities = 19/51 (37%), Positives = 25/51 (49%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
L V L +N + E+ FS GEVES + D G S G+ FV + K
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAK 54
>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 = 36.6 bits (84), Expect = 0.001
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
C ++ GG+T+ ++EQ +R FS +G I E + D KG+ F+ F+ A +
Sbjct: 1 CTVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIV 54
Query: 161 N 161
+
Sbjct: 55 S 55
>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 = 36.9 bits (86), Expect = 0.001
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEF--QQPF------DKSKNMKKGFCFISFDDQNV 154
I++ GL +++E + + F G I P DK KG +++DD +
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETE-PKGEATVTYDDPSA 59
Query: 155 AEQV 158
A+
Sbjct: 60 AQAA 63
>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 = 36.9 bits (85), Expect = 0.001
Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
++F+G L R+ E E+ + G++ + + D G +RG+AFVTF+ ++ + +
Sbjct: 3 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQ 61
Query: 78 GDHY 81
++Y
Sbjct: 62 LNNY 65
Score = 30.7 bits (69), Expect = 0.14
Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
C+IF+G L ++ E ++ + G I E + D + N +G+ F++F ++ A+ +
Sbjct: 2 CEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAI 59
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a
transcription coactivator of LEF-1 and AML-1 for the
TCRalpha enhancer function. In addition, THOC4
specifically binds to rhesus (RH) promoter in
erythroid, and might be a novel transcription cofactor
for erythroid-specific genes. SKAR shows high sequence
homology with THOC4 and possesses one RRM as well. SKAR
is widely expressed and localizes to the nucleus. It
may be a critical player in the function of S6K1 in
cell and organism growth control by binding the
activated, hyperphosphorylated form of S6K1 but not
S6K2. Furthermore, SKAR functions as a protein partner
of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 36.4 bits (85), Expect = 0.001
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
+L V LH + E+++ + F + GEV+ + I D +G+S G A V F ++A+
Sbjct: 2 RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59
Score = 27.2 bits (61), Expect = 2.7
Identities = 12/57 (21%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
++ V L +++E+D+ + F + G + + + +D+S +G + F+ + AE+
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGR-SEGTADVVFEKREDAER 56
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved
poly(A) binding protein containing poly(A) tails that
can be attached to the 3'-ends of mRNAs. The yeast PABP
and its homologs may play important roles in the
initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 77
Score = 36.8 bits (86), Expect = 0.001
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+F+ L ++ K + D FS +G + S + D G S+G+ FV F T++A
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAV 57
>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 = 36.9 bits (86), Expect = 0.001
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 17/78 (21%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDP-----------------HTGQSRG 59
R +FVG L T +K++ F Q+G +ES+ ++ P H +
Sbjct: 1 RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60
Query: 60 FAFVTFTTQKAVDDLLAA 77
A+V F +++ + L
Sbjct: 61 NAYVVFKEEESAEKALKL 78
Score = 28.0 bits (63), Expect = 1.5
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQ---PFDKSKNMKKGF 144
+FVG L ++D++ F Q+G I + P + K KK
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVA 47
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 of SRSF1, also termed alternative-splicing factor
1 (ASF-1), or pre-mRNA-splicing factor SF2, P33
subunit. SRSF1 is a splicing regulatory serine/arginine
(SR) protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich
in serine-arginine dipeptides. .
Length = 73
Score = 36.3 bits (84), Expect = 0.001
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRG--FAFVTFTTQKAVDDLL 75
+++VG L + K+I D F +YG + I +KN RG FAFV F + +D +
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKN------RRGPPFAFVEFEDPRDAEDAV 54
Query: 76 AAGDHY 81
D Y
Sbjct: 55 YGRDGY 60
Score = 35.1 bits (81), Expect = 0.004
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG-FCFISFDDQNVAE 156
+I+VG L +I +D+ D F +YG+I + KN + F F+ F+D AE
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDL-----KNRRGPPFAFVEFEDPRDAE 51
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 36.6 bits (85), Expect = 0.001
Identities = 18/81 (22%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++ V + + D+R F Q+G I + + F++ + KGF F++F + A++
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS--KGFGFVTFANSADADRA--- 56
Query: 162 PKQVICGKEVDVKRVKFNPET 182
++ + G V+ ++++ N T
Sbjct: 57 -REKLHGTVVEGRKIEVNNAT 76
Score = 30.1 bits (68), Expect = 0.27
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISI-KNDPHTGQSRGFAFVTFTT 67
++L V + + ++ F Q+G + + I N+ S+GF FVTF
Sbjct: 1 KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNER---GSKGFGFVTFAN 49
>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 = 36.3 bits (84), Expect = 0.001
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
++VG + +E+ +F G V ++I D +G +GFA++ F+ +++V LA
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61
Query: 79 DHYIGNK--KIDPKR 91
+ + K+ PKR
Sbjct: 62 ESLFRGRQIKVMPKR 76
Score = 31.3 bits (71), Expect = 0.076
Identities = 17/71 (23%), Positives = 33/71 (46%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
++VG + + +++ +F GS+ DK KGF +I F D+ LA
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61
Query: 163 KQVICGKEVDV 173
+ + G+++ V
Sbjct: 62 ESLFRGRQIKV 72
>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 = 36.2 bits (84), Expect = 0.001
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
+FV L G K++ + F G+V IK D G+SRG V F
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEH 48
Score = 27.7 bits (62), Expect = 1.8
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
IFV L ++ + +++ F G + DK +G + F+
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGK-SRGMGVVQFE 47
>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 = 36.3 bits (84), Expect = 0.002
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQP--FDKSKNMKKGFCFISF 149
KI V L E +++DVR FS YG + + P FD+S +GF F+ F
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQS---ARGFAFVEF 48
Score = 34.8 bits (80), Expect = 0.006
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K+ V L +K++ FS YG+++S+ + +RGFAFV F+T K + + A
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKK-FDQSARGFAFVEFSTAKEALNAMNA 60
Query: 78 --GDHYIG 83
H +G
Sbjct: 61 LKDTHLLG 68
>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 = 36.1 bits (84), Expect = 0.002
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
++VG L ++E + + FSQ G I + + + + F+ + D A L
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGND---PYAFVEYYDHRSAAAALQTM 57
Query: 161 NPKQVICGKEVDV 173
N + I G+E+ V
Sbjct: 58 NGRL-ILGQEIKV 69
Score = 33.0 bits (76), Expect = 0.021
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 12/74 (16%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISI----KNDPHTGQSRGFAFVTFTT-QKAVDD 73
L+VG L R E + + FSQ G ++S + NDP +AFV + + A
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP-------YAFVEYYDHRSAAAA 53
Query: 74 LLAAGDHYIGNKKI 87
L I ++I
Sbjct: 54 LQTMNGRLILGQEI 67
>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 = 36.6 bits (84), Expect = 0.002
Identities = 18/58 (31%), Positives = 34/58 (58%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+FVG L+ EI+ D++ F+ +G I++ + D + KG+ F+SF ++ AE +
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61
Score = 35.4 bits (81), Expect = 0.004
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA- 77
+FVG L +I F+ +G + + D TG+S+G+ FV+F + ++ +
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 78 GDHYIGNKKIDPKRVTK 94
G ++G ++I T+
Sbjct: 64 GGQWLGGRQIRTNWATR 80
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast
pre-mRNA-splicing factor Cwc2 and similar proteins.
This subfamily corresponds to the RRM of yeast protein
Cwc2, also termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and an intervening loop,
also termed RNA-binding loop or RB loop, between ZnF
and RRM, all of which are necessary and sufficient for
RNA binding. The ZnF is also responsible for mediating
protein-protein interaction. The C-terminal flexible
region of Cwc2 interacts with the WD40 domain of Prp19.
Length = 78
Score = 36.1 bits (84), Expect = 0.002
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 10/56 (17%)
Query: 17 RKLFVGGLHRNTGEKEIND----YFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
R L+VGG+ + K+I + +F ++G++E I S+G AFV + +
Sbjct: 2 RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDI------RVLPSKGIAFVRYKYR 51
>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 = 36.2 bits (83), Expect = 0.002
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQK 69
+ + L V L +N ++E+ F GE+ES + D TGQS G+ FV + +K
Sbjct: 2 DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61
Query: 70 AVDDL 74
A++ L
Sbjct: 62 AINTL 66
>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 = 36.1 bits (83), Expect = 0.002
Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 11/78 (14%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-- 159
++++G L+ + E+D++ +F YG + E ++K G+ F+ F+D A+ +
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEI--------DLKNGYGFVEFEDSRDADDAVYE 52
Query: 160 ANPKQVICGKEVDVKRVK 177
N K +CG+ V V+ +
Sbjct: 53 LNGKD-LCGERVIVEHAR 69
Score = 34.1 bits (78), Expect = 0.008
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
++++G L + EK+I +F YG++ I +KN G+ FV F + DD
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLKN--------GYGFVEFEDSRDADD 48
>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 = 36.1 bits (84), Expect = 0.002
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSR-GFAFVTFTTQKAVDD 73
+ R ++VG + +T E+ F +GE+E I++ H + FVT+
Sbjct: 1 ERRVIYVGKIPIDTTRSELRQRFQPFGEIEEITL----HFRDDGDNYGFVTYRYACDAFR 56
Query: 74 LLAAGDH 80
+ G+
Sbjct: 57 AIEHGND 63
>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 = 35.7 bits (83), Expect = 0.002
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE 129
K+FVG L + +++R F +YG++TE
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTE 28
Score = 35.7 bits (83), Expect = 0.002
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 10/66 (15%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
KLFVG L T +E+ F +YG V E +KN + FV ++ +D +
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN---------YGFVHMEEEEDAEDAIK 51
Query: 77 AGDHYI 82
A + Y
Sbjct: 52 ALNGYE 57
>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 = 36.3 bits (83), Expect = 0.002
Identities = 18/64 (28%), Positives = 32/64 (50%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K +++ GL ++QD+ YG I + DK+ N KG+ F+ FD A++ +
Sbjct: 7 KTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV 66
Query: 160 ANPK 163
+ K
Sbjct: 67 SALK 70
Score = 30.9 bits (69), Expect = 0.15
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L++ GL NT ++++ YG++ S D T + +G+ FV F + QKAV L
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69
Query: 75 LAAG 78
A+G
Sbjct: 70 KASG 73
>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 = 35.9 bits (83), Expect = 0.002
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 21 VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD-LLAAG 78
V L E++I D+FS G++E + I+ G+ A+VTF +A + LL +G
Sbjct: 3 VTNLSPKATERDIYDFFSFSGDIEYVEIQRS---GEQSQTAYVTFKDPQAQETALLLSG 58
Score = 28.2 bits (63), Expect = 0.96
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 7/57 (12%)
Query: 105 VGGLTTEISEQDVRDYFSQYGSI--TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
V L+ + +E+D+ D+FS G I E Q+ ++S+ +++F D E L
Sbjct: 3 VTNLSPKATERDIYDFFSFSGDIEYVEIQRSGEQSQ-----TAYVTFKDPQAQETAL 54
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 36.0 bits (84), Expect = 0.002
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 10/62 (16%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF---CFISFDDQNVAEQVL 159
+FV L +E+++R FS+ Q F + K KG CF+ F+D + A Q L
Sbjct: 5 LFVANLGPNTTEEELRQLFSR-------QPGFRRLKMHNKGGGPVCFVEFEDVSFATQAL 57
Query: 160 AN 161
+
Sbjct: 58 NS 59
>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 = 35.7 bits (83), Expect = 0.002
Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R L+V L +E+ D F +YG + I I N T RG AFV + + + D
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVY---EDIYDAKN 56
Query: 77 AGDHYIG 83
A DH G
Sbjct: 57 ACDHLSG 63
Score = 26.4 bits (59), Expect = 4.5
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
++V L +IS +++ D F +YG+I + + K +G F+ ++D
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE---TRGTAFVVYED 50
>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 = 35.6 bits (83), Expect = 0.002
Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI 87
++N++FS++G + +I + +P + A V F+T + + + N+ I
Sbjct: 16 ITKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKAYRSPEAVFNNRFI 67
Score = 33.3 bits (77), Expect = 0.016
Identities = 9/49 (18%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 117 VRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQV 165
+ ++FS++G+I Q ++ + F A++ +P+ V
Sbjct: 19 LNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKAYRSPEAV 61
>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 = 35.6 bits (83), Expect = 0.002
Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
++VGGL S ++ F ++G+I +D +N + +I ++ A+
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRID--YDPGRN----YAYIEYESIEAAQA 49
Score = 30.6 bits (70), Expect = 0.12
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
L+VGGL T E+ F ++G + I DP R +A++ + + ++ AA
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIR--RIDYDPG----RNYAYIEYES---IEAAQAA 50
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and
similar proteins. This subfamily corresponds to the
RRM of Nab3p, an acidic nuclear polyadenylated
RNA-binding protein encoded by Saccharomyces cerevisiae
NAB3 gene that is essential for cell viability. Nab3p
is predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA
processing. Nab3p contains an N-terminal
aspartic/glutamic acid-rich region, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal region rich in glutamine and proline
residues. .
