RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6490
(398 letters)
>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 = 143 bits (363), Expect = 9e-43
Identities = 51/74 (68%), Positives = 64/74 (86%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
KIFVGG+S +T+ ++VK YFSQFGKVE+ +++ D+QT RHRGFGFVTFE+E+VVD +CEI
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 311 HFHMIKNKKVECKK 324
HFH I NK VECKK
Sbjct: 61 HFHEINNKMVECKK 74
Score = 84.0 bits (208), Expect = 3e-20
Identities = 31/73 (42%), Positives = 48/73 (65%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGLS T+ + +++YF FG V D ++M D T R RGFGF+TF + V+KV ++
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 223 PIHTLDGKKIDPK 235
H ++ K ++ K
Sbjct: 61 HFHEINNKMVECK 73
>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 = 136 bits (346), Expect = 3e-40
Identities = 47/72 (65%), Positives = 57/72 (79%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LF+GGLSW T+ E LREYF +G V D +IMKDPIT RSRGFGF+TFA+P +V+KVL
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 224 IHTLDGKKIDPK 235
H LDG++IDPK
Sbjct: 61 PHVLDGREIDPK 72
Score = 96.5 bits (241), Expect = 6e-25
Identities = 28/72 (38%), Positives = 48/72 (66%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+F+GG+S DT+ E ++ YFS++G+V + V++ D T R RGFGFVTF + VD +
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 312 FHMIKNKKVECK 323
H++ ++++ K
Sbjct: 61 PHVLDGREIDPK 72
>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 = 131 bits (330), Expect = 8e-38
Identities = 45/74 (60%), Positives = 60/74 (81%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+F+GGLSWQT++E LREYF FG + + ++M+DP T+RSRGFGF+TF++P +V+KVL
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 224 IHTLDGKKIDPKHA 237
H LDGKKIDPK A
Sbjct: 61 PHELDGKKIDPKVA 74
Score = 75.2 bits (185), Expect = 4e-17
Identities = 32/74 (43%), Positives = 50/74 (67%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+F+GG+S T+AE ++ YFS+FG+++E +++ D TKR RGFGFVTF + VD +
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 312 FHMIKNKKVECKKA 325
H + KK++ K A
Sbjct: 61 PHELDGKKIDPKVA 74
>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 = 123 bits (309), Expect = 6e-35
Identities = 54/78 (69%), Positives = 65/78 (83%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
RTKKIFVGG+S +T E+VK YF QFGKVE+ +++ D+ T RHRGFGFVTFENE+VV+ +
Sbjct: 2 RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61
Query: 308 CEIHFHMIKNKKVECKKA 325
CEIHFH I NK VECKKA
Sbjct: 62 CEIHFHEINNKMVECKKA 79
Score = 75.1 bits (184), Expect = 5e-17
Identities = 34/77 (44%), Positives = 49/77 (63%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ K+FVGGLS T E +++YF FG V D ++M D T R RGFGF+TF + VEKV
Sbjct: 3 TKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVC 62
Query: 221 KVPIHTLDGKKIDPKHA 237
++ H ++ K ++ K A
Sbjct: 63 EIHFHEINNKMVECKKA 79
>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 = 120 bits (302), Expect = 6e-34
Identities = 47/74 (63%), Positives = 62/74 (83%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
KIFVGG+S +T+ E+VK YF QFGKV++ +++ D+ T RHRGFGFVTFE+E++V+ +CEI
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 311 HFHMIKNKKVECKK 324
HFH I NK VECKK
Sbjct: 61 HFHEINNKMVECKK 74
Score = 77.4 bits (190), Expect = 6e-18
Identities = 33/73 (45%), Positives = 48/73 (65%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGLS T+ E +++YF FG V D ++M D T R RGFGF+TF + VEKV ++
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 223 PIHTLDGKKIDPK 235
H ++ K ++ K
Sbjct: 61 HFHEINNKMVECK 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 = 117 bits (294), Expect = 2e-32
Identities = 43/80 (53%), Positives = 58/80 (72%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
RTKKIFVGG+ + + +++ YFSQFG V E V++ D + KR RGFGF+TFE+E+ VD +
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60
Query: 308 CEIHFHMIKNKKVECKKAQP 327
HFH I KKVE K+A+P
Sbjct: 61 VNEHFHDINGKKVEVKRAEP 80
Score = 92.0 bits (229), Expect = 3e-23
Identities = 35/79 (44%), Positives = 52/79 (65%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ K+FVGGL + LR+YF FG VT+V++M D +R RGFGFITF ++V++V+
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61
Query: 221 KVPIHTLDGKKIDPKHATP 239
H ++GKK++ K A P
Sbjct: 62 NEHFHDINGKKVEVKRAEP 80
>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 = 110 bits (277), Expect = 4e-30
Identities = 46/78 (58%), Positives = 54/78 (69%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVGGLSW+T+ E LR YF +G V D +IMKD T RSRGFGF+ F +P V VL
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 223 PIHTLDGKKIDPKHATPK 240
HTLDG+ IDPK TP+
Sbjct: 61 GPHTLDGRTIDPKPCTPR 78
Score = 67.9 bits (166), Expect = 2e-14
Identities = 29/78 (37%), Positives = 49/78 (62%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+FVGG+S +T+ E ++ YFSQ+G+V + V++ D+ T R RGFGFV F++ V +
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60
Query: 311 HFHMIKNKKVECKKAQPK 328
H + + ++ K P+
Sbjct: 61 GPHTLDGRTIDPKPCTPR 78
>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 = 107 bits (270), Expect = 5e-29
Identities = 37/78 (47%), Positives = 57/78 (73%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLF+GGLS++T+ + L+ YF +G +TD ++MKDP T+RSRGFGF+TFA V+ +
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 223 PIHTLDGKKIDPKHATPK 240
H +DG++++PK A P+
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
Score = 79.7 bits (197), Expect = 9e-19
Identities = 33/78 (42%), Positives = 52/78 (66%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+F+GG+S +T+ + +K YFSQ+G++ + V++ D TKR RGFGFVTF + VD
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
Query: 311 HFHMIKNKKVECKKAQPK 328
H + ++VE K+A P+
Sbjct: 61 RPHKVDGREVEPKRAVPR 78
>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 = 107 bits (268), Expect = 8e-29
Identities = 44/77 (57%), Positives = 59/77 (76%), Gaps = 1/77 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+F+GGL+W+T+ + LREYFG FG VTD +M+D T RSRGFGF+TF +P++V +V+K
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60
Query: 224 IHTLDGKKIDPKHATPK 240
H LDGK IDPK A P+
Sbjct: 61 -HILDGKIIDPKRAIPR 76
Score = 68.4 bits (167), Expect = 1e-14
Identities = 26/77 (33%), Positives = 51/77 (66%), Gaps = 1/77 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+F+GG++ +T+ + ++ YF QFG+V + ++ D T R RGFGF+TF+ + V+ + +
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60
Query: 312 FHMIKNKKVECKKAQPK 328
H++ K ++ K+A P+
Sbjct: 61 -HILDGKIIDPKRAIPR 76
>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 = 104 bits (260), Expect = 1e-27
Identities = 45/75 (60%), Positives = 59/75 (78%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+F+GGLSWQTS + LR+YF FG + + ++M+DP T+RSRGFGF+TFA+P +V+KVL
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 223 PIHTLDGKKIDPKHA 237
P H LD K IDPK A
Sbjct: 61 PHHELDSKTIDPKVA 75
Score = 66.3 bits (161), Expect = 6e-14
Identities = 31/75 (41%), Positives = 49/75 (65%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+F+GG+S TS + ++ YFS+FG++ E +++ D TKR RGFGFVTF + VD +
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 311 HFHMIKNKKVECKKA 325
H + +K ++ K A
Sbjct: 61 PHHELDSKTIDPKVA 75