Length = 71
Score = 35.5 bits (82), Expect = 0.003
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 9/61 (14%)
Query: 18 KLFVGGL-HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+LF+G L + ++++ FS YGE+ I +KN + FV F + ++ + +
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKN--------AYGFVQFDSPESCANAIN 52
Query: 77 A 77
Sbjct: 53 C 53
Score = 35.5 bits (82), Expect = 0.003
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 9/50 (18%)
Query: 102 KIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
++F+G L T+ +S++D+ FS YG + + +K + F+ FD
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQI--------VLKNAYGFVQFD 42
>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 = 35.6 bits (82), Expect = 0.003
Identities = 16/53 (30%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
++FVG + R+ E E+ F + G++ + + +G++RG+AFV +TT++
Sbjct: 2 CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKE 53
Score = 29.1 bits (65), Expect = 0.52
Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF---DDQNVAEQ 157
C++FVG + ++ E ++ F + G I EF+ + S +G+ F+ + ++ +A +
Sbjct: 2 CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGE-NRGYAFVMYTTKEEAQLAIR 60
Query: 158 VLAN 161
+L N
Sbjct: 61 ILNN 64
>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 = 35.1 bits (80), Expect = 0.004
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
+ + L V L +N ++E F GE+ES + D TGQS G+ FV + D
Sbjct: 1 DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDAD 59
>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 = 34.9 bits (80), Expect = 0.005
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
+R LFVG L E+ + + F Q G + ++I D G+ + F FV F ++V
Sbjct: 1 DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESV 55
Score = 27.6 bits (61), Expect = 2.1
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+FVG L + E+ + + F Q G +T+ DK K F F+ F
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGK-PKSFGFVCF 49
>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 = 34.9 bits (81), Expect = 0.005
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFT 66
+FVG L + + + + F Y V + DP TG+S+G+ FV F
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFG 52
Score = 31.5 bits (72), Expect = 0.092
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQ-YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
IFVG L ++++ +++ F Y S+ + D KG+ F+ F D++ E+
Sbjct: 2 HSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDED--ERDR 59
Query: 160 A 160
A
Sbjct: 60 A 60
>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 = 34.4 bits (80), Expect = 0.006
Identities = 15/55 (27%), Positives = 27/55 (49%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
++VG L+ +E+ + + FS+ G I D+ GFCF+ + + AE
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAEN 55
Score = 32.9 bits (76), Expect = 0.022
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
L+VG L T E++I + FS+ G+++ I + D T GF FV + T+
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTR 50
>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 = 34.9 bits (80), Expect = 0.006
Identities = 17/47 (36%), Positives = 23/47 (48%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+V L R E E+ F YG + ++ D TG RG AFV +
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRY 49
Score = 34.5 bits (79), Expect = 0.008
Identities = 16/64 (25%), Positives = 34/64 (53%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
++V L +++E ++R F YG+I + DKS + +G F+ +D + A+ +++
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 163 KQVI 166
I
Sbjct: 63 NGTI 66
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B).
This subgroup corresponds to the RRM of Setd1B, also
termed SET domain-containing protein 1B (Set1B), or
lysine N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits
high homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone
H3 at Lys4. Set1B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), an N- SET
domain, and a C-terminal catalytic SET domain followed
by a post-SET domain. .
Length = 93
Score = 35.0 bits (80), Expect = 0.007
Identities = 18/50 (36%), Positives = 24/50 (48%)
Query: 24 LHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
L+ N E + D +YGEVE + I +P + G A V F T K D
Sbjct: 10 LNDNIRENFLTDMCKKYGEVEEVEILYNPKNKKHLGIAKVVFATVKGAKD 59
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 34.1 bits (79), Expect = 0.008
Identities = 16/54 (29%), Positives = 28/54 (51%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
++VG L E+ + + F Q G V ++ I D T +G+ FV F +++ D
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDAD 54
Score = 34.1 bits (79), Expect = 0.008
Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF---DDQNVAEQVL 159
++VG L +++E+ + + F Q G + P D+ +G+ F+ F +D + A +++
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 160 ANPKQVICGKEVDVKR 175
K + GK + V +
Sbjct: 61 NMIK--LYGKPIRVNK 74
>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 = 34.2 bits (78), Expect = 0.010
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTF 65
D +FV GL + + + DYF Q G +++ I++ D TG+ +G A V+F
Sbjct: 1 DNNTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 59
Score = 33.4 bits (76), Expect = 0.018
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSI---TEFQQPF-----DKSKNMKKGFCFISFDD 151
IFV GL +++ + V DYF Q G I + QP D+ KG +SFDD
Sbjct: 5 IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 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 = 33.9 bits (78), Expect = 0.010
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTT 67
+ + GL + E++I + +G E + + + TG SRGFAFV F +
Sbjct: 5 IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMS 54
Score = 27.3 bits (61), Expect = 2.8
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISF 149
I + GL ++E+D+R+ +G + + K+ +GF F+ F
Sbjct: 5 IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEF 52
>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 = 33.8 bits (78), Expect = 0.011
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 12/60 (20%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ----KAVDDL 74
L+V L +T E+++ + FS+YGEVE + D +AFV F + KA++++
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55
Score = 31.8 bits (73), Expect = 0.054
Identities = 12/57 (21%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
++V L +E+ +R+ FS+YG + ++ D + F+ F++++ A + +
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAM 52
>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 = 33.6 bits (77), Expect = 0.012
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
K+FVG + +T ++E+ F YG V S ++ R FAFV
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFV 39
Score = 30.6 bits (69), Expect = 0.15
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
KIFVG + + S++++R F YG++ S + + F F+ + A++ +
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVL--------SCAVMRQFAFVHLRGEAAADRAIE 52
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 33.7 bits (78), Expect = 0.014
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 10/69 (14%)
Query: 106 GGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQV 165
GGL +S +++ F +YG++ + P K +CF+S+ A
Sbjct: 9 GGLGNGVSREELLRVFEKYGTVEDLVMPPGKP------YCFVSYSSIEDAAAAYDA---- 58
Query: 166 ICGKEVDVK 174
+ GKE+++
Sbjct: 59 LNGKELELP 67
>gnl|CDD|191721 pfam07292, NID, Nmi/IFP 35 domain (NID). This family represents a
domain of approximately 90 residues that is tandemly
repeated within interferon-induced 35 kDa protein (IFP
35) and the homologous N-myc-interactor (Nmi). This
domain mediates Nmi-Nmi protein interactions and
subcellular localisation.
Length = 88
Score = 33.6 bits (77), Expect = 0.014
Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 23/92 (25%)
Query: 61 AFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPL-------------KCKIFVGG 107
A +TF ++ ++L+ +H++ + RV + PL K KI V G
Sbjct: 1 ALITFEKEEVAQNVLSMKEHHV-QMEDCRLRVQAQPVPLNSGVRFQVSVQVSKMKINVTG 59
Query: 108 LTTEISEQDVRDYFSQYGSITEFQQPFDKSKN 139
+ +SE+ +RD + + F KS+N
Sbjct: 60 IPDRLSEEQLRD---------KLELSFGKSRN 82
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 33.5 bits (76), Expect = 0.015
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
++VG L+ +++E + FSQ G + D + N +CF+ F + A LA
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGN--DPYCFVEFFEHRHAAASLAAM 59
Query: 161 NPKQVICGKEVDV 173
N ++++ GKEV V
Sbjct: 60 NGRKIM-GKEVKV 71
Score = 28.5 bits (63), Expect = 0.92
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L+VG L R+ E I FSQ G +S + D T + + FV F + LAA
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAA- 58
Query: 79 DHYIGNKKIDPKRV 92
+ +KI K V
Sbjct: 59 ---MNGRKIMGKEV 69
>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 = 33.6 bits (76), Expect = 0.015
Identities = 18/64 (28%), Positives = 32/64 (50%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
K +++ GL ++QD+ YG I + DK+ N KG+ F+ FD + A++ +
Sbjct: 1 KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60
Query: 160 ANPK 163
K
Sbjct: 61 TALK 64
Score = 32.8 bits (74), Expect = 0.028
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDDL 74
L++ GLH T ++++ YG++ S D T + +G+ FV F QKAV L
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63
Query: 75 LAAG 78
A+G
Sbjct: 64 KASG 67
>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 = 33.4 bits (76), Expect = 0.015
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 7/77 (9%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+ LFV GL +T E+ + + F G + + I D TG S+GF FV F++++
Sbjct: 1 KTLFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAK---- 53
Query: 77 AGDHYIGNKKIDPKRVT 93
A + + +ID +VT
Sbjct: 54 AAKEAMEDGEIDGNKVT 70
Score = 26.5 bits (58), Expect = 5.0
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV GL+ + +E+ +++ F GSI + D+ KGF F+ F + A+
Sbjct: 3 LFVKGLSEDTTEETLKESFD--GSIAA-RIVTDRDTGSSKGFGFVDFSSEEDAKAA---- 55
Query: 163 KQVICGKEVDVKRVKFN 179
K+ + E+D +V +
Sbjct: 56 KEAMEDGEIDGNKVTLD 72
>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 = 33.3 bits (76), Expect = 0.016
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS-KNMKKGFCFISFDDQNVAEQVLAN 161
++VG L ++E ++ F G + + DK+ K + G F+ + + AE L
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYG--FVEYHQSHDAEIAL-- 56
Query: 162 PKQVICGKEVDVKRVKFN 179
Q + G++++ ++ N
Sbjct: 57 --QTLNGRQIENNEIRVN 72
Score = 25.6 bits (56), Expect = 10.0
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
L+VG L E + F G V+++ I D + + + FV +
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEY 46
>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 = 33.3 bits (77), Expect = 0.016
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 19 LFVGGLHRNTGEKEINDYFSQY-GEVESISIKNDPHTGQSRGFAFVTFTTQ 68
LF+ L T ++ + F+Q+ G E + RG AFV F T+
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR-------RGIAFVEFETE 48
>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 = 33.3 bits (76), Expect = 0.017
Identities = 14/57 (24%), Positives = 24/57 (42%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
I+V G T ++E+ +++ F Q + P D +CF+ F A L
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAAL 57
Score = 27.9 bits (62), Expect = 1.2
Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF-TTQKAVDDL 74
++V G ++ E+ + + F Q ++E+I + D +G+ + F+ F +Q A L
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAAL 57
>gnl|CDD|241190 cd12746, RRM2_RBM12B, RNA recognition motif 2 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM2 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 78
Score = 33.2 bits (76), Expect = 0.017
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
LF+ GL + E + D+FS I +KN G + G + V F T++ + L
Sbjct: 2 LFLRGLPFSVTEDNVRDFFSGLKVDGVIFLKN--RRGLNNGNSMVKFATKEDAIEGLKRD 59
Query: 79 DHYIGNKKIDPKRVT 93
Y+G++ I+ R T
Sbjct: 60 RQYMGSRYIEISRTT 74
>gnl|CDD|240992 cd12548, RRM_Set1A, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1A (Set1A).
This subgroup corresponds to the RRM of Setd1A, also
termed SET domain-containing protein 1A (Set1A), or
lysine N-methyltransferase 2F, or Set1/Ash2 histone
methyltransferase complex subunit Set1, a ubiquitously
expressed vertebrates histone methyltransferase that
exhibits high homology to yeast Set1. Set1A is
localized to euchromatic nuclear speckles and
associates with a complex containing six human homologs
of the yeast Set1/COMPASS complex, including CXXC
finger protein 1 (CFP1; homologous to yeast Spp1),
Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to
yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82
(homologous to yeast Swd2). Set1A contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
an N- SET domain, and a C-terminal catalytic SET domain
followed by a post-SET domain. In contrast to Set1B,
Set1A additionally contains an HCF-1 binding motif that
interacts with HCF-1 in vivo. .
Length = 95
Score = 33.8 bits (77), Expect = 0.017
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 24 LHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
L+ N E + D ++GEVE + I P T + G A V FT+ + D
Sbjct: 10 LNDNVREPFLADMCRKFGEVEEVEILLHPKTRKHLGLARVLFTSTRGAKD 59
>gnl|CDD|240991 cd12547, RRM1_2_PAR10, RNA recognition motif 1 and 2 in poly
[ADP-ribose] polymerase 10 (PARP-10) and similar
proteins. This subgroup corresponds to the RRM1 and
RRM2 of PARP-10, a novel oncoprotein c-Myc-interacting
protein with poly(ADP-ribose) polymerase activity. It is
localized to the nuclear and cytoplasmic compartments.
In addition to the PARP activity, PARP-10 is also
involved in the control of cell proliferation by
inhibiting c-Myc- and E1A-mediated cotransformation of
primary cells. PARP-10 may play a role in nuclear
processes including the regulation of chromatin, gene
transcription, and nuclear/cytoplasmic transport. It
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two overlapping C-terminal
domains composed of a glycine-rich region and a region
with homology to catalytic domains of PARP enzymes (PARP
domain). In addition, PARP-10 contains two
ubiquitin-interacting motifs (UIM). .
Length = 71
Score = 33.0 bits (76), Expect = 0.017
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 14/80 (17%)
Query: 101 CKIFVGGLTTEISEQDVRDYF-----SQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
I V G + + S++ + YF S G I ++ DK I+F+D VA
Sbjct: 1 RTIEVSGFSPDTSDETLELYFENKRRSGGGEIESIERKGDK--------VLITFEDPAVA 52
Query: 156 EQVLANPKQVICGKEVDVKR 175
E+VL + G + VK
Sbjct: 53 ERVLKR-THGLNGATLTVKP 71
>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 = 33.4 bits (76), Expect = 0.017
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
K++VG L G+ E+ FS YG + ++ I +P GFAFV F + +D
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAED 51
Score = 30.4 bits (68), Expect = 0.23
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 6/74 (8%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ-VLA 160
K++VG L T + ++ FS YG + + GF F+ F+D AE V
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 55
Query: 161 NPKQVICGKEVDVK 174
+VICG V V+
Sbjct: 56 LDGKVICGSRVRVE 69
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 of MRN1, also termed multicopy
suppressor of RSC-NHP6 synthetic lethality protein 1,
or post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 33.2 bits (76), Expect = 0.018
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 10/62 (16%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVD 72
R +++G L + E+E+ + ++G ++ I I + + AFV F K V
Sbjct: 4 RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKVVT 57
Query: 73 DL 74
L
Sbjct: 58 TL 59
Score = 32.0 bits (73), Expect = 0.051
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISF 149
+++G L SE+++R+ ++G I D+ K +K K F+ F
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPI-------DQIKIVKEKNIAFVHF 46
>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 = 32.8 bits (75), Expect = 0.021
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 13/76 (17%)
Query: 19 LFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
LFV G T E++I F +G + I+ + FAFV F + L A
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR--------KTFAFVEFEDSEDATKALEA 53
Query: 78 GDHYIGNKKIDPKRVT 93
+ +ID +T
Sbjct: 54 ----LHGSRIDGSVLT 65
Score = 29.7 bits (67), Expect = 0.31
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 9/67 (13%)
Query: 112 ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-ANPKQVICGKE 170
E+D+ F +G + ++K F F+ F+D A + L A I G
Sbjct: 12 TREEDIEKLFEPFGPLVRCD--------IRKTFAFVEFEDSEDATKALEALHGSRIDGSV 63
Query: 171 VDVKRVK 177
+ V+ VK
Sbjct: 64 LTVEFVK 70
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 35.4 bits (82), Expect = 0.022
Identities = 11/43 (25%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
E++I ++FS G++E + ++++ Q A+VTF + +
Sbjct: 18 ERDIKEFFSFSGDIEYVEMQSENERSQ---IAYVTFKDPQGAE 57
>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 = 32.9 bits (75), Expect = 0.023
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 11/56 (19%)
Query: 17 RKLFVG-----GLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
R +++G G RN EKE+ +YGE+ESI I + + AF+ F
Sbjct: 3 RNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRIL------REKACAFINFMN 52
>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 = 33.1 bits (76), Expect = 0.025
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L + L + ++E F G V++ I D TG S GF FV + + Q+A+ L
Sbjct: 3 LIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTL 62
Query: 75 LAAGDHYIGNKKI 87
+ NK+I
Sbjct: 63 ---NGLQLQNKRI 72
>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 = 33.1 bits (75), Expect = 0.026
Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
R +F L +++ D+FS G+V + I +D ++ +S+G A+V F ++V
Sbjct: 2 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 56
Score = 30.4 bits (68), Expect = 0.21
Identities = 12/51 (23%), Positives = 24/51 (47%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+F L I +D+ D+FS G + + + D++ KG ++ F +
Sbjct: 4 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 54
>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 = 33.1 bits (75), Expect = 0.028
Identities = 14/55 (25%), Positives = 30/55 (54%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
R +F L +++ ++FS G+V + + +D ++ +S+G A+V F +V
Sbjct: 2 RTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSV 56
Score = 30.8 bits (69), Expect = 0.14
Identities = 15/72 (20%), Positives = 32/72 (44%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+F L I +D+ ++FS G + + + D++ KG ++ F D + +
Sbjct: 4 VFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLT 63
Query: 163 KQVICGKEVDVK 174
Q + G + V+
Sbjct: 64 GQRVLGVPIIVQ 75
>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 = 32.7 bits (74), Expect = 0.030
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD-QNVAE 156
PL CK++VG L ++ ++ F YG + ++N GF F+ F+D ++ A+
Sbjct: 2 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV----ARN-PPGFAFVEFEDPRDAAD 56
Query: 157 QVLANPKQVICGKEVDVK 174
V + +CG V V+
Sbjct: 57 AVRELDGRTLCGCRVRVE 74
Score = 31.9 bits (72), Expect = 0.052
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 11/62 (17%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
K++VG L N + E+ F YG + S+ + +P GFAFV F +D A
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEF------EDPRDA 54
Query: 78 GD 79
D
Sbjct: 55 AD 56
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 32.5 bits (74), Expect = 0.032
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
++VG + ++ D+ F +G I EF+ D +GF F+ D
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLD 44
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 32.7 bits (75), Expect = 0.032
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 10/84 (11%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
L++ L + E+++ YG+V S I D GQSRG F +++ +D++
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDS-KGQSRGVGFARMESREKCEDII--- 58
Query: 79 DHYIGNKKIDPKRVTKRVNPLKCK 102
K + K + PL K
Sbjct: 59 ------SKFNGKYLKGEGEPLLVK 76
>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 = 32.7 bits (75), Expect = 0.032
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
L++G L E I F+ GE V S+ I + TG G+ FV F + + L
Sbjct: 2 LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCL 59
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast
nucleolar protein 3 (Npl3p) and similar proteins. This
subfamily corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or
nuclear polyadenylated RNA-binding protein 1. Npl3p is
a major yeast RNA-binding protein that competes with
3'-end processing factors, such as Rna15, for binding
to the nascent RNA, protecting the transcript from
premature termination and coordinating transcription
termination and the packaging of the fully processed
transcript for export. It specifically recognizes a
class of G/U-rich RNAs. Npl3p is a multi-domain protein
containing two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a short
linker and a C-terminal domain rich in glycine,
arginine and serine residues. .
Length = 67
Score = 32.0 bits (73), Expect = 0.035
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 12/61 (19%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDD 73
+L+V +T E I + FS YG V+ + + + FAFV F + +A D
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRAKDS 52
Query: 74 L 74
+
Sbjct: 53 V 53
Score = 31.2 bits (71), Expect = 0.088
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 8/56 (14%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
+++V + SE +R+ FS YG++ E + M F F+ F+ A +
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVK--------MISNFAFVEFESLESAIR 48
>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 = 32.1 bits (73), Expect = 0.037
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
R +F G + + EI F +YG V+ + +K+ GFAFV ++ +D +
Sbjct: 1 RPVFCGNFEYDARQSEIERLFGKYGRVDRVDMKS--------GFAFVYMEDERDAEDAIR 52
Query: 77 AGDHY 81
D++
Sbjct: 53 GLDNF 57
Score = 29.8 bits (67), Expect = 0.32
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+F G + + ++ F +YG + +MK GF F+ +D+ AE
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRV--------DMKSGFAFVYMEDERDAE 48
>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 = 32.2 bits (74), Expect = 0.039
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
+L V L + E E+ ++FS+ GE+ + + G+SR AF+ + T++ +
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEE---EAQK 57
Query: 77 AGDH----YIGNKKI 87
A D+ YI KI
Sbjct: 58 AKDYFNNTYINTSKI 72
Score = 25.7 bits (57), Expect = 7.7
Identities = 11/58 (18%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQ-YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
++ V L ++E +++++FS+ G IT+ + + + FI + + A++
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKA 58
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM1 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 32.2 bits (74), Expect = 0.040
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF-TTQKAVDDLLA 76
++ V L + E + ++F GEV + + G+SR F FV F + + A +
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVKY 60
Query: 77 AGDHYIGNKKI 87
+I KI
Sbjct: 61 FNKTFIDTSKI 71
Score = 25.6 bits (57), Expect = 9.7
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 13/65 (20%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG------FCFISFDDQNVA 155
+I V L ++E +R++F G +T+ K M+ F F+ F + A
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTD-------VKVMRTRDGKSRRFGFVGFKSEEDA 54
Query: 156 EQVLA 160
+Q +
Sbjct: 55 QQAVK 59
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding
protein 19 (RBM19) and similar proteins. This
subfamily corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). .
Length = 72
Score = 32.0 bits (73), Expect = 0.040
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 23 GLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYI 82
G N EK I ++FS + +I I + H G+ GFAFV +++ + L Y+
Sbjct: 7 GAPFNVKEKHIREFFSPL-KPVAIRIVKNDH-GRKTGFAFVDLKSEEDLKKALKRNKDYM 64
Query: 83 GNKKID 88
G + I+
Sbjct: 65 GGRYIE 70
>gnl|CDD|205803 pfam13625, Helicase_C_3, Helicase conserved C-terminal domain.
This domain family is found in a wide variety of
helicases and helicase-related proteins.