>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 = 103 bits (258), Expect = 2e-27
Identities = 38/75 (50%), Positives = 54/75 (72%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
KIFVGG+S +T+ E+++ YF +FG + E + MD++T + RGF F+TF++EE V I E
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 311 HFHMIKNKKVECKKA 325
FH+I KKVE KKA
Sbjct: 61 QFHVIGGKKVEVKKA 75
Score = 88.2 bits (219), Expect = 7e-22
Identities = 36/75 (48%), Positives = 51/75 (68%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGLS +T+ EK+REYFG FG + ++ + D T + RGF FITF E V+K+L+
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 223 PIHTLDGKKIDPKHA 237
H + GKK++ K A
Sbjct: 61 QFHVIGGKKVEVKKA 75
>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 = 103 bits (257), Expect = 3e-27
Identities = 42/74 (56%), Positives = 51/74 (68%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+FVGGLSW T+ + L+EYF FG V D I DP+T RSRGFGF+ F + +VEKVL
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 224 IHTLDGKKIDPKHA 237
H LDG+ IDPK A
Sbjct: 61 EHKLDGRVIDPKRA 74
Score = 67.6 bits (165), Expect = 2e-14
Identities = 28/74 (37%), Positives = 49/74 (66%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+FVGG+S DT+ +++K YFS+FG+V + + +D T R RGFGFV F++ V+ + +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 312 FHMIKNKKVECKKA 325
H + + ++ K+A
Sbjct: 61 EHKLDGRVIDPKRA 74
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 75
Score = 102 bits (255), Expect = 4e-27
Identities = 45/75 (60%), Positives = 53/75 (70%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGLSW TS + L++YF FG VTD I DP T RSRGFGFI F + +VEKVL+
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 223 PIHTLDGKKIDPKHA 237
H LDG+ IDPK A
Sbjct: 61 KEHRLDGRLIDPKKA 75
Score = 72.3 bits (177), Expect = 3e-16
Identities = 31/75 (41%), Positives = 50/75 (66%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+FVGG+S DTS +++K YF++FG+V + + MD T R RGFGF+ F++ V+ + E
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 311 HFHMIKNKKVECKKA 325
H + + ++ KKA
Sbjct: 61 KEHRLDGRLIDPKKA 75
>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 = 102 bits (255), Expect = 4e-27
Identities = 46/75 (61%), Positives = 57/75 (76%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+F+GGLSWQT+ E LREYFG FG V + L+M+DP+T+RSRGFGF+TF + V+KVL
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 223 PIHTLDGKKIDPKHA 237
H LD K IDPK A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 70.0 bits (171), Expect = 3e-15
Identities = 32/75 (42%), Positives = 50/75 (66%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+F+GG+S T+ E ++ YF QFG+V+E +++ D TKR RGFGFVTF ++ VD +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 311 HFHMIKNKKVECKKA 325
H + +K ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
>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 = 98.2 bits (245), Expect = 2e-25
Identities = 36/75 (48%), Positives = 48/75 (64%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
KIFVGG+ D + EE K YFSQFGKV + ++ D T R RGFGFVTF++E V+ +
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 311 HFHMIKNKKVECKKA 325
+ K+VE K+A
Sbjct: 61 GMLELGGKQVEVKRA 75
Score = 90.1 bits (224), Expect = 1e-22
Identities = 34/75 (45%), Positives = 46/75 (61%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGL + E+ +EYF FG V D +M+D T RSRGFGF+TF VE+V
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 223 PIHTLDGKKIDPKHA 237
+ L GK+++ K A
Sbjct: 61 GMLELGGKQVEVKRA 75
>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 = 97.8 bits (243), Expect = 2e-25
Identities = 42/75 (56%), Positives = 52/75 (69%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+F+GGLSW TS + L EY FG V D I DP+T RSRGFGF+ F + +V+KVL++
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 223 PIHTLDGKKIDPKHA 237
H LDGK IDPK A
Sbjct: 61 KEHKLDGKLIDPKRA 75
Score = 69.6 bits (170), Expect = 4e-15
Identities = 30/76 (39%), Positives = 49/76 (64%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+F+GG+S DTS +++ Y S+FG+V + + D T R RGFGFV F++ VD + E+
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 311 HFHMIKNKKVECKKAQ 326
H + K ++ K+A+
Sbjct: 61 KEHKLDGKLIDPKRAK 76
>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 = 93.5 bits (232), Expect = 7e-24
Identities = 40/74 (54%), Positives = 52/74 (70%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+F+GGLSW T+ + L++YF FG V D + DPIT RSRGFGF+ F E E+V+KV+
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 224 IHTLDGKKIDPKHA 237
H L+GK IDPK A
Sbjct: 61 EHKLNGKVIDPKRA 74
Score = 68.5 bits (167), Expect = 9e-15
Identities = 30/74 (40%), Positives = 49/74 (66%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+F+GG+S DT+ +++K YFS+FG+V + + +D T R RGFGFV F+ E VD + +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 312 FHMIKNKKVECKKA 325
H + K ++ K+A
Sbjct: 61 EHKLNGKVIDPKRA 74
>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 = 92.3 bits (230), Expect = 2e-23
Identities = 31/73 (42%), Positives = 49/73 (67%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+FVGG+ +D + E+++ YFSQ+G VE ++ D++T + RGF FVTF++ + VD I
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 311 HFHMIKNKKVECK 323
+H I +VE K
Sbjct: 61 KYHTINGHRVEVK 73
Score = 81.9 bits (203), Expect = 1e-19
Identities = 31/73 (42%), Positives = 46/73 (63%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVGGL + E LREYF +G V V I+ D T + RGF F+TF + + V+K++
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60
Query: 223 PIHTLDGKKIDPK 235
HT++G +++ K
Sbjct: 61 KYHTINGHRVEVK 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 = 91.7 bits (228), Expect = 3e-23
Identities = 33/78 (42%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
L V GL W+T+ + L++YF FG + V + KDP T +S+GFGF+ FA+ E KVL
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60
Query: 223 PIHTLDGKKIDPKHATPK 240
H +DG+ D K K
Sbjct: 61 R-HMIDGRWCDVKIPNSK 77
Score = 60.1 bits (146), Expect = 9e-12
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
+ V G+ T+ +++K YFS FG++ + D +T + +GFGFV F + E +
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60
Query: 311 HFHMIKNKKVECKKAQPK 328
HMI + + K K
Sbjct: 61 R-HMIDGRWCDVKIPNSK 77
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 88.4 bits (220), Expect = 5e-22
Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
LFVG L T+ E+LRE F FG V V +++D T +S+GF F+ F E EK L+
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 222 VPIHTLDGKKID 233
+ LDG+ +
Sbjct: 61 LNGKELDGRPLK 72
Score = 85.7 bits (213), Expect = 5e-21
Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
+FVG + DT+ EE++ FS+FGKVE ++ D++T + +GF FV FE+EE + E
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 311 -HFHMIKNKKVEC 322
+ + + ++
Sbjct: 61 LNGKELDGRPLKV 73
>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 = 87.9 bits (217), Expect = 1e-21
Identities = 35/78 (44%), Positives = 56/78 (71%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLF+GGLS++T+ E LR Y+ +G +TD ++M+DP ++RSRGFGF+TF+ V+ +
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63
Query: 223 PIHTLDGKKIDPKHATPK 240
HT+DG+ ++PK A +
Sbjct: 64 RPHTIDGRVVEPKRAVAR 81
Score = 66.7 bits (162), Expect = 5e-14
Identities = 31/76 (40%), Positives = 48/76 (63%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+K+F+GG+S +T+ E ++ Y+ Q+GK+ + V++ D +KR RGFGFVTF VD
Sbjct: 3 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62
Query: 310 IHFHMIKNKKVECKKA 325
H I + VE K+A
Sbjct: 63 ARPHTIDGRVVEPKRA 78
>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 = 87.4 bits (216), Expect = 2e-21
Identities = 35/78 (44%), Positives = 56/78 (71%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLF+GGLS++T+ E LR +F +G +TD ++M+DP T+RSRGFGF+T++ E V+ +
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63
Query: 223 PIHTLDGKKIDPKHATPK 240
H +DG+ ++PK A +
Sbjct: 64 RPHKVDGRVVEPKRAVSR 81
Score = 66.2 bits (161), Expect = 7e-14
Identities = 30/76 (39%), Positives = 50/76 (65%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+K+F+GG+S +T+ E ++++F Q+G + + V++ D TKR RGFGFVT+ + E VD
Sbjct: 3 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62
Query: 310 IHFHMIKNKKVECKKA 325
H + + VE K+A
Sbjct: 63 ARPHKVDGRVVEPKRA 78
>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 = 85.5 bits (211), Expect = 9e-21
Identities = 35/78 (44%), Positives = 57/78 (73%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLF+GGLS++T+ + LRE+F +G +TD ++M+DP T+RSRGFGF+T++ E V+ +
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63
Query: 223 PIHTLDGKKIDPKHATPK 240
H +DG+ ++PK A +
Sbjct: 64 RPHKVDGRVVEPKRAVSR 81
Score = 62.8 bits (152), Expect = 1e-12
Identities = 29/76 (38%), Positives = 49/76 (64%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+K+F+GG+S +T+ + ++ +F ++G + + V++ D QTKR RGFGFVT+ E VD
Sbjct: 3 RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62
Query: 310 IHFHMIKNKKVECKKA 325
H + + VE K+A
Sbjct: 63 ARPHKVDGRVVEPKRA 78
>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 = 81.9 bits (202), Expect = 1e-19
Identities = 36/79 (45%), Positives = 50/79 (63%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+FVGG+ D ++ +FSQFG VE+ ++ D+QT + RGFGFV F+N + D +
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 311 HFHMIKNKKVECKKAQPKE 329
FH I +VE KKA PKE
Sbjct: 61 KFHPINGHRVEVKKAVPKE 79
Score = 62.6 bits (152), Expect = 1e-12
Identities = 29/78 (37%), Positives = 42/78 (53%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVGGL L E+F FG V ++ D T + RGFGF+ F ++ +K V
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60
Query: 223 PIHTLDGKKIDPKHATPK 240
H ++G +++ K A PK
Sbjct: 61 KFHPINGHRVEVKKAVPK 78
>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 = 80.2 bits (198), Expect = 6e-19
Identities = 34/75 (45%), Positives = 53/75 (70%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVGGL+ +TS LR +F +G +T+ ++M DP T+RSRGFGFITF+ + ++ ++
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63
Query: 223 PIHTLDGKKIDPKHA 237
H++DG +I+ K A
Sbjct: 64 QPHSIDGNQIELKRA 78
Score = 73.7 bits (181), Expect = 2e-16
Identities = 30/78 (38%), Positives = 50/78 (64%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
+ K+FVGG++ TS ++ +F+++GK+ E V+++D TKR RGFGF+TF + + D
Sbjct: 1 QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60
Query: 308 CEIHFHMIKNKKVECKKA 325
E H I ++E K+A
Sbjct: 61 MEAQPHSIDGNQIELKRA 78
>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 = 80.4 bits (198), Expect = 6e-19
Identities = 33/80 (41%), Positives = 50/80 (62%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
KKIFVGG+ +DT ++ YF ++GK+E ++ D+Q+ + RGF FVTF++ + VD I
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 310 IHFHMIKNKKVECKKAQPKE 329
+H I E KKA K+
Sbjct: 61 QKYHTINGHNCEVKKALSKQ 80
Score = 67.3 bits (164), Expect = 2e-14
Identities = 28/78 (35%), Positives = 47/78 (60%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGG+ T LR+YF +G + + +M+D + + RGF F+TF + +TV+K++
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61
Query: 223 PIHTLDGKKIDPKHATPK 240
HT++G + K A K
Sbjct: 62 KYHTINGHNCEVKKALSK 79
>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 = 79.2 bits (196), Expect = 1e-18
Identities = 32/73 (43%), Positives = 47/73 (64%), Gaps = 4/73 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFV GLS +T+ ++L F FG V +VL+MKDP T SRGFGF+TF E + ++
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR- 61
Query: 223 PIHTLDGKKIDPK 235
L+GK+++ +
Sbjct: 62 ---DLNGKELEGR 71
Score = 66.9 bits (164), Expect = 4e-14
Identities = 27/52 (51%), Positives = 40/52 (76%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K+FV G+S T+ +E++A FS+FG+VEE +++ D +T RGFGFVTFE+ E
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVE 54
>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 = 78.8 bits (195), Expect = 2e-18
Identities = 25/71 (35%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
L+VG L + + E L++ FG FG VT ++ D T RSRGFGF+ E
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA--- 57
Query: 223 PIHTLDGKKID 233
I L+G
Sbjct: 58 -IEKLNGTDFG 67
Score = 64.6 bits (158), Expect = 2e-13
Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++VG + + + E++K F QFG+V ++ D++T R RGFGFV E E +
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEAN 55
>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 = 77.7 bits (191), Expect = 5e-18
Identities = 30/76 (39%), Positives = 47/76 (61%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
KKIFVGG+ +DT ++ YF Q+GK+E ++ D+ + + RGF FVTF++ + VD I
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60
Query: 310 IHFHMIKNKKVECKKA 325
+H + E +KA
Sbjct: 61 QKYHTVNGHNCEVRKA 76
Score = 63.9 bits (155), Expect = 5e-13
Identities = 26/75 (34%), Positives = 45/75 (60%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGG+ T LR+YF +G + + IM D + + RGF F+TF + ++V+K++
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61
Query: 223 PIHTLDGKKIDPKHA 237
HT++G + + A
Sbjct: 62 KYHTVNGHNCEVRKA 76
>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 = 75.8 bits (187), Expect = 2e-17
Identities = 28/71 (39%), Positives = 42/71 (59%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVG L W S++L+EYF FG V + D T S+G+GF++F+ + +E L+
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 223 PIHTLDGKKID 233
H L+G K+
Sbjct: 61 QKHILEGNKLQ 71
Score = 70.0 bits (172), Expect = 2e-15
Identities = 23/73 (31%), Positives = 47/73 (64%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+FVG + ++E+K YFSQFGKV+ + D++T +G+GFV+F + + +++ +
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 311 HFHMIKNKKVECK 323
H+++ K++ +
Sbjct: 61 QKHILEGNKLQVQ 73
>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 = 76.0 bits (187), Expect = 2e-17
Identities = 30/77 (38%), Positives = 52/77 (67%), Gaps = 1/77 (1%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV-EKVL 220
KLF+GGLS+ T+ + L + F +G +++V+++KD TQRSRGFGF+TF P+ + ++
Sbjct: 1 GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60
Query: 221 KVPIHTLDGKKIDPKHA 237
+ ++DG++I A
Sbjct: 61 AMNGKSVDGRQIRVDQA 77
Score = 69.1 bits (169), Expect = 6e-15
Identities = 25/52 (48%), Positives = 42/52 (80%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K+F+GG+S DT+ + ++ FS++G++ E V++ D++T+R RGFGFVTFEN +
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPD 53
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic
RNA-binding protein RBM24, RBM38 and similar proteins.