Length = 128
Score = 33.3 bits (77), Expect = 0.046
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 12/60 (20%)
Query: 114 EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVD 172
+RD ++G + + K ++ DD V E++LA+ K + + +
Sbjct: 76 LYLIRDVARRHGRLR-----------LGKAGLYLRSDDPAVLEELLADKKLAPLLLRRIA 124
>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 = 32.0 bits (72), Expect = 0.046
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
R L+V GL T ++ + FS+YG+V + + + +R + FVT +T
Sbjct: 2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMST 52
>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 = 32.2 bits (73), Expect = 0.048
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 13/79 (16%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDD 73
++FVG + R+ E E+ F G + + + D G++RG+AFV +T ++AV +
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVRE 61
Query: 74 LLAAGDHYIGNKKIDPKRV 92
L N +I P R+
Sbjct: 62 L--------NNYEIRPGRL 72
Score = 29.2 bits (65), Expect = 0.58
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD-KSKNMKKGFCFISFDDQNVAEQVL 159
C++FVG + ++ E ++ F G I E + D KN +G+ F+ + ++ A++ +
Sbjct: 2 CEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKN--RGYAFVMYTQKHEAKRAV 59
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 32.0 bits (73), Expect = 0.049
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSI---TEFQQP-----FDKSKNMKKGFCFISFDDQNV 154
+FV L +EQD+ ++F G I + +P DK KG +++DD +
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 155 AE 156
A
Sbjct: 61 AS 62
Score = 30.5 bits (69), Expect = 0.22
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEV--------ESISIKNDPHTGQSRGFAFVTF 65
+FV L NT E+++ ++F G + I + D TG+ +G A VT+
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTY 55
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 31.9 bits (72), Expect = 0.049
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 10/74 (13%)
Query: 102 KIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
++F+G L T + + DV FS+YG I ++ KGF F+ + ++ A +A
Sbjct: 3 RVFIGNLNTLVVKKSDVEAIFSKYGKIV--------GCSVHKGFAFVQYVNERNARAAVA 54
Query: 161 NPK-QVICGKEVDV 173
++I G+ +D+
Sbjct: 55 GEDGRMIAGQVLDI 68
Score = 26.1 bits (57), Expect = 4.9
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 18 KLFVGGLHRNTGEK-EINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
++F+G L+ +K ++ FS+YG++ S+ +GFAFV + ++ +A
Sbjct: 3 RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVA 54
Query: 77 AGD 79
D
Sbjct: 55 GED 57
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit
4 (THOC4) and similar proteins. This subgroup
corresponds to the RRM of THOC4, also termed
transcriptional coactivator Aly/REF, or ally of AML-1
and LEF-1, or bZIP-enhancing factor BEF, an mRNA
transporter protein with a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It is
involved in RNA transportation from the nucleus. THOC4
was initially identified as a transcription coactivator
of LEF-1 and AML-1 for the TCRalpha enhancer function.
In addition, THOC4 specifically binds to rhesus (RH)
promoter in erythroid. It might be a novel
transcription cofactor for erythroid-specific genes. .
Length = 75
Score = 31.8 bits (73), Expect = 0.050
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
KL V L + +I + F+++G ++ ++ D +G+S G A V F + D L A
Sbjct: 2 KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRA---DALKA 57
Query: 78 GDHYIG 83
Y G
Sbjct: 58 MKQYNG 63
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 31.9 bits (72), Expect = 0.050
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+FV L G K++ + FS G V+ IK D G+SRG VTF
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKED-KDGKSRGMGTVTF 48
>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 = 32.2 bits (74), Expect = 0.051
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+FVG + +S+ +R + G + +++ D S K F F F+D E L
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFED---PEGAL- 56
Query: 161 NPKQVICGKEVDVKR--VKFNPET 182
+++ G E+ K+ VK + +T
Sbjct: 57 RALRLLNGLELGGKKLLVKVDAKT 80
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 31.9 bits (72), Expect = 0.052
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV--L 159
+IFV L +++ Q +++ FSQ G + + + K+ KG + FD AE+ L
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMENGKS--KGCGTVRFDSPESAEKACRL 58
Query: 160 ANPKQVICGKEVDVK 174
N + I G+E+DV+
Sbjct: 59 MNGIK-INGREIDVR 72
>gnl|CDD|241209 cd12765, RRM2_SRSF5, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM2 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5), is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 75
Score = 32.0 bits (72), Expect = 0.054
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 15/80 (18%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSIT--EFQQPFDKSKNMKKGFC-FISFDDQNVAEQV 158
++ V L++ +S QD++D+ Q G +T + +P + +G F S+ D
Sbjct: 5 RLIVENLSSRVSWQDLKDFMRQAGEVTFADAHRP-----KLNEGVVEFASYSD------- 52
Query: 159 LANPKQVICGKEVDVKRVKF 178
L N + + GKE++ +++K
Sbjct: 53 LKNAIEKLSGKEINGRKIKL 72
>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM2 of 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 has 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 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. The
second subfamily includes CPEB-2, CPEB-3, CPEB-4, and
related protiens. Due to the 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. 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 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 = 81
Score = 31.9 bits (73), Expect = 0.055
Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 5/77 (6%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQ----KAV 71
R +FVGGL E+ + YG V + I D G A VTF + KAV
Sbjct: 1 RTVFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKAV 60
Query: 72 DDLLAAGDHYIGNKKID 88
++ NK++
Sbjct: 61 SEVFVELPFNDINKRVR 77
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La
or LARP3) and similar proteins. This subfamily
corresponds to the RRM1 of La autoantigen, also termed
Lupus La protein, or La ribonucleoprotein, or Sjoegren
syndrome type B antigen (SS-B), a highly abundant
nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. La contains an N-terminal La motif
(LAM), followed by two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also possesses a short
basic motif (SBM) and a nuclear localization signal
(NLS) at the C-terminus. .
Length = 72
Score = 31.8 bits (73), Expect = 0.055
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
++V G ++ +I ++F ++G+V +I ++ D + +G FV F T++ L
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLD-KKFKGSVFVEFKTEEDAKKFLEK 59
Score = 28.7 bits (65), Expect = 0.63
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
++V G + + D++++F ++G + + D K K G F+ F + A++ L
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFK-GSVFVEFKTEEDAKKFLEKE 60
Query: 163 KQVICGKEVDVK 174
K KE+ V
Sbjct: 61 KLKYKEKELTVM 72
>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 = 31.9 bits (73), Expect = 0.060
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISI---KNDPHTGQSRGFAFVTFTTQKAVDDLL 75
L+VG L+ E+ + F ++G + S+ I + + ++R FV F + + L
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 76 AAGDHYI 82
D
Sbjct: 64 DELDGKD 70
Score = 28.8 bits (65), Expect = 0.87
Identities = 13/62 (20%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQ--QPFDKSKNMKKGFC-FISFDDQNVAEQVL 159
++VG L +++E+ + F ++G + + P + + + C F++F ++ AE+ L
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 160 AN 161
Sbjct: 64 DE 65
>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 = 32.0 bits (72), Expect = 0.063
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
++VG L+ +++E + FSQ G + + + N +CF+ F + A LA
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAM 59
Query: 161 NPKQVICGKEVDV 173
N ++++ GKEV V
Sbjct: 60 NGRKIL-GKEVKV 71
Score = 27.0 bits (59), Expect = 3.0
Identities = 21/64 (32%), Positives = 27/64 (42%), Gaps = 12/64 (18%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISI-----KNDPHTGQSRGFAFVTFTTQKAVDD 73
L+VG L R+ E I FSQ G +S + NDP + FV F +
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-------YCFVEFYEHRDAAA 54
Query: 74 LLAA 77
LAA
Sbjct: 55 ALAA 58
>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 = 31.5 bits (71), Expect = 0.064
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ-PFDKSKNMKKGFCFISFDDQNVAEQVL 159
C ++ GG+ + ++EQ +R FS +G I E + P +KG+ FI F A +
Sbjct: 1 CTVYCGGIASGLTEQLMRQTFSPFGQIMEIRVFP-------EKGYSFIRFSTHESAAHAI 53
Query: 160 AN 161
+
Sbjct: 54 VS 55
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 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 = 85
Score = 31.7 bits (72), Expect = 0.064
Identities = 17/83 (20%), Positives = 39/83 (46%), Gaps = 11/83 (13%)
Query: 103 IFVGGLTTEISEQDVRDYFSQY-------GSITEFQQPFDKSKNMK----KGFCFISFDD 151
+++G L+ +++ +R +F IT P K+K KGF ++ F
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60
Query: 152 QNVAEQVLANPKQVICGKEVDVK 174
Q + +A ++++ G+++ +K
Sbjct: 61 QEATKAAIALSEKILNGRKLLIK 83
Score = 26.7 bits (59), Expect = 4.1
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 56 QSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKID 88
Q++GFA+V FT+Q+A +A + G K +
Sbjct: 49 QNKGFAYVDFTSQEATKAAIALSEKILNGRKLLI 82
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for
growth. Srp1p is closely related to the SR protein
family found in metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. Some family members also contain another RRM
domain.
Length = 78
Score = 31.7 bits (72), Expect = 0.068
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
L+V G T +++ F +YG + I P T QSR FAFV + + + +D
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDIP-PPRTFQSRPFAFVEYESHRDAED 55
>gnl|CDD|218575 pfam05390, KRE9, Yeast cell wall synthesis protein KRE9/KNH1. This
family contains several KRE9 and KNH1 proteins which are
involved in encoding cell surface O glycoproteins, which
are required for beta -1,6-glucan synthesis in yeast.
Length = 107
Score = 32.3 bits (73), Expect = 0.075
Identities = 20/50 (40%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 218 YAGYAATDYGYTAGSYDAYATAYPGYDY---SAMGYAYPAAATSYGGGKY 264
YA A T Y + D + T PG+ Y SA+ YA PA S GG Y
Sbjct: 39 YATSAVTYYSTLRSTPDQHTTLTPGWSYTISSAVNYATPAPMPSDNGGWY 88
>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 = 31.4 bits (72), Expect = 0.083
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 113 SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
+ D+RD F QYG I + P + N + FC++ F A +A
Sbjct: 13 DQSDIRDLFEQYGEILSIRFPSLRF-NKTRRFCYVQFTSPESAAAAVA 59
Score = 26.8 bits (60), Expect = 3.8
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 14/74 (18%)
Query: 30 EKEINDYFSQYGEVESI---SIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK 86
+ +I D F QYGE+ SI S++ ++R F +V FT+ ++ +A N K
Sbjct: 14 QSDIRDLFEQYGEILSIRFPSLR----FNKTRRFCYVQFTSPESAAAAVAL-----LNGK 64
Query: 87 IDPKR--VTKRVNP 98
+ V K +P
Sbjct: 65 LGEGYKLVVKISDP 78
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 31.5 bits (72), Expect = 0.084
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
P C +++ GL ++EQ + +FS+YG + D+ ++G + FD A+
Sbjct: 6 PTNC-VWLDGLDESVTEQYLTRHFSRYGPVVHVV--IDR----QRGQALVFFDKVEAAQA 58
Query: 158 VLANPK-QVICGKEVDV 173
+ K + + G+++ V
Sbjct: 59 AVNEMKGRKLGGRKLQV 75
>gnl|CDD|241170 cd12726, RRM2_CPEB2_like, RNA recognition motif 2 found in
cytoplasmic polyadenylation element-binding protein
CPEB-2, CPEB-3, CPEB-4 and similar protiens. This
subgroup corresponds to the RRM2 of the paralog
proteins CPEB-2, CPEB-3 and CPEB-4, all well conserved
in both, vertebrates and invertebrates. Due to the high
sequence similarity, members in this family may share
similar expression patterns and functions. CPEB-2 is an
RNA-binding protein that is abundantly expressed in
testis and localized in cytoplasm in transfected HeLa
cells. It preferentially binds to poly(U) RNA oligomers
and may regulate the translation of stored mRNAs during
spermiogenesis. Moreover, CPEB-2 impedes target RNA
translation at elongation; it directly interacts with
the elongation factor, eEF2, to reduce
eEF2/ribosome-activated GTP hydrolysis in vitro and
inhibit peptide elongation of CPEB2-bound RNA in vivo.
CPEB-3 is a sequence-specific translational regulatory
protein that regulates translation in a
polyadenylation-independent manner. It functions as a
translational repressor that governs the synthesis of
the AMPA receptor GluR2 through binding GluR2 mRNA. It
also represses translation of a reporter RNA in
transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All family members contain an
N-terminal unstructured region, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a Zn-finger
motif. In addition, they do have conserved nuclear
export signals that are not present in CPEB-1. .
Length = 81
Score = 31.3 bits (71), Expect = 0.094
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
+ +FVGG+ R E+ + YG V I DP +G V F+ Q++
Sbjct: 1 KTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQS 55
>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 = 31.4 bits (71), Expect = 0.095
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 43 VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
V +I + D T Q+RGFAFV ++ LL
Sbjct: 31 VSNIRLIKDKQTQQNRGFAFVQLSSALEASQLL 63
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 31.4 bits (72), Expect = 0.10
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQY----GSITEFQQPFDKSK-NMKKGFCFISF 149
+++VG L I+E+++ D+F+Q G P + N +K F F+ F
Sbjct: 3 RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEF 55
Score = 31.0 bits (71), Expect = 0.13
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 9/58 (15%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHT-------GQSRGFAFVTFTT 67
R+L+VG L E+E+ D+F+Q + + + P + FAFV F T
Sbjct: 2 RRLYVGNLPPGITEEELVDFFNQA--MLAAGLNQAPGNPVLSVQINPEKNFAFVEFRT 57
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 31.0 bits (71), Expect = 0.11
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQY-GSITEFQQPFD----KSKNMKKGFCFISFDDQNVA 155
+++V L+ ++E+D+ F ++ S +E + FD MK G F++F + +A
Sbjct: 2 KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMK-GQAFVTFPSEEIA 60
Query: 156 EQVL 159
+ L
Sbjct: 61 TKAL 64
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in
Saccharomyces cerevisiae protein Nrd1,
Schizosaccharomyces pombe Rpb7-binding protein seb1 and
similar proteins. This subfamily corresponds to the
RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous
nuclear ribonucleoprotein (hnRNP)-like RNA-binding
protein encoded by gene NRD1 (for nuclear pre-mRNA
down-regulation) from yeast S. cerevisiae. It is
implicated in 3' end formation of small nucleolar and
small nuclear RNAs transcribed by polymerase II, and
plays a critical role in pre-mRNA metabolism. Nrd1
contains an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a short arginine-, serine-, and glutamate-rich
segment similar to the regions rich in RE and RS
dipeptides (RE/RS domains) in many metazoan splicing
factors, and a proline- and glutamine-rich C-terminal
domain (P+Q domain) similar to domains found in several
yeast hnRNPs. Disruption of NRD1 gene is lethal to
yeast cells. Its N-terminal domain is sufficient for
viability, which may facilitate interactions with RNA
polymerase II where Nrd1 may function as an auxiliary
factor. By contrast, the RRM, RE/RS domains, and P+Q
domain are dispensable. Seb1 is an RNA-binding protein
encoded by gene seb1 (for seven binding) from fission
yeast S. pombe. It is essential for cell viability and
bound directly to Rpb7 subunit of RNA polymerase II.
Seb1 is involved in processing of polymerase II
transcripts. It also contains one RRM motif and a
region rich in arginine-serine dipeptides (RS domain).
Length = 79
Score = 31.0 bits (70), Expect = 0.11
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKND 51
R LF GG+ N E ++ F ++GEV+S + ND
Sbjct: 3 SRTLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNND 38
>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 = 31.2 bits (70), Expect = 0.11
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
+FV L ++ E + F +G V ++ + D +T + +GF FVT T
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMT 53
Score = 26.2 bits (57), Expect = 6.4
Identities = 15/59 (25%), Positives = 29/59 (49%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
IFV L+ + E + F +G++ + D + N KGF F++ + + A +A+
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64
>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 = 30.9 bits (70), Expect = 0.12
Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 8/70 (11%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
++ G T DV+ F G + + + FI+F++ A+ +
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRT----VQPHAFITFENLEAAQLAIET- 56
Query: 163 KQVICGKEVD 172
+ G VD
Sbjct: 57 ---LNGASVD 63
Score = 28.9 bits (65), Expect = 0.48
Identities = 9/54 (16%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
++ G + ++ F G V +++ + + AF+TF +A
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR----TVQPHAFITFENLEAAQ 51
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 30.7 bits (69), Expect = 0.13
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
K+++G L+ ++ +D+R F + + P +K G+ F+ + DQN A
Sbjct: 3 KLYIGNLSPAVTAEDLRQLFG------DRKLPLTGQVLLKSGYAFVDYPDQNWA 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 = 31.1 bits (70), Expect = 0.13
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
R LF+G L E ++ F ++G + + IK P GQ+ + F+ F
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVDIKR-PGRGQTSTYGFLKF 55
Score = 30.3 bits (68), Expect = 0.28
Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 14/80 (17%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVAEQ--- 157
+F+G L ++E D+R F ++G ITE ++P + + F+ F++ ++A +
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIKRP---GRGQTSTYGFLKFENLDMAHRAKL 66
Query: 158 ------VLANPKQVICGKEV 171
+ NP ++ GK
Sbjct: 67 AMSGKVLRRNPIKIGYGKAT 86
>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 = 31.0 bits (71), Expect = 0.13
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 121 FSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
FS++G P D++ KG+ F+ F A++ +
Sbjct: 28 FSKFGVGKIVGIYMPVDETG-KTKGYAFVEFATPEEAKEAVKA 69
Score = 28.3 bits (64), Expect = 1.1
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 40 YGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
G++ I + D TG+++G+AFV F T + + + A + K+D K+ T VN
Sbjct: 33 VGKIVGIYMPVDE-TGKTKGYAFVEFATPEEAKEAVKA----LNGYKLD-KKHTFAVN 84
>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 = 30.8 bits (69), Expect = 0.14
Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+F+ L ++ E + F +G V ++ + D +T + +GF FVT T + +A+
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
Query: 79 DHY-IGNK 85
+ Y +G+K
Sbjct: 64 NGYRLGDK 71
Score = 25.8 bits (56), Expect = 9.2
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
IF+ L + E + F +G++T + D + N KGF F++ + A +A+
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIAS 62
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 30.7 bits (70), Expect = 0.15
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 16 ERKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
E LFVG L + + ++ ++FS+ Y + + D G SRG+ FV F+ +
Sbjct: 1 EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRA 59
Query: 75 LAAGDHYIG 83
L G
Sbjct: 60 LTEMQGASG 68
Score = 29.2 bits (66), Expect = 0.50
Identities = 14/54 (25%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQ-YGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
+FVG LT ++ + + ++FS+ Y S + D +G+ F+ F D++
Sbjct: 2 FSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDES 54
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 30.3 bits (69), Expect = 0.15
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
+ V L + +E +R +F G I E
Sbjct: 1 LTVKVKNLPKDTTENKIRQFFKDCGEIRE 29
Score = 29.9 bits (68), Expect = 0.21
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
V L ++T E +I +F GE+ + I A + F T+ D+ LAA
Sbjct: 4 KVKNLPKDTTENKIRQFFKDCGEIREVKIVESE----GGLVAVIEFETE---DEALAA 54
>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 = 30.2 bits (68), Expect = 0.16
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
KIFVG ++ + ++R F ++G + E + K + F+ + + A +
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVEC--------DKVKDYAFVHMEREEEALAAIEA 53
Query: 162 PKQVICGKEVDVKRV 176
+ GKEV +R+
Sbjct: 54 ----LNGKEVKGRRI 64
>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 = 30.6 bits (70), Expect = 0.18
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 36 YFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
FSQ+G V I T + RG AFV F
Sbjct: 23 LFSQFGPVLDIVASK---TLKMRGQAFVVFKD 51
>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 = 30.2 bits (68), Expect = 0.19
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-AN 161
+ V L +S D+ F YG I E ++ + N K+ FI F D AE L A
Sbjct: 4 LVVFNLDPSVSNDDLHQIFGAYGEIKEIRE----TPN-KRHHKFIEFYDVRSAEAALKAL 58
Query: 162 PKQVICGKEVDVK 174
+ I GK + ++
Sbjct: 59 NRSEIAGKRIKLE 71
>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 = 31.0 bits (71), Expect = 0.19
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 34 NDYFSQYGEVESISIKNDPHTGQSRG---FAFVTFTTQ 68
+YF QYG+++ I I + S+G A+VT++ +
Sbjct: 26 PEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRK 63
>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 = 30.2 bits (68), Expect = 0.19
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
D R LFV L N E+ + F ++ S K G S+G A++ F T+ +
Sbjct: 2 DARTLFVKNLPYNITVDELKEVFEDAVDIRLPSGK----DGSSKGIAYIEFKTEAEAEKA 57
Query: 75 L 75
L
Sbjct: 58 L 58
>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM2 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 93
Score = 30.7 bits (70), Expect = 0.20
Identities = 13/81 (16%), Positives = 37/81 (45%), Gaps = 10/81 (12%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF------AFVTFTTQKAVD 72
++ G L + ++++ ++F Y E + A VT T++ +D
Sbjct: 5 VYCGKLPKKVTDEDLREFFKDYNPQEIWIFRTRKSKRNPLQLHRHFTAALVTLDTEETLD 64
Query: 73 DLLAAGDHYIGNKKIDPKRVT 93
+++ + + +KK++ K+++
Sbjct: 65 EIIES----LKSKKLNGKKIS 81
>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 = 30.3 bits (69), Expect = 0.20
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDDL 74
++E+ FSQ+GEV+ I+ P + FV F + A+D L
Sbjct: 15 DQELRSLFSQFGEVK--DIRETPLRPSQK---FVEFYDIRAAEAALDAL 58
Score = 26.0 bits (58), Expect = 6.1
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
+ V L + IS+Q++R FSQ+G + + ++ + +K F+ F D AE L
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEVKDIRE--TPLRPSQK---FVEFYDIRAAEAALDAL 58
Query: 162 PKQVICGKEVDVK 174
+ G + VK
Sbjct: 59 NGRPFLGGRLKVK 71
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44
(RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 30.3 bits (68), Expect = 0.20
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE-QVLAN 161
+ VGGL+ +SE D+R +F +Y + + + FD + A V
Sbjct: 2 VHVGGLSPSVSEGDLRSHFQKYQVSVISLCKLSNYR-----YASLHFDRASDALLAVKKM 56
Query: 162 PKQVICGKEVDVKRVK 177
V+ G + V+ VK
Sbjct: 57 NGGVLSGLSIKVRMVK 72
>gnl|CDD|199208 cd08964, L-asparaginase_II, Type II (periplasmic) bacterial
L-asparaginase. Asparaginases (amidohydrolases, E.C.
3.5.1.1) are enzymes that catalyze the hydrolysis of
asparagine to aspartic acid and ammonia. In bacteria,
there are two classes of amidohydrolases. This model
represents type II L-asparaginases, which tend to be
highly specific for asparagine and localized to the
periplasm. They are potent antileukemic agents and have
been used in the treatment of acute lymphoblastic
leukemia (ALL), but not without severe side effects.
Tumor cells appear to have a heightened dependence on
exogenous L-aspartate, and depleting their surroundings
of L-aspartate may starve cancerous ALL cells. Type II
L-asparaginase acts as a tetramer, which is actually a
dimer of two tightly bound dimers. A conserved threonine
residue is thought to supply the nucleophile
hydroxy-group that attacks the amide bond. Many
bacterial L-asparaginases have both L-asparagine and
L-glutamine hydrolysis activities, to a different
degree, and some of them are annotated as
asparaginase/glutaminase.