This subfamily corresponds to the RRM of RBM24 and RBM38
from vertebrate, SUPpressor family member SUP-12 from
Caenorhabditis elegans and similar proteins. Both, RBM24
and RBM38, are preferentially expressed in cardiac and
skeletal muscle tissues. They regulate myogenic
differentiation by controlling the cell cycle in a
p21-dependent or -independent manner. RBM24, also termed
RNA-binding region-containing protein 6, interacts with
the 3'-untranslated region (UTR) of myogenin mRNA and
regulates its stability in C2C12 cells. RBM38, also
termed CLL-associated antigen KW-5, or HSRNASEB, or
RNA-binding region-containing protein 1(RNPC1), or
ssDNA-binding protein SEB4, is a direct target of the
p53 family. It is required for maintaining the stability
of the basal and stress-induced p21 mRNA by binding to
their 3'-UTRs. It also binds the AU-/U-rich elements in
p63 3'-UTR and regulates p63 mRNA stability and
activity. SUP-12 is a novel tissue-specific splicing
factor that controls muscle-specific splicing of the
ADF/cofilin pre-mRNA in C. elegans. All family members
contain a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 75.7 bits (187), Expect = 2e-17
Identities = 29/69 (42%), Positives = 47/69 (68%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGL + T+ + LR+YF FG + + +++ D T +SRG+GF+TF + E+ E+ K
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61
Query: 223 PIHTLDGKK 231
P +DG+K
Sbjct: 62 PNPIIDGRK 70
Score = 75.3 bits (186), Expect = 3e-17
Identities = 31/76 (40%), Positives = 50/76 (65%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
KIFVGG+ T+ + ++ YFSQFG++EE V++ D+QT + RG+GFVTF+++E + C+
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 310 IHFHMIKNKKVECKKA 325
+I +K A
Sbjct: 61 DPNPIIDGRKANVNLA 76
>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 = 73.9 bits (181), Expect = 9e-17
Identities = 34/75 (45%), Positives = 48/75 (64%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
K+FVGG+S DT+ E++K YF FG++E + MD +T RGF FVT+ +EE V + E
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 311 HFHMIKNKKVECKKA 325
+H I + K E K A
Sbjct: 61 RYHQIGSGKCEIKVA 75
Score = 66.2 bits (161), Expect = 6e-14
Identities = 30/75 (40%), Positives = 47/75 (62%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGLS T+ E+++EYFG FG + ++ + D T RGF F+T+ + E V+K+L+
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60
Query: 223 PIHTLDGKKIDPKHA 237
H + K + K A
Sbjct: 61 RYHQIGSGKCEIKVA 75
>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 = 73.4 bits (181), Expect = 1e-16
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 5/70 (7%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFVG L T+ E L++ F FG + + I++D T RS+GF F+ F + E EK L+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALE-- 57
Query: 224 IHTLDGKKID 233
L+GK++
Sbjct: 58 --ALNGKELG 65
Score = 69.5 bits (171), Expect = 3e-15
Identities = 22/71 (30%), Positives = 43/71 (60%), Gaps = 2/71 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
+FVG + DT+ E++K FS+FG +E + ++ +T R +GF FV FE+EE + + +
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIES-IRIVRDETGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 311 HFHMIKNKKVE 321
+ + +++
Sbjct: 60 NGKELGGRELR 70
>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 = 72.7 bits (179), Expect = 3e-16
Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 6/70 (8%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVG L+ + E LR+YF FG VTDV I K R F F+TFA+PE + +
Sbjct: 2 KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCG- 55
Query: 223 PIHTLDGKKI 232
H + G +
Sbjct: 56 EDHIIKGVSV 65
Score = 65.8 bits (161), Expect = 7e-14
Identities = 27/71 (38%), Positives = 42/71 (59%), Gaps = 6/71 (8%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+K+FVG +++D + E+++ YFSQFG+V + + K R F FVTF + EV +C
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI-----PKPFRAFAFVTFADPEVAQSLCG 55
Query: 310 IHFHMIKNKKV 320
H+IK V
Sbjct: 56 -EDHIIKGVSV 65
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 72.7 bits (178), Expect = 3e-16
Identities = 37/80 (46%), Positives = 51/80 (63%), Gaps = 1/80 (1%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
DP K+FVGGL+ + + EK+REYFG FG + + + DP T + RGF FITF E + V+
Sbjct: 2 DPVK-KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVK 60
Query: 218 KVLKVPIHTLDGKKIDPKHA 237
KVL+ H + G K + K A
Sbjct: 61 KVLEKKFHNVSGSKCEIKVA 80
Score = 71.9 bits (176), Expect = 6e-16
Identities = 31/76 (40%), Positives = 49/76 (64%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
KKIFVGG++ + + E+++ YF +FG++E + MD +T + RGF F+TF+ E+ V + E
Sbjct: 5 KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64
Query: 310 IHFHMIKNKKVECKKA 325
FH + K E K A
Sbjct: 65 KKFHNVSGSKCEIKVA 80
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM2
of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Overexpression of hnRNP
A2/B1 has been described in many cancers. It functions
as a nuclear matrix protein involving in RNA synthesis
and the regulation of cellular migration through
alternatively splicing pre-mRNA. It may play a role in
tumor cell differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 80
Score = 72.8 bits (178), Expect = 4e-16
Identities = 30/80 (37%), Positives = 51/80 (63%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
KK+FVGG+ +DT ++ YF ++GK++ ++ D+Q+ + RGFGFVTF++ + VD I
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60
Query: 310 IHFHMIKNKKVECKKAQPKE 329
+H I E +KA ++
Sbjct: 61 QKYHTINGHNAEVRKALSRQ 80
Score = 60.5 bits (146), Expect = 8e-12
Identities = 27/78 (34%), Positives = 46/78 (58%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVGG+ T LR+YF +G + + I+ D + + RGFGF+TF + + V+K++
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61
Query: 223 PIHTLDGKKIDPKHATPK 240
HT++G + + A +
Sbjct: 62 KYHTINGHNAEVRKALSR 79
>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 = 72.3 bits (177), Expect = 4e-16
Identities = 35/75 (46%), Positives = 47/75 (62%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
KIFVGG+S DT E+++ YF FG+VE + MD +T + RGF F+TF+ EE V I E
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 311 HFHMIKNKKVECKKA 325
+H + K E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
Score = 65.8 bits (160), Expect = 9e-14
Identities = 35/75 (46%), Positives = 46/75 (61%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+FVGGLS T EK+REYFG FG V + + D T + RGF FITF E E V+K+++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 223 PIHTLDGKKIDPKHA 237
H + K + K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
>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 = 71.2 bits (175), Expect = 8e-16
Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 5/72 (6%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFVG L T+ E LRE F FG + V I++D +S+GF F+ F PE EK L+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALE-- 57
Query: 224 IHTLDGKKIDPK 235
L+GK++D +
Sbjct: 58 --ALNGKELDGR 67
Score = 66.2 bits (162), Expect = 5e-14
Identities = 21/73 (28%), Positives = 43/73 (58%), Gaps = 2/73 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I 310
+FVG + DT+ E+++ FS+FG++E ++ D + + +GF FV FE+ E + E +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59
Query: 311 HFHMIKNKKVECK 323
+ + +K++
Sbjct: 60 NGKELDGRKLKVS 72
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 76.5 bits (187), Expect = 1e-15
Identities = 46/239 (19%), Positives = 88/239 (36%), Gaps = 30/239 (12%)
Query: 92 PNSNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQ------LVLVNGKS 145
+ L + + K + + + K + + +S
Sbjct: 42 NSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRS 101
Query: 146 SGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
S + ++ + LFVG L + + E LRE F FG V V +++D T +SRGF
Sbjct: 102 SESPKSRQKSKEENNT--LFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGF 159
Query: 206 GFITFAEPETVEKVLKVPIHT-LDGKKIDPKHATPKNRPKI------------------- 245
F+ F E+ EK ++ L+G+ + + A P ++P+
Sbjct: 160 AFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKA 219
Query: 246 --GNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++ ++VG + T+ EE+ F G + + + K + FV E +
Sbjct: 220 LLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASK 278
Score = 74.6 bits (182), Expect = 7e-15
Identities = 29/92 (31%), Positives = 52/92 (56%), Gaps = 1/92 (1%)
Query: 238 TPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVT 297
+PK+R K +FVG + D + E+++ F +FG V+ ++ D++T + RGF FV
Sbjct: 104 SPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVE 163
Query: 298 FENEEVVDHICEI-HFHMIKNKKVECKKAQPK 328
FE+EE + E + ++ + + +KAQP
Sbjct: 164 FESEESAEKAIEELNGKELEGRPLRVQKAQPA 195
>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 = 70.9 bits (174), Expect = 1e-15
Identities = 30/71 (42%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
LFVG LSW E L+ F FG V ++ D T RSRGFG++ F PE +K
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKA--- 57
Query: 223 PIHTLDGKKID 233
I +DGK++D
Sbjct: 58 -IEAMDGKELD 67
Score = 53.5 bits (129), Expect = 2e-09
Identities = 22/52 (42%), Positives = 32/52 (61%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FVG +S E +KA F +FG V ++ D++T R RGFG+V FE+ E
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPE 52
>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 = 77.9 bits (192), Expect = 2e-15
Identities = 61/239 (25%), Positives = 101/239 (42%), Gaps = 40/239 (16%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L+V L + +KLRE F FG +T +MKD + RSRGF F+ F + E K
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKA---- 235
Query: 224 IHTLDGKKIDP----------------------------KHATPKNRPKIGNRTKKIFVG 255
+ ++GKKI K + + N ++V
Sbjct: 236 VEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVN----LYVK 291
Query: 256 GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEIHFHM 314
+ + E+++ FS+ G++ +++D++ RGFGFV F N EE + E+H M
Sbjct: 292 NLDDTVTDEKLRELFSECGEITSAKVMLDEK-GVSRGFGFVCFSNPEEANRAVTEMHGRM 350
Query: 315 IKNKKVECKKAQPKEAVQANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQV 373
+ K + AQ KE +A+L + + L P ++ +P+ A Q Q
Sbjct: 351 LGGKPLYVALAQRKEQRRAHLQD-QFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQ 408
Score = 62.9 bits (153), Expect = 1e-10
Identities = 48/149 (32%), Positives = 71/149 (47%), Gaps = 17/149 (11%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL- 220
A L+VG L + KL + F FG V V + +D +T+RS G+G++ F P E+ L
Sbjct: 1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE 60
Query: 221 KVPIHTLDGKKI-------DPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQF 273
+ L GK I DP R +GN IFV + + + + FS+F
Sbjct: 61 TMNFKRLGGKPIRIMWSQRDPS----LRRSGVGN----IFVKNLDKSVDNKALFDTFSKF 112
Query: 274 GKVEETVMLMDQQTKRHRGFGFVTFENEE 302
G + + D + + RG+GFV FE EE
Sbjct: 113 GNILSCKVATD-ENGKSRGYGFVHFEKEE 140
Score = 61.0 bits (148), Expect = 4e-10
Identities = 43/180 (23%), Positives = 83/180 (46%), Gaps = 10/180 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK-VLKV 222
+FV L ++ L + F FG + + D +SRG+GF+ F + E+ + + KV
Sbjct: 91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149
Query: 223 PIHTLDGKKIDPKHATPKNRPKIGNRTK--KIFVGGVSQDTSAEEVKAYFSQFGKVEETV 280
L+ K++ K+ + K ++V + + ++++ F++FG++
Sbjct: 150 NGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA 209
Query: 281 MLMDQQTKRHRGFGFVTFENEE----VVDHICEIHFHMIKN-KKVECKKAQPKEAVQANL 335
++ D + R RGF FV FE E V+ + + K KK+ +AQ + +A L
Sbjct: 210 VMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAEL 268
Score = 51.3 bits (123), Expect = 5e-07
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 5/74 (6%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
L+V L + EKLRE F G +T +M D SRGFGF+ F+ PE + +
Sbjct: 286 VNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVT 344
Query: 222 VPIHTLDGKKIDPK 235
+ G+ + K
Sbjct: 345 ----EMHGRMLGGK 354
Score = 30.9 bits (70), Expect = 1.3
Identities = 11/58 (18%), Positives = 13/58 (22%), Gaps = 3/58 (5%)
Query: 39 NGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNN 96
NG P A PP + P Q PQP+
Sbjct: 435 NGLAPMNAVRAPSRNAQNAAQKPPMQPV---MYPPNYQSLPLSQDLPQPQSTASQGGQ 489
Score = 30.2 bits (68), Expect = 2.3
Identities = 12/83 (14%), Positives = 14/83 (16%), Gaps = 7/83 (8%)
Query: 22 TMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQ 81
Q P L P G P P Q
Sbjct: 402 GQGPQQQFNGQP-LGWPRMSMMPTPMG---PGGPLRPNGLAPMN---AVRAPSRNAQNAA 454
Query: 82 PPQPQPRDLQPNSNNQLVLVNGK 104
P + P + L L
Sbjct: 455 QKPPMQPVMYPPNYQSLPLSQDL 477
>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 = 70.0 bits (172), Expect = 3e-15
Identities = 31/78 (39%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++FVGG+ T+ E+LR++F FG+V DV I+ D S+G+GF+TF E EK+L +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGV-SKGYGFVTFETQEDAEKILAM 62
Query: 223 PIHTLDGKKIDPKHATPK 240
GKK++ A K
Sbjct: 63 GNLNFRGKKLNIGPAIRK 80
Score = 66.1 bits (162), Expect = 6e-14
Identities = 27/75 (36%), Positives = 46/75 (61%), Gaps = 1/75 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
+IFVGG+ DT+ EE++ +FS+FG V++ ++ D + +G+GFVTFE +E + I +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62
Query: 311 HFHMIKNKKVECKKA 325
+ KK+ A
Sbjct: 63 GNLNFRGKKLNIGPA 77
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 69.3 bits (169), Expect = 3e-14
Identities = 33/76 (43%), Positives = 44/76 (57%), Gaps = 4/76 (5%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
S KLF+GGLSW T LR+ F FG V D ++ D T RSRGFGF+ F + E
Sbjct: 34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFND----EGAA 89
Query: 221 KVPIHTLDGKKIDPKH 236
I +DGK+++ +H
Sbjct: 90 TAAISEMDGKELNGRH 105
Score = 54.3 bits (130), Expect = 4e-09
Identities = 21/53 (39%), Positives = 35/53 (66%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
+ K+F+GG+S T ++ F+ FG V + +++D++T R RGFGFV F +E
Sbjct: 34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDE 86
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 66.8 bits (164), Expect = 3e-14
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV- 222
L+V L + E LRE+F +G V V ++++ R RGF F+ FA PE E LK
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58
Query: 223 PIHTLDGKKI 232
LDG+ +
Sbjct: 59 NGLVLDGRTL 68
Score = 62.2 bits (152), Expect = 1e-12
Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
++V + + E+++ +FS +GKVE ++ ++ R RGF FV F + E + +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58
Query: 312 -FHMIKNKKVE 321
++ + +
Sbjct: 59 NGLVLDGRTLR 69
>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 = 66.1 bits (162), Expect = 7e-14
Identities = 21/49 (42%), Positives = 34/49 (69%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
V G+S T+ +++ FS++G +E+ ++ DQ+T R RGFGFV FE+ E
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVE 52
Score = 54.2 bits (131), Expect = 1e-09
Identities = 25/54 (46%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
L V GLS T+ LRE F +G + V ++ D T RSRGFGF+ F E+VE
Sbjct: 2 LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYF---ESVE 52
>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 = 65.8 bits (161), Expect = 8e-14
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L V L+++T+ + LR F +G V DV I +D T+ SRGF F+ F + E
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA---- 56
Query: 224 IHTLDGKKIDPKH 236
+ +DGK++D +
Sbjct: 57 MDAMDGKELDGRE 69
Score = 42.3 bits (100), Expect = 1e-05
Identities = 14/63 (22%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF-ENEEVVDHICEIHF 312
V ++ T+ ++++ F ++G+V + + D+ T+ RGF FV F + + D + +
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 313 HMI 315
+
Sbjct: 63 KEL 65
>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 = 65.3 bits (160), Expect = 2e-13
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 4/70 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFV L++ T+ KLR F +G + + +++D T + RG+ FI F E+ +K
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEH----ERDMKAA 59
Query: 224 IHTLDGKKID 233
DGKKID
Sbjct: 60 YKYADGKKID 69
Score = 56.1 bits (136), Expect = 3e-10
Identities = 15/53 (28%), Positives = 34/53 (64%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K +FV ++ DT+ +++ F ++G ++ ++ D++T + RG+ F+ FE+E
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER 54
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 70.7 bits (173), Expect = 3e-13
Identities = 48/173 (27%), Positives = 80/173 (46%), Gaps = 26/173 (15%)
Query: 149 SGRSTP---TGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGF 205
SGR+T T + +FV L+ + L E+F G V DV +KD ++RS+G
Sbjct: 74 SGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGV 133
Query: 206 GFITFAEPETV--------EKVLKVPIHTLDGKKIDPKHATPKNR--------PKIGNRT 249
++ F + E+V + +L PI + A KNR P
Sbjct: 134 AYVEFYDVESVIKALALTGQMLLGRPI------IVQSSQAE-KNRAAKAATHQPGDIPNF 186
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K++VG + + + +E++ F FG +E+ + D +T R +GFGF+ F + E
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAE 239
Score = 62.2 bits (151), Expect = 2e-10