Length = 319
Score = 32.5 bits (75), Expect = 0.21
Identities = 18/65 (27%), Positives = 22/65 (33%), Gaps = 7/65 (10%)
Query: 183 MGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPG 242
G+V A+ A R + G VV G YGY G+ A A A
Sbjct: 241 AGNVPPALVEALERAVAKGIP-------VVRSSRVGNGRVLPVYGYGGGADLAEAGAIFA 293
Query: 243 YDYSA 247
D S
Sbjct: 294 GDLSP 298
>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 = 30.3 bits (69), Expect = 0.23
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 17 RKLFVGGLHRN-TGEKEINDYFSQYGEVE--SISIKNDPHTGQSRGFAFVTFTT 67
R LFV L + + FSQ G+ ++I + GQ RGFAFV + T
Sbjct: 3 RCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPN---GQPRGFAFVEYAT 53
>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 = 30.4 bits (68), Expect = 0.24
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
IFV L+ E E + F +G++T + D + N KGF F++ + + A +A+
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIAS 62
Score = 28.9 bits (64), Expect = 0.69
Identities = 15/48 (31%), Positives = 23/48 (47%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
+FV L E + F +G V ++ + D T + +GF FVT T
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMT 51
>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 = 30.0 bits (68), Expect = 0.24
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
FVG L NT + +++ F V+S+ + D T + +GF +V F +++ + L
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE 60
>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 = 30.1 bits (68), Expect = 0.25
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 8/51 (15%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESI-SIKNDPHTGQSRGFAFVTFT 66
R +++G + + E+++ + FSQYGE+ES+ ++ + AFV FT
Sbjct: 4 RNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLRE-------KNCAFVNFT 47
Score = 26.6 bits (59), Expect = 4.2
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 6/47 (12%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
+++G + ++E+ +R+ FSQYG I + + KN F++F
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESVN--YLREKNC----AFVNF 46
>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 = 30.4 bits (68), Expect = 0.26
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 24 LHRNTGEKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH 80
L +N E +I ++G + + + + +GQSRGFAFV F + + A H
Sbjct: 10 LPQNATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQH 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 = 29.9 bits (68), Expect = 0.26
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 9/54 (16%)
Query: 17 RKLFVGGLHRNTGEKE-INDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
R+L V G +K+ + +F+Q+GE+E + + + +TF T+K
Sbjct: 6 RQLSVTGF--TEEDKDELLAHFAQFGEIEDVEVDEEGLH------LVITFKTRK 51
>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 = 30.0 bits (68), Expect = 0.27
Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDP-HTGQSRGFAFVTFTTQKAVDDLLAAG 78
++G L + E++I ++F V S+ + +P G+ RGF + F + ++ L+
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLN 63
Query: 79 DHYIGNKKI 87
D + N++I
Sbjct: 64 DESLKNRRI 72
Score = 28.5 bits (64), Expect = 0.83
Identities = 13/71 (18%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 104 FVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLANP 162
++G L +++E+D++++F +++ + P + + +GF + F+D++ Q L+
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLN 63
Query: 163 KQVICGKEVDV 173
+ + + + V
Sbjct: 64 DESLKNRRIRV 74
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a
specific inhibitory effect on oestrogen action, SLTM is
shown to exert a generalized inhibitory effect on gene
expression associated with induction of apoptosis in a
wide range of cell lines. .
Length = 74
Score = 30.0 bits (67), Expect = 0.27
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
L+V GL NT ++ + F +YG+V S + + + ++ + VT ++ V
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEV 54
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 29.9 bits (68), Expect = 0.28
Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 14/80 (17%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSIT--EFQQPFDKSKNMKKGFCFISFDDQNVA--- 155
C + G+ + S +D+++ F ++G + +F ++ +G ++ F ++N A
Sbjct: 2 CVLHFSGVGEQTSREDLKEAFEEFGEVAWVDF------ARGQTEG--YVRFKEENAAKEA 53
Query: 156 -EQVLANPKQVICGKEVDVK 174
E++ I G EV VK
Sbjct: 54 LEKLKEAKNLKIKGSEVTVK 73
>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 = 30.2 bits (68), Expect = 0.28
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGE--VESISIKNDP-HTGQ--SRGFAFVTFTTQKAVDD 73
LFV L+ +T + + D F + K DP GQ S GF FV F T++
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 74 LLAAGDHYI 82
L A D ++
Sbjct: 63 ALKAMDGFV 71
>gnl|CDD|240956 cd12512, RRM3_RBM12, RNA recognition motif 3 in RNA-binding
protein 12 (RBM12) and similar proteins. This
subfamily corresponds to the RRM3 of RBM12. RBM12, also
termed SH3/WW domain anchor protein in the nucleus
(SWAN), is ubiquitously expressed. It contains five
distinct RNA binding motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. The biological role of
RBM12 remains unclear. .
Length = 101
Score = 30.3 bits (68), Expect = 0.35
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
+++ GL K + D+F + VE SI I P+ G++ G FV F + L
Sbjct: 12 VYLKGLPYEAENKHVIDFFKKLDIVEDSIYIAYGPN-GKATGEGFVEFRNEADYKAALCR 70
Query: 78 GDHYIGNKKIDPKRVTKR 95
Y+GN+ I +TK+
Sbjct: 71 HKQYMGNRFIQVHPITKK 88
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family. This subfamily corresponds to the RRM2
of hnRNP H protein family which includes hnRNP H (also
termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP
H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA
only in the presence of cap-binding proteins.
Furthermore, hnRNP H and hnRNP H2 are almost identical;
both have been found to bind nuclear-matrix proteins.
hnRNP H activates exon inclusion by binding G-rich
intronic elements downstream of the 5' splice site in
the transcripts of c-src, human immunodeficiency virus
type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences
exons when bound to exonic elements in the transcripts
of beta-tropomyosin, HIV-1, and alpha-tropomyosin.
hnRNP H2 has been implicated in pre-mRNA 3' end
formation. hnRNP H3 may be involved in the splicing
arrest induced by heat shock. Most family members
contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and they
play an important role in efficiently silencing the
exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction
with the exonic GGG motifs. The lack of RRM1 could
account for the reduced silencing activity within hnRNP
H3. In addition, the family members have an extensive
glycine-rich region near the C-terminus, which may
allow them to homo- or heterodimerize. .
Length = 77
Score = 29.7 bits (67), Expect = 0.36
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 23 GLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHY 81
GL ++EI +FS V I++ D G+S G A+V F +Q++ + L
Sbjct: 7 GLPFGCSKEEIAQFFSGLEIVPNGITLPMDYR-GRSTGEAYVQFASQESAERALGKHKEK 65
Query: 82 IGNKKID 88
IG++ I+
Sbjct: 66 IGHRYIE 72
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 86
Score = 29.7 bits (66), Expect = 0.37
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
+FV L + E + F +G V ++ + D +T + +GF FVT T
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMT 53
Score = 27.8 bits (61), Expect = 1.7
Identities = 16/59 (27%), Positives = 29/59 (49%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
IFV L + E + F +G++T + D + N KGF F++ + + A +A+
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 29.6 bits (66), Expect = 0.39
Identities = 18/73 (24%), Positives = 42/73 (57%), Gaps = 11/73 (15%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL--A 160
+FV L T ++E+ + FS++G + ++ K +K + F+ F++++ A + +
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKL-------ERVKKLKD-YAFVHFEERDAAVRAMDEM 55
Query: 161 NPKQVICGKEVDV 173
N K+ I G+E+++
Sbjct: 56 NGKE-IEGEEIEI 67
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM4 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 98
Score = 29.9 bits (68), Expect = 0.39
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 54 TGQSRGFAFVTFT 66
G+S+G+ FV FT
Sbjct: 53 KGKSKGYGFVEFT 65
>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 = 29.9 bits (67), Expect = 0.40
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 43 VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
V +I + D T Q+RGFAFV ++ LL
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQLSSALEASQLL 63
>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly
[ADP-ribose] polymerase PARP-10, RNA recognition motif 2
in PARP-14, RNA recognition motif in N-myc-interactor
(Nmi), interferon-induced 35 kDa protein (IFP 35),
RNA-binding protein 43 (RBM43) and similar proteins.
This subfamily corresponds to the RRM1 and RRM2 of
PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi),
interferon-induced 35 kDa protein (IFP 35) and
RNA-binding protein 43 (RBM43). PARP-10 is a novel
oncoprotein c-Myc-interacting protein with
poly(ADP-ribose) polymerase activity. It is localized to
the nuclear and cytoplasmic compartments. In addition to
PARP activity, PARP-10 is also involved in the control
of cell proliferation by inhibiting c-Myc- and
E1A-mediated cotransformation of primary cells. PARP-10
may also play a role in nuclear processes including the
regulation of chromatin, gene transcription, and
nuclear/cytoplasmic transport. PARP-10 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two overlapping C-terminal domains composed of
a glycine-rich region and a region with homology to
catalytic domains of PARP enzymes (PARP domain). In
addition, PARP-10 contains two ubiquitin-interacting
motifs (UIM). PARP-14, also termed aggressive lymphoma
protein 2, is a member of the B aggressive lymphoma
(BAL) family of macrodomain-containing PARPs. Like
PARP-10, PARP-14 also includes two RRMs at the
N-terminus. Nmi, also termed N-myc and STAT interactor,
is an interferon inducible protein that interacts with
c-Myc, N-Myc, Max and c-Fos, and other transcription
factors containing bHLH-ZIP, bHLH or ZIP domains.
Besides binding Myc proteins, Nmi also associates with
all the Stat family of transcription factors except
Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma)
stimulation, Nmi can enhance Stat-mediated
transcriptional activity through recruiting the Stat1
and Stat5 transcriptional coactivators, CREB-binding
protein (CBP) and p300. IFP 35 is an interferon-induced
leucine zipper protein that can specifically form
homodimers. Distinct from known bZIP proteins, IFP 35
lacks a basic domain critical for DNA binding. In
addition, IFP 35 may negatively regulate other bZIP
transcription factors by protein-protein interaction.
For instance, it can form heterodimers with B-ATF, a
member of the AP1 transcription factor family. Both Nmi
and IFP35 harbor one RRM. RBM43 is a putative
RNA-binding protein containing one RRM, but its
biological function remains unclear. .
Length = 74
Score = 29.2 bits (66), Expect = 0.40
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 11/77 (14%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQY-----GSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
+ V GL +S+ + YF G +T Q +K + ++F D VAE
Sbjct: 2 CVLVAGLPETVSDDKLELYFENKRRSGGGDVTRVQYLREKGSAL------VTFADFKVAE 55
Query: 157 QVLANPKQVICGKEVDV 173
+V+ K + G ++ V
Sbjct: 56 RVVKQKKHPLNGTQLSV 72
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B shows high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 29.4 bits (66), Expect = 0.41
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
+F+ GL E ++ ++F +VE + H G++ G A V F T + + L
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGL-DVEDVIFLKR-HNGRNNGNAIVKFATFQDAKEALKRH 59
Query: 79 DHYIGNKKI 87
+G++ I
Sbjct: 60 RELMGSRYI 68
>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 617
Score = 31.7 bits (72), Expect = 0.43
Identities = 20/67 (29%), Positives = 24/67 (35%), Gaps = 7/67 (10%)
Query: 215 PSTYAGY---AATDYGYTAGSYDAYATA---YPGYDYSAMGYAYPAAATSYGGGKYREAA 268
Y GY A D D TA YP Y A+P AA Y G + +
Sbjct: 115 RRPYEGYGGPRADDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPRAADDY-GWQQQRLG 173
Query: 269 YTRHAPY 275
+ APY
Sbjct: 174 FPPRAPY 180
>gnl|CDD|240936 cd12492, RRM2_RBM46, RNA recognition motif 2 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM2 of RBM46, also termed
cancer/testis antigen 68 (CT68). It is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 85
Score = 29.6 bits (66), Expect = 0.44
Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGE--VESISIKNDPHTGQSRGFAFVTFTTQKA 70
D +LF+G + + ++EI + + E ++ I + ++RGFAFV + + +A
Sbjct: 1 DNCRLFIGSIPKEKKKEEILEEMKKVTEGVMDVIVYPSATDRTKNRGFAFVEYESHRA 58
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
In the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its
C-terminal RRM motif. .
Length = 72
Score = 29.3 bits (66), Expect = 0.45
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN 50
R L V G+ ++ + + F + G+V+ I +K
Sbjct: 2 RYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKK 35
Score = 28.5 bits (64), Expect = 0.77
Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
+ V G+ ++S ++++ F + G + + K + KG +SF D
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDV----KGIFVKKLLSKGIVIVSFHD 48
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM1 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding protein family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 71
Score = 29.1 bits (65), Expect = 0.47
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
R LFV + R+ E + F YG+V + + S G V F
Sbjct: 2 RSLFVINVPRDVTESTLRRLFEVYGDVRGVQTER-----ISEGIVTVHF 45
>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 = 29.5 bits (66), Expect = 0.48
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
+ R ++VG + +T E+ D F +GE+E ++ N G S GF +T
Sbjct: 1 ERRVIYVGKIRPDTTRTELRDRFEVFGEIEECTV-NLRDDGDSYGFITYRYT 51
>gnl|CDD|240934 cd12490, RRM2_ACF, RNA recognition motif 2 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM2 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 85
Score = 29.3 bits (65), Expect = 0.52
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQY--GEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
D +LFVGG+ + +EI + G ++ I + ++RGFAFV + + +A
Sbjct: 1 DNCRLFVGGIPKTKKREEILAEMKKVTDGVLDVIVYPSAADKAKNRGFAFVEYESHRA 58
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein
zinc fingers (zf-RanBP), and an asparagine-rich region.
It may possess RNA-binding and zinc ion binding
activities. Additional research had indicated that ARP
may function as a factor involved in the stress
response. .
Length = 88
Score = 29.0 bits (65), Expect = 0.67
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 8/85 (9%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESI------SIKNDPHTG-QSRGFAFVTFTTQKAV 71
L++ L +T + E+ +F+QYG V + + D + + F F + +
Sbjct: 3 LYISNLPPDTTQLELESWFTQYG-VRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEA 61
Query: 72 DDLLAAGDHYIGNKKIDPKRVTKRV 96
+ LA +G + I+ + + RV
Sbjct: 62 MEALALNGRCLGERAIEVQPSSSRV 86
Score = 29.0 bits (65), Expect = 0.71
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGS----ITEFQQPFDKSKNMKK--GFCFISFDDQNVAE 156
+++ L + ++ ++ +F+QYG + P + + K F F A
Sbjct: 3 LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62
Query: 157 QVLA 160
+ LA
Sbjct: 63 EALA 66
>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 = 28.8 bits (65), Expect = 0.68
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 8/54 (14%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
L+V G E+ + FS +G + +IS++ + + FVTF ++ D
Sbjct: 7 LYVHG--YGLTEEILKKAFSPFGNIINISMEKE------KNCGFVTFEKMESAD 52
Score = 26.8 bits (60), Expect = 3.3
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 10/59 (16%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFC-FISFDDQNVAEQVLA 160
++V G ++E+ ++ FS +G+I +K KN C F++F+ A++ +A
Sbjct: 7 LYVHG--YGLTEEILKKAFSPFGNIINIS--MEKEKN-----CGFVTFEKMESADRAIA 56
>gnl|CDD|224643 COG1729, COG1729, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 262
Score = 30.9 bits (70), Expect = 0.69
Identities = 25/84 (29%), Positives = 34/84 (40%), Gaps = 11/84 (13%)
Query: 187 SGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDYS 246
S +V G GA V+ A Y AA Y + DY ++ A+ YP Y+
Sbjct: 128 SASVDGDGAPVSPATKLYNAA----------LDLYKSGDYAEAEQAFQAFIKKYPNSTYT 177
Query: 247 AMGYAYPAAATSYGGGKYREAAYT 270
Y Y + Y G Y +AAY
Sbjct: 178 PNAY-YWLGESLYAQGDYEDAAYI 200
>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 = 28.8 bits (64), Expect = 0.71
Identities = 21/72 (29%), Positives = 40/72 (55%), Gaps = 9/72 (12%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT-TQKAVDDL--L 75
L+VG + + ++++ + F ++G++ESI++ RG A+V Q A L L
Sbjct: 5 LWVGQVDKKATQQDLTNLFEEFGQIESINMI------PPRGCAYVCMVHRQDAYRALQKL 58
Query: 76 AAGDHYIGNKKI 87
++G + IG+K I
Sbjct: 59 SSGSYKIGSKVI 70
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 86
Score = 28.9 bits (65), Expect = 0.76
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 10/84 (11%)
Query: 19 LFVGGLHRNTGEKEIN----DYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT-QKAVDD 73
+FV L + + E+ ++FS+YG + + + D + R +AFV FT A +
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNA 61
Query: 74 LLAAGDHYIGNKKIDPKRVTKRVN 97
L + + I +R +VN
Sbjct: 62 LAKGQGTILDGRHIRCERA--KVN 83
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 28.1 bits (63), Expect = 1.2
Identities = 10/43 (23%), Positives = 21/43 (48%)
Query: 119 DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
+YF + G I + +N K+G +I+F+ A + + +
Sbjct: 14 EYFGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVD 56
>gnl|CDD|240426 PTZ00466, PTZ00466, actin-like protein; Provisional.
Length = 380
Score = 30.3 bits (68), Expect = 1.2
Identities = 22/90 (24%), Positives = 43/90 (47%), Gaps = 15/90 (16%)
Query: 110 TEISEQDVRDYFS----QYGSITEFQQPFDKSKNMKKGFCFISFD---DQNVAEQ----- 157
T+++ +D+ Y + G + + KNMK+ C++SF+ ++N +E+
Sbjct: 184 TDVAGRDITTYLGYLLRKNGHLFNTSAEMEVVKNMKENCCYVSFNMNKEKNSSEKALTTL 243
Query: 158 --VLANPKQVICGKE-VDVKRVKFNPETMG 184
+L + Q++ G E V FNP +G
Sbjct: 244 PYILPDGSQILIGSERYRAPEVLFNPSILG 273
>gnl|CDD|192529 pfam10309, DUF2414, Protein of unknown function (DUF2414). This is
a family of proteins conserved from fungi to mammals.
One mouse member is referred to as ELG protein but this
is not a homologue of human ELG protein. The function is
not known.
Length = 62
Score = 27.7 bits (62), Expect = 1.3
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 16/57 (28%)
Query: 111 EISEQDVRDYFSQYGSITEFQQPF------DKSKNMKKGFCFISFDDQNVAEQVLAN 161
E+S D++ Y +Y + PF D S N I F ++ A++ L
Sbjct: 15 ELSTDDIKAYVKEYFDE---EIPFRIEWIDDTSAN-------IVFKSEDTAQRALVA 61
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 28.3 bits (64), Expect = 1.4
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 110 TEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
EI ++DV + S++G + + DK N +G ++ F A++
Sbjct: 22 DEI-KEDVLEECSKFGPVEHIK--VDK--NSPEGVVYVKFKTVEAAQK 64
>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 = 28.0 bits (62), Expect = 1.4
Identities = 17/75 (22%), Positives = 39/75 (52%), Gaps = 12/75 (16%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
+FV L ++E+ + F Q+G + ++ K +K + FI FD+++ A + +
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKL-------ERVKKLKD-YAFIHFDERDGAVKAMEE- 54
Query: 163 KQVICGKEVDVKRVK 177
+ GKE++ + ++
Sbjct: 55 ---MNGKELEGENIE 66
>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast
sporulation-specific protein 2 (Ssp2) and similar
protein. This subfamily corresponds to the RRM of the
lineage specific yeast sporulation-specific protein 2
(Ssp2) and similar proteins. Ssp2 is encoded by a
sporulation-specific gene necessary for outer spore wall
assembly in the yeast Saccharomyces cerevisiae. It
localizes to the spore wall and may play an important
role after meiosis II and during spore wall formation.
Ssp2 contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 28.1 bits (63), Expect = 1.4
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 15/64 (23%)
Query: 107 GLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVI 166
L ++ ++++D F+ +G I + + C F A+ + I
Sbjct: 1 VLPSDFDVEELKDDFTVFGEIVDISPIIS------RKLCVSIF---------FADIRSAI 45
Query: 167 CGKE 170
KE
Sbjct: 46 RAKE 49
>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM2 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 89
Score = 28.1 bits (62), Expect = 1.5
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGE--VESISIKNDPHTGQSRGFAFVTFTTQKA 70
+LF+GG+ + +EI + S+ E ++ I + ++RGFAFV + + +A
Sbjct: 3 RLFIGGIPKMKKREEILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRA 57
>gnl|CDD|234363 TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood
CpaE-like protein. Members of this protein family
belong to the MinD/ParA family of P-loop NTPases, and in
particular show homology to the CpaE family of pilus
assembly proteins (see PMID:12370432). Nearly all
members are found, not only in a gene context consistent
with pilus biogenesis or a pilus-like secretion
apparatus, but also near a DEAD/DEAH-box helicase,
suggesting an involvement in DNA transfer activity. The
model describes a clade restricted to the
Actinobacteria.
Length = 322
Score = 29.6 bits (67), Expect = 1.6
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 185 SVSGAVRGAGARVASAGTAYAAA 207
+V G GAGA +A A AAA
Sbjct: 97 AVIGGRGGAGASTLAAALALAAA 119
>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 = 27.7 bits (62), Expect = 1.6
Identities = 7/31 (22%), Positives = 15/31 (48%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ 132
KI + + + +D+ S YG++ +Q
Sbjct: 2 KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQ 32
>gnl|CDD|233567 TIGR01773, GABAperm, gamma-aminobutyrate permease. GABA permease
(gabP) catalyzes the translocation of 4-aminobutyrate
(GABA) across the plasma membrane, with homologues
expressed in Gram-negative and Gram-positive organisms.
This permease is a highly hydrophobic transmembrane
protein consisting of 12 transmembrane domains with
hydrophilic N- and C-terminal ends. Induced by
nitrogen-limited culture conditions in both Escherichia
coli and Bacillus subtilis, gabP is an energy dependent
transport system stimulated by membrane potential and
has been observed adjacent and distant from other GABA
degradation proteins. GabP is highly homologous to amino
acid permeases from B. subtilis, E. coli, as well as to
other members of the amino acid permease family
(pfam00324). A member of the APC
(amine-polyamine-choline) transporter superfamily, GABA
permease possesses a "consensus amphiphatic region"
(CAR) found to be evolutionarily conserved within this
transport family. This amphiphatic region is located
between helix 8 and cytoplasmic loop 8-9, forming a
potential channel domain and suggested to play a
significant role in ligand recognition and
translocation. Unique to GABA permeases, a conserved
cysteine residue (CYS-300, E.coli) located at the
beginning of the amphiphatic domain, has been determined
to be critical for catalytic specificity [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 452
Score = 29.8 bits (67), Expect = 1.7
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 182 TMGSVSGAVRGAGARVASAGTAYAAAPGRVVAY 214
TM S++G + GAG V S +A P ++AY
Sbjct: 20 TMLSIAGVI-GAGLFVGSGSAIASAGPAALLAY 51
>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 = 1.7
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 14/79 (17%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVE--------SISIKNDPHTGQSRGFAFVTF----T 66
++V GL+ N +E+ D+F G V+ ++I D TG+ +G A V++ +
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62
Query: 67 TQKAVDDLLAAGDHYIGNK 85
+ AV+ G + G+K
Sbjct: 63 AKAAVE--WFDGKDFQGSK 79
Score = 26.8 bits (59), Expect = 3.9
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 12/83 (14%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSI---TEFQQPF-----DKSKNMKKGFCFISFDDQNV 154
I+V GL ++ +++ D+F G + QP DK KG +S++D
Sbjct: 3 IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62
Query: 155 AEQVLANPKQVICGKEVDVKRVK 177
A+ + + GK+ ++K
Sbjct: 63 AKAAV----EWFDGKDFQGSKLK 81
>gnl|CDD|237627 PRK14155, PRK14155, heat shock protein GrpE; Provisional.
Length = 208
Score = 29.2 bits (65), Expect = 1.7
Identities = 22/57 (38%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 181 ETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYA 237
E MG + VR A VA+ G+ AAP A + YA AA D + GS+D A
Sbjct: 156 ELMGRL---VRPAMVAVAAKGSTGPAAPAEPAAGANPYAS-AAADGDGSGGSFDTKA 208
>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 = 27.6 bits (62), Expect = 1.7
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
E E+ FS+YG+V + + + + +G A V F ++KA +
Sbjct: 18 EDELRKIFSKYGDVSDVVVSS-----KKKGSAIVEFASKKAAE 55
>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 = 28.0 bits (63), Expect = 1.8
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 15/75 (20%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDP-------------HTGQSRGF--A 61
R LFV + E+ + FS+ G+VES+ ++ P +GF A
Sbjct: 1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVA 60
Query: 62 FVTFTTQKAVDDLLA 76
+V F ++ L
Sbjct: 61 YVVFKKPSSLSRALK 75
>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 = 27.4 bits (61), Expect = 2.0
Identities = 18/66 (27%), Positives = 29/66 (43%)
Query: 23 GLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYI 82
GL + E +I D+F V+ + G+ G A+V F T + + L I
Sbjct: 8 GLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKHREEI 67
Query: 83 GNKKID 88
GN+ I+
Sbjct: 68 GNRYIE 73
>gnl|CDD|222042 pfam13313, DUF4082, Domain of unknown function (DUF4082). This
family appears to be a parallel beta-helix repeated
region that sits between successive Cadherin domains,
pfam00028.