Identities = 29/67 (43%), Positives = 43/67 (64%)
Query: 156 GDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
GD P KL+VG L + + ++LR+ F FG + DV + +DP T RS+GFGFI F + E
Sbjct: 181 GDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEE 240
Query: 216 VEKVLKV 222
++ L+V
Sbjct: 241 AKEALEV 247
Score = 43.3 bits (102), Expect = 2e-04
Identities = 15/66 (22%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 265 EVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKK 324
++ +FS+ GKV + + D+ ++R +G +V F + E V + M+ + +
Sbjct: 105 DLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPI---I 161
Query: 325 AQPKEA 330
Q +A
Sbjct: 162 VQSSQA 167
>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 = 63.1 bits (154), Expect = 7e-13
Identities = 31/77 (40%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFVG LSW + L E+F G V DV I +D RS+GFG + FA E +K L+
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEKS 60
Query: 224 IHTLDGKKIDPKHATPK 240
L G++I AT +
Sbjct: 61 GEELLGREIRVDLATER 77
Score = 44.6 bits (106), Expect = 3e-06
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+FVG +S ++++ +F + G+V + V + R +GFG V F EE E
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVD-VRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60
Query: 312 FHMIKNKKVECKKAQPK 328
+ +++ A +
Sbjct: 61 GEELLGREIRVDLATER 77
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
L+VG L + + + LR F FG + V + +DP T RS+G+GFI FA+ E +K L
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKAL 57
Score = 47.3 bits (113), Expect = 2e-07
Identities = 14/51 (27%), Positives = 31/51 (60%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++VG + + + ++++ F FG++E + D +T R +G+GF+ F + E
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAE 51
>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 = 67.4 bits (164), Expect = 4e-12
Identities = 54/238 (22%), Positives = 97/238 (40%), Gaps = 43/238 (18%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-K 221
+++VG +S++ + +R F FG + + + DP T + +GF F+ + PE + L +
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 222 VPIHTLDGKKIDPKHATPKNRP----------KIGNRTKKIFVGGVSQDTSAEEVKAYFS 271
+ L G+ I K P N P + + +I+V V D S ++K+ F
Sbjct: 169 MNGQMLGGRNI--KVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFE 226
Query: 272 QFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAV 331
FG++ + + + H+G+GF+ + N ++Q +
Sbjct: 227 AFGEIVKCQLARAPTGRGHKGYGFIEYNN----------------------LQSQSEAIA 264
Query: 332 QANLL--------VGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVA 381
NL VGK V L+ A + I A +AA + A+ A A A
Sbjct: 265 SMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGAA 322
>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 = 60.3 bits (147), Expect = 6e-12
Identities = 18/51 (35%), Positives = 34/51 (66%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++VGG++++ + + A F FG +++ + +D +T++HRGF FV FE E
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51
Score = 57.2 bits (139), Expect = 7e-11
Identities = 22/51 (43%), Positives = 30/51 (58%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
L+VGGL+ + + L F FG + D+ I D TQ+ RGF F+ F EPE
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51
>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 = 65.7 bits (160), Expect = 7e-12
Identities = 39/151 (25%), Positives = 74/151 (49%), Gaps = 12/151 (7%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
+ L V L + E++R F G + +++D +T +S G+GF+ + PE EK
Sbjct: 2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61
Query: 220 LKVPIHTLDG-----KKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFG 274
+++L+G K I +A P + G ++V G+ + + E+++ FS FG
Sbjct: 62 ----VNSLNGLRLQNKTIKVSYARPSSDSIKG---ANLYVSGLPKTMTQHELESIFSPFG 114
Query: 275 KVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++ + +L D T +G GF+ F+ + D
Sbjct: 115 QIITSRILSDNVTGLSKGVGFIRFDKRDEAD 145
Score = 48.0 bits (114), Expect = 5e-06
Identities = 32/147 (21%), Positives = 47/147 (31%), Gaps = 19/147 (12%)
Query: 82 PPQPQPRDLQPN----SNNQLVLVNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQ 137
P + L N Q V + + P + G V Q
Sbjct: 171 PSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQ 230
Query: 138 LVLVNGKSSGDSGRSTPTGD---------------DPTSAKLFVGGLSWQTSSEKLREYF 182
+ S P D D +FV LS T L + F
Sbjct: 231 QQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLF 290
Query: 183 GMFGAVTDVLIMKDPITQRSRGFGFIT 209
G FGAV +V I++D T + +G+GF++
Sbjct: 291 GPFGAVQNVKIIRDLTTNQCKGYGFVS 317
Score = 42.2 bits (99), Expect = 3e-04
Identities = 28/94 (29%), Positives = 42/94 (44%), Gaps = 6/94 (6%)
Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
P+ D A L+V GL + +L F FG + I+ D +T S+G GFI F +
Sbjct: 82 PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKR 141
Query: 214 ETVEKVLKVPIHTLDGKKIDPKHATPKNRPKIGN 247
+ ++ +K TL+G P T K N
Sbjct: 142 DEADRAIK----TLNGTT--PSGCTEPITVKFAN 169
Score = 38.4 bits (89), Expect = 0.005
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
IFV +S DT + F FG V+ ++ D T + +G+GFV+ N +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYD 322
>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 = 60.3 bits (147), Expect = 9e-12
Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
+F+ L + + E+L+E F FG V I+KD +T S+G F+ F E+ +K L+
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Score = 54.1 bits (131), Expect = 1e-09
Identities = 19/60 (31%), Positives = 33/60 (55%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
+ +F+ + D + EE+K FSQFG+V+ ++ D+ T +G FV F+ +E E
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 59.5 bits (145), Expect = 2e-11
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
++V L EKL+E FG +G +T +MKD +S+GFGF+ F E +K ++
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVE-- 60
Query: 224 IHTLDGKKIDPK 235
L+GK+++ K
Sbjct: 61 --ELNGKEVNGK 70
Score = 52.2 bits (126), Expect = 5e-09
Identities = 25/81 (30%), Positives = 44/81 (54%), Gaps = 8/81 (9%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE----VVDHI 307
++V + +D E++K F ++GK+ ++ D + K +GFGFV FEN E V+
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKS-KGFGFVNFENHEAAQKAVE-- 60
Query: 308 CEIHFHMIKNKKVECKKAQPK 328
E++ + KK+ +AQ K
Sbjct: 61 -ELNGKEVNGKKLYVGRAQKK 80
>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 = 59.3 bits (144), Expect = 2e-11
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 7/73 (9%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG-FGFITFAEPETVEKVLKV 222
+FV G TS E+L +YF FG V +V++ KD +G + + F E V+KVL
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDKVLSE 58
Query: 223 PIHTLDGKKIDPK 235
P HTL+G ++ +
Sbjct: 59 PQHTLNGHRLRVR 71
Score = 43.5 bits (103), Expect = 5e-06
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+FV G + TS E++ YFS FG V +M + K + V F+++E VD +
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFGPVMNVIM---DKDKGV--YAIVEFDSKEGVDKVLSEP 59
Query: 312 FHMIKNKKVECKKAQ 326
H + ++ + +
Sbjct: 60 QHTLNGHRLRVRPRE 74
>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 = 58.3 bits (142), Expect = 3e-11
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 169 LSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLD 228
LS + LRE F FG ++ V + KD T +SRGF F+TF E E+ ++ L+
Sbjct: 7 LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE----KLN 62
Query: 229 GKKID 233
G D
Sbjct: 63 GFGYD 67
Score = 46.8 bits (112), Expect = 4e-07
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 257 VSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+S+D ++++ F FG + + D++T + RGF FVTF E
Sbjct: 7 LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTRE 52
>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 = 57.6 bits (140), Expect = 7e-11
Identities = 18/52 (34%), Positives = 33/52 (63%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K+FVG + + + E+V+A F ++G +EE ++ D+ T + +G FV F + E
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSRE 52
Score = 56.8 bits (138), Expect = 1e-10
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVG L + E +R F +G + +V I++D T +S+G F+ F+ E +K
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKA--- 57
Query: 223 PIHTLDGKKIDP 234
I L GK P
Sbjct: 58 -IEALHGKVTMP 68
>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 = 57.0 bits (138), Expect = 9e-11
Identities = 24/69 (34%), Positives = 42/69 (60%), Gaps = 4/69 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+FVG LS + +E LR F FG ++D ++KD T +S+G+GF++F + E E
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENA---- 57