Length = 149
Score = 28.7 bits (65), Expect = 2.2
Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 15/72 (20%)
Query: 199 SAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPG------YDYSAMGYAY 252
+AGT Y V +Y + Y+AT +T G + TA G Y Y A G A+
Sbjct: 85 TAGTTY------VASYHTPNGHYSATGGYFTTGVDNGPLTALAGAGGNGVYAYGA-GSAF 137
Query: 253 PAAATSYGGGKY 264
P + SY Y
Sbjct: 138 PTS--SYQASNY 147
>gnl|CDD|222144 pfam13458, Peripla_BP_6, Periplasmic binding protein. This family
includes a diverse range of periplasmic binding
proteins.
Length = 343
Score = 29.2 bits (66), Expect = 2.3
Identities = 20/102 (19%), Positives = 33/102 (32%), Gaps = 16/102 (15%)
Query: 146 FISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYA 205
+ DDQ+ ++ A ++++ VD G ++ AV A A
Sbjct: 45 LVVADDQSDPDRAAAAARRLVDQDGVDA--------IFGGLTSAVALAVA-------PVL 89
Query: 206 AAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDYSA 247
G + PS G + + G A DY A
Sbjct: 90 EKKGVPLIGPSALEGEECSPNVFYTG-ATPNQQAAALVDYLA 130
>gnl|CDD|131032 TIGR01977, am_tr_V_EF2568, cysteine desulfurase family protein.
This model describes a subfamily of probable pyridoxal
phosphate-dependent enzymes in the aminotransferase
class V family. Related families contain members active
as cysteine desulfurases, selenocysteine lyases, or
both. The members of this family form a distinct clade
and all are shorter at the N-terminus. The function of
this subfamily is unknown [Unknown function, Enzymes of
unknown specificity].
Length = 376
Score = 29.3 bits (66), Expect = 2.4
Identities = 16/43 (37%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 233 YDAYATAYPGYD--YSAMGYAYPAAATSYGGGKYREAAYTRHA 273
+D AT YP D Y AM Y S G G+YR A
Sbjct: 3 FDNAATTYPKPDEVYEAMADFYKNYGGSPGRGRYRLALRASRE 45
>gnl|CDD|241175 cd12731, RRM2_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM2 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth
factor receptor 2 (FGFR2) transcripts. The presence of
Fox 2 can allows hnRNP H and hnRNP F to better compete
with the SR protein ASF/SF2 for binding to FGFR2 exon
IIIc. Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently
silencing the exon. In addition, the family members
have an extensive glycine-rich region near the
C-terminus, which may allow them to homo- or
heterodimerize. .
Length = 83
Score = 27.3 bits (60), Expect = 2.4
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 23 GLHRNTGEKEINDYFSQYGEVES-ISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHY 81
GL ++EI +FS V + I++ D G+S G AFV F +Q+ + L
Sbjct: 8 GLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQ-GRSTGEAFVQFASQEIAEKALKKHKER 66
Query: 82 IGNKKID 88
IG++ I+
Sbjct: 67 IGHRYIE 73
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It 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. Rrp7p contains an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal RRP7 domain. .
Length = 96
Score = 27.4 bits (61), Expect = 2.7
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDP 52
R LF+ L +T E+ + F G +ES+ +
Sbjct: 1 RTLFLVNLPVDTTERHLRKLFGSGGGIIESVVFVEEL 37
>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 = 27.0 bits (60), Expect = 3.5
Identities = 13/61 (21%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
++ ++V + +++E+ + FS G + + + D + ++ F FI F D+ A
Sbjct: 1 IRRTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLR--FAFIEFTDEEGARAA 58
Query: 159 L 159
L
Sbjct: 59 L 59
>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 = 27.2 bits (60), Expect = 3.9
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
+ R +++G + E+ D FS +GE+E +I + + FVT+
Sbjct: 1 ERRVVYIGKIPSRMTRSELKDRFSVFGEIEECTIH---FRSEGDNYGFVTY 48
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 26.7 bits (60), Expect = 4.1
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
++V GL +I+ ++ + FS+ G I E
Sbjct: 2 TNVYVSGLPLDITVEEFVEVFSKCGIIKE 30
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM3 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 = 86
Score = 26.8 bits (60), Expect = 4.2
Identities = 6/27 (22%), Positives = 11/27 (40%)
Query: 51 DPHTGQSRGFAFVTFTTQKAVDDLLAA 77
D + G+AF+ F + + A
Sbjct: 36 DFKNKCNVGYAFINFVNPEYAEKFYKA 62
Score = 26.4 bits (59), Expect = 5.7
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 133 PFDKSKNMKKGFCFISFDDQNVAEQ 157
P D G+ FI+F + AE+
Sbjct: 34 PIDFKNKCNVGYAFINFVNPEYAEK 58
>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage
factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar
proteins. This subgroup corresponds to the RRM of
CFIm59. 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. The two separate genes,
CPSF6 and CPSF7, code for two isoforms of the large
subunit, CFIm68 and CFIm59. The family includes CFIm59,
also termed cleavage and polyadenylation specificity
factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59). CFIm59 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. The N-terminal
RRM of CFIm59 mediates the interaction with CFIm25. It
also serves to enhance RNA binding and facilitate RNA
looping. .
Length = 90
Score = 26.8 bits (59), Expect = 4.2
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 55 GQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
GQS+G+A V ++ +V LL + K ++ ++V R
Sbjct: 42 GQSKGYAEVVVASENSVHKLL----ELLPGKVLNGEKVDVR 78
>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM2 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4), a splicing
regulatory serine/arginine (SR) protein that plays an
important role in both constitutive splicing and
alternative splicing of many pre-mRNAs. For instance, it
interacts with heterogeneous nuclear ribonucleoproteins,
hnRNP G and hnRNP E2, and further regulates the 5'
splice site of tau exon 10, whose misregulation causes
frontotemporal dementia. SFRS4 also induces production
of HIV-1 vpr mRNA through the inhibition of the
5'-splice site of exon 3. In addition, SRSF4 activates
splicing of the cardiac troponin T (cTNT) alternative
exon by direct interactions with the cTNT exon 5
enhancer RNA. SRSF4 can shuttle between the nucleus and
cytoplasm. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine-rich region, an
internal region homologous to the RRM, and a very long,
highly phosphorylated C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 26.6 bits (58), Expect = 4.5
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
++ V L++ S QD++DY Q G +T K + + F S+ D A + L
Sbjct: 2 RLIVENLSSRCSWQDLKDYMRQAGEVTYADA--HKGRKNEGVIEFRSYSDMKRALEKLD- 58
Query: 162 PKQVICGKEVDVKRVKF 178
G EV+ ++++
Sbjct: 59 ------GTEVNGRKIRL 69
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also
stimulate translation initiation. It contains a five
stranded beta sheet which forms an atypical RNA
recognition motif.
Length = 102
Score = 26.9 bits (60), Expect = 5.2
Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 16/82 (19%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
L GL++ T ++I + FSQ+GEV+ + G R F T +KA++
Sbjct: 4 LKFSGLNKPTSREDIKEAFSQHGEVKYVDFLEGDKEGYVR------FKTPEAAKKALEKA 57
Query: 75 LAAGDHYIGNKKIDPKRVTKRV 96
A KI VT +
Sbjct: 58 TEAK------LKIKEAEVTLEL 73
>gnl|CDD|226675 COG4222, COG4222, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 391
Score = 28.2 bits (63), Expect = 5.4
Identities = 16/77 (20%), Positives = 22/77 (28%), Gaps = 6/77 (7%)
Query: 167 CGKEVDVKRVKFNPETMGSVSGA-VRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATD 225
GK + R G SG RG G + G G + P +A +D
Sbjct: 34 VGKAILAARA----AATGPASGKFNRGTGGGLPFNGQPVGGFSG-ITYDPQGDGYWALSD 88
Query: 226 YGYTAGSYDAYATAYPG 242
G + T
Sbjct: 89 NGRGSKLNSRDYTLRLY 105
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 77
Score = 26.1 bits (57), Expect = 5.8
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDDL 74
L + L +++ + +G +E + TG S+G+ FV + + +A DL
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61
Query: 75 L 75
L
Sbjct: 62 L 62
>gnl|CDD|237529 PRK13841, PRK13841, conjugal transfer protein TrbL; Provisional.
Length = 391
Score = 27.9 bits (62), Expect = 6.3
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 185 SVSGAV-RGAGARVASAGTAYA-AAPGRVVAYPSTYAG 220
S++GA RG GA + SAG+A AA + + P YAG
Sbjct: 324 SLAGAALRGMGAGIGSAGSAAGSAAKEKAIGSPGAYAG 361
>gnl|CDD|131966 TIGR02920, acc_sec_Y2, accessory Sec system translocase SecY2.
Members of this family are restricted to the Firmicutes
lineage (low-GC Gram-positive bacteria) and appear to be
paralogous to, and much more divergent than, the
preprotein translocase SecY. Members include the SecY2
protein of the accessory Sec system in Streptococcus
gordonii, involved in export of the highly glycosylated
platelet-binding protein GspB [Protein fate, Protein and
peptide secretion and trafficking].
Length = 395
Score = 27.4 bits (61), Expect = 8.3
Identities = 16/71 (22%), Positives = 24/71 (33%), Gaps = 4/71 (5%)
Query: 34 NDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT 93
FS + I I S F FV ++ +G+ YI I P + T
Sbjct: 267 VFQFS-FSSPVGILIYLILQMLLSYFFTFVNINPKEISKSFRKSGN-YIPG--IAPGKDT 322
Query: 94 KRVNPLKCKIF 104
+R + F
Sbjct: 323 QRYLNRLARRF 333
>gnl|CDD|241176 cd12732, RRM2_hnRNPH3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H') and hnRNP F. This
family is involved in mRNA processing and exhibit
extensive sequence homology. Currently, little is known
about the functions of hnRNP H3 except for its role in
the splicing arrest induced by heat shock. In addition,
the typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and play an important role in efficiently
silencing the exon. Members in this family can regulate
the alternative splicing of the fibroblast growth
factor receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction
with the exonic GGG motifs. The lack of RRM1 could
account for the reduced silencing activity within hnRNP
H3. In addition, like other hnRNP H protein family
members, hnRNP H3 has an extensive glycine-rich region
near the C-terminus, which may allow it to homo- or
heterodimerize. .
Length = 96
Score = 26.1 bits (57), Expect = 8.8
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 4 RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES-ISIKNDPHTGQSRGFAF 62
+ NG + + + GL ++EI +FS V + I++ D + G+S G AF
Sbjct: 6 KHNGPTDYDGSSGGTVRLRGLPFGCSKEEIVQFFSGLEIVPNGITLTMD-YQGRSTGEAF 64
Query: 63 VTFTTQKAVDDLLAAGDHYIGNKKID 88
V F +++ ++ L IG++ I+
Sbjct: 65 VQFASKEIAENALGKHKERIGHRYIE 90
>gnl|CDD|227806 COG5519, COG5519, Superfamily II helicase and inactivated
derivatives [DNA replication, recombination, and
repair].
Length = 562
Score = 27.4 bits (61), Expect = 9.6
Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 10/62 (16%)
Query: 81 YIGNKKIDPKRVTKRVNPLK--CKIFV--------GGLTTEISEQDVRDYFSQYGSITEF 130
I K PK VN IF+ G +++ + + G++ E+
Sbjct: 96 LIDYSKYLPKEFVAVVNGWGWDNGIFILPQEVMGDGKKDIFSNDEKLTKGYRSKGTLKEW 155
Query: 131 QQ 132
Q+
Sbjct: 156 QK 157
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
0.316 0.133 0.392
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,255,547
Number of extensions: 1355199
Number of successful extensions: 2407
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2246
Number of HSP's successfully gapped: 686
Length of query: 275
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 179
Effective length of database: 6,679,618
Effective search space: 1195651622
Effective search space used: 1195651622
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 (21.6 bits)
S2: 58 (26.3 bits)