Query: 224 IHTLDGKKI 232
I +++G+ +
Sbjct: 58 IQSMNGQWL 66
Score = 50.4 bits (121), Expect = 2e-08
Identities = 19/51 (37%), Positives = 34/51 (66%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
IFVG +S + E ++A F+ FG++ + ++ D QT + +G+GFV+F +E
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKE 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 = 56.5 bits (137), Expect = 2e-10
Identities = 27/68 (39%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
+LFV L + T+ E+LRE F FG +++V + D T+RS+GF F++F PE K
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYS- 59
Query: 223 PIHTLDGK 230
LDG
Sbjct: 60 ---ELDGS 64
Score = 55.4 bits (134), Expect = 4e-10
Identities = 19/52 (36%), Positives = 33/52 (63%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++FV + T+ EE++ F FG++ E + +D++TKR +GF FV+F E
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPE 52
>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 = 56.5 bits (137), Expect = 2e-10
Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V 222
LFV L + T+ E+L E+F G + ++KD +++ RGFG++TFA E ++ L+
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 223 PIHTLDGKKIDPKHATPK 240
G+KI + A K
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79
Score = 56.1 bits (136), Expect = 2e-10
Identities = 19/51 (37%), Positives = 35/51 (68%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FV + DT+ E+++ +FS+ G ++ ++ D+ +K+ RGFG+VTF EE
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEE 52
>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 = 55.7 bits (135), Expect = 3e-10
Identities = 18/52 (34%), Positives = 34/52 (65%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+I+V V D S +++K+ F FGK++ + D +T +H+G+GF+ +EN +
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQ 53
Score = 43.0 bits (102), Expect = 9e-06
Identities = 13/55 (23%), Positives = 29/55 (52%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
+++V + S + ++ F FG + + DP T + +G+GFI + P++ +
Sbjct: 2 RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQ 56
>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 = 55.2 bits (134), Expect = 4e-10
Identities = 25/68 (36%), Positives = 38/68 (55%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
FVG L + E+LR++F G V V I++D T +GFG++ F ++V LK+
Sbjct: 3 FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62
Query: 225 HTLDGKKI 232
L G+KI
Sbjct: 63 IKLKGRKI 70
Score = 42.1 bits (100), Expect = 2e-05
Identities = 18/54 (33%), Positives = 32/54 (59%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
+FVG + D EE++ +F G VE ++ D++T +GFG+V F+ ++ V
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVA 55
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 55.2 bits (133), Expect = 5e-10
Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE-TVEKVLKV 222
LFV L++ + E L ++F + +++ DP T SRG+GF+TFA E E + K+
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 223 PIHTLDGKKIDPKHATPK 240
L G+ + A +
Sbjct: 62 KNKKLHGRILRLDIAERR 79
Score = 52.5 bits (126), Expect = 5e-09
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FV ++ + E++ +FS ++ V++ D +T RG+GFVTF E
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLE 52
>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 = 55.2 bits (133), Expect = 6e-10
Identities = 22/59 (37%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
++FVGG+ ++T+ LR++F +G V +V I+ D S+G+GF+TF E +K+L+
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQ 61
Score = 48.6 bits (116), Expect = 1e-07
Identities = 22/57 (38%), Positives = 38/57 (66%), Gaps = 1/57 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
+IFVGG+ T+ +++ +FSQ+G V+E V +++ + +G+GFVTFE +E I
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKE-VKIVNDRAGVSKGYGFVTFETQEDAQKI 59
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 55.1 bits (133), Expect = 6e-10
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
P S +LFVG L + ++L+E+F FG V +V I R FGF+ F +PE V+K
Sbjct: 1 PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60
Query: 219 VL-KVPIHTLDGKKID 233
+L PI+ +++
Sbjct: 61 ILANKPIYFRGDHRLN 76
Score = 47.4 bits (113), Expect = 3e-07
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 3/77 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
++FVG + D + +E+K +F +FG V E + R FGFV F++ E V I
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64
Query: 311 HFHMIKNKK---VECKK 324
+ VE KK
Sbjct: 65 KPIYFRGDHRLNVEEKK 81
>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 = 54.7 bits (132), Expect = 8e-10
Identities = 26/69 (37%), Positives = 38/69 (55%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFVG L + T++E L +F GA V ++ D T +S+G F+ F E + K LK+
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 224 IHTLDGKKI 232
L G+KI
Sbjct: 63 HTLLKGRKI 71
Score = 50.0 bits (120), Expect = 2e-08
Identities = 21/69 (30%), Positives = 40/69 (57%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+FVG + DT+AE++ A+F G +L D++T + +G FV F+ E + ++H
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 312 FHMIKNKKV 320
++K +K+
Sbjct: 63 HTLLKGRKI 71
>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 = 54.6 bits (132), Expect = 8e-10
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
+L V L ++ + L++ F FG V +V I + P + +GF F+ F EK +K
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIK- 58
Query: 223 PIHTLDGKKID 233
++GKKI
Sbjct: 59 ---GVNGKKIK 66
Score = 38.8 bits (91), Expect = 3e-04
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
++ V + + ++K FS FG V E + + +GF FV F +
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTS 49
>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 = 54.2 bits (131), Expect = 1e-09
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FVG + D + E++ FS+ G V ++ D+ T + +G+GF FE+ E
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIE 51
Score = 51.5 bits (124), Expect = 9e-09
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
FVG + + + E+L E F G V ++ D T + +G+GF F + ET
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAA 54
>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 = 53.9 bits (130), Expect = 1e-09
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 14/83 (16%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
++G L+W + + +RE+F +T V + D T +GFG + FA+ E+++ LK
Sbjct: 3 YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALK--- 58
Query: 225 HTLDGKKIDPKHATPKNRP-KIG 246
LDG + RP +I
Sbjct: 59 --LDGTVL-------CGRPIRIA 72
Score = 42.4 bits (100), Expect = 1e-05
Identities = 14/54 (25%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
+++G ++ D + ++V+ +F ++ + D++T +GFG V F +EE +D
Sbjct: 2 VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLD 54
>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 = 54.1 bits (131), Expect = 1e-09
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVT--DVLIMKDPITQRSRGFGFITFAEPETVEK 218
+ L + GL T+ E + + +V DV +++D +T SRGF F+ F E +
Sbjct: 2 TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61
Query: 219 VLK----VPIHTLDGKKI 232
+ + +DG+ +
Sbjct: 62 WMDALNNLDPFVIDGRVV 79
Score = 34.8 bits (81), Expect = 0.008
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 6/83 (7%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVE-ETVMLM-DQQTKRHRGFGFVTF----ENEE 302
T + + G+ T+ E++ S V + V L+ D+ T RGF FV F + +
Sbjct: 2 TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61
Query: 303 VVDHICEIHFHMIKNKKVECKKA 325
+D + + +I + V A
Sbjct: 62 WMDALNNLDPFVIDGRVVRVSYA 84
>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 = 53.8 bits (130), Expect = 2e-09
Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
L+V L E+LRE F FG +T +M D RS+GFGF+ F+ PE K
Sbjct: 2 VNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATK--- 57
Query: 222 VPIHTLDGKKIDPK 235
+ ++G+ I K
Sbjct: 58 -AVTEMNGRIIGGK 70
Score = 40.3 bits (95), Expect = 9e-05
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
++V + E ++ FS FG + ++ D++ R +GFGFV F + EE + E
Sbjct: 3 NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAVTE 61
Query: 310 IHFHMIKNK 318
++ +I K
Sbjct: 62 MNGRIIGGK 70
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM2
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA). However, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 75
Score = 53.3 bits (128), Expect = 2e-09
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+FVG LS + + L F F + +D +M D + RSRG+GF++F + E
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENA---- 57
Query: 224 IHTLDGK 230
I+ ++GK
Sbjct: 58 INEMNGK 64
Score = 48.3 bits (115), Expect = 1e-07
Identities = 17/51 (33%), Positives = 31/51 (60%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
IFVG +S + + + A FS F + ++ D ++ R RG+GFV+F +++
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQ 52
>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 = 52.8 bits (127), Expect = 4e-09
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ +LFV L + + L + F FG +++V + D + +S+GF ++ F +PE K
Sbjct: 2 TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61
Query: 221 KVPIHTLDGKK 231
K LDGK
Sbjct: 62 K----ELDGKV 68
Score = 47.0 bits (112), Expect = 4e-07
Identities = 13/50 (26%), Positives = 31/50 (62%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
T ++FV + ++++ FS+FG++ E + +D+++ + +GF +V F
Sbjct: 2 TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF 51
>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 = 52.6 bits (127), Expect = 5e-09
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 11/86 (12%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
++FVG L + + E L F + + +++D T +S+G+GF++F++P
Sbjct: 3 PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62
Query: 218 KVLKVPIHTLDGKKIDPKHATPKNRP 243
K +K ++GK + NRP
Sbjct: 63 KAMK----EMNGKYVG-------NRP 77
Score = 41.4 bits (98), Expect = 4e-05
Identities = 17/76 (22%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
+IFVG + + + E + FS++ ++ ++ D++T + +G+GFV+F + + + + E
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67
Query: 310 IHFHMIKNKKVECKKA 325
++ + N+ ++ +K+
Sbjct: 68 MNGKYVGNRPIKLRKS 83
>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 = 52.3 bits (126), Expect = 5e-09
Identities = 17/69 (24%), Positives = 38/69 (55%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
IFVG V T+ EE++ +F G + +L D+ T + +GF ++ F ++ V++ ++
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61
Query: 312 FHMIKNKKV 320
+ +++
Sbjct: 62 ESEFRGRQI 70
Score = 48.1 bits (115), Expect = 2e-07
Identities = 21/68 (30%), Positives = 38/68 (55%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
FVG + + T+ E+L+E+F G + + I+ D T + +GF +I F + +VE L +
Sbjct: 3 FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62
Query: 225 HTLDGKKI 232
G++I
Sbjct: 63 SEFRGRQI 70
>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 = 52.0 bits (125), Expect = 8e-09
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L+V ++ T + LR FG +G + DV I D T+R RGF ++ F + E L
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL--- 59
Query: 224 IHTLDGKKI 232
+ LD +
Sbjct: 60 -YYLDRTRF 67
Score = 44.3 bits (105), Expect = 4e-06
Identities = 18/78 (23%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHIC 308
++V V+ T ++++ F ++G + + + +D T+R RGF +V FE+ + D +
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60
Query: 309 EIHFHMIKNKKVECKKAQ 326
+ +++E + AQ
Sbjct: 61 YLDRTRFLGREIEIQFAQ 78
>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 = 51.6 bits (124), Expect = 9e-09
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
IFVG +S D + EE+ FS+ GK+ E ++ ++ F F+ FE E+ E
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63
Query: 312 FH-MIKNK--KVECK 323
H M+KNK V+ K
Sbjct: 64 NHSMLKNKTMHVQYK 78
Score = 40.8 bits (96), Expect = 6e-05
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 4/64 (6%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
D S +FVG LS + E+L E F G + +V ++K + F FI F +
Sbjct: 2 DKYS--IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRA--NHTNAFAFIKFEREQAAA 57
Query: 218 KVLK 221
+ ++
Sbjct: 58 RAVE 61
>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 = 51.2 bits (123), Expect = 1e-08
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
++VGG+ + ++ +++R YF G + ++ +M P T R RG FITF E ++ L
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA-- 58
Query: 224 IHTLDGKKID 233
LDG+ +
Sbjct: 59 ---LDGEDMG 65
Score = 46.2 bits (110), Expect = 7e-07
Identities = 19/52 (36%), Positives = 34/52 (65%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
++VGG+ ++ +E+++YFS G++EE ++ T R RG F+TF+ EE
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEA 52
>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 = 51.5 bits (124), Expect = 1e-08
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 9/77 (11%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR------GFGFITFAEPETV 216
+++V L ++ + LR F FG V + I P Q + GF F+TF + +
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRI---PKKQDEKQGRLNNGFAFVTFKDASSA 58
Query: 217 EKVLKVPIHTLDGKKID 233
E L++ L G+KI
Sbjct: 59 ENALQLNGTELGGRKIS 75
Score = 45.3 bits (108), Expect = 2e-06
Identities = 18/74 (24%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHR---GFGFVTFENEEVVDHI 307
+I+V + ++++ FS+FG+VE + Q K+ R GF FVTF++ ++
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 308 CEIHFHMIKNKKVE 321
+++ + +K+
Sbjct: 62 LQLNGTELGGRKIS 75
>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 = 51.0 bits (123), Expect = 1e-08
Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVEC 322
E++ YFSQFG V + ++T + +G+ FV FE+ EV + E ++ +++ + ++C
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKC 73
Query: 323 K 323
K
Sbjct: 74 K 74
Score = 45.6 bits (109), Expect = 1e-06
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 176 EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDG 229
+LR+YF FG VT + + + T +S+G+ F+ F PE V K+ T++
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE----VAKIVAETMNN 63
>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 = 50.4 bits (121), Expect = 2e-08
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFVG LS+ + + E FG +G ++ V + DP + R +GFG++ F+ E + L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 224 IHT-LDGKKI 232
T L G+ +
Sbjct: 61 GGTDLLGRPV 70
Score = 43.5 bits (103), Expect = 5e-06
Identities = 15/52 (28%), Positives = 29/52 (55%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
+FVG +S D + + F ++G++ + D + R +GFG+V F ++E
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEA 52
>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 = 50.7 bits (122), Expect = 2e-08
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV 304
+FV +S ++ +FS+ GKV + ++ D+ ++R +G +V F +EE V
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54
Score = 48.4 bits (116), Expect = 1e-07
Identities = 20/56 (35%), Positives = 31/56 (55%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
FV LS + L E+F G V DV I++D ++RS+G ++ F + E+V L
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL 58
>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 = 50.5 bits (121), Expect = 2e-08
Identities = 22/61 (36%), Positives = 34/61 (55%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFVG LS++T+ ++LR +FG G + V +M + + +GF F+ F E E LK
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60
Query: 224 I 224
Sbjct: 61 H 61
Score = 46.3 bits (110), Expect = 6e-07
Identities = 17/51 (33%), Positives = 33/51 (64%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FVG +S +T+ +E++A+F + G++ M+ + + + +GF FV FE E
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE 51
>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 = 50.3 bits (121), Expect = 2e-08
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
++ V L + ++LRE+F G VTDV +M+ +SR FGF+ F E ++ +K
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVK 59
Score = 34.1 bits (79), Expect = 0.015
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+I V + + + + ++ +F G+V + V +M + + R FGFV F++EE
Sbjct: 2 RIIVKNLPKYVTEDRLREHFESKGEVTD-VKVMRTRDGKSRRFGFVGFKSEE 52
>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 = 50.1 bits (120), Expect = 3e-08
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
S +LF+ L++ + E L + F +G +++V + D +T++ +GF F+T+ PE K
Sbjct: 2 SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAF 61
Query: 221 KVPIHTLDG 229
LDG
Sbjct: 62 A----ELDG 66
Score = 47.4 bits (113), Expect = 3e-07
Identities = 14/50 (28%), Positives = 33/50 (66%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
+ ++F+ ++ + E+++ FS++G + E + +D+ TK+ +GF FVT+
Sbjct: 2 SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog of
DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 50.2 bits (120), Expect = 4e-08
Identities = 23/69 (33%), Positives = 43/69 (62%), Gaps = 2/69 (2%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+FVGG+ + ++R +F +G+V +V I+ D T S+G+GF++F + V+K+++
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66
Query: 224 IHTLDGKKI 232
I GKK+
Sbjct: 67 I-NFHGKKL 74
Score = 46.0 bits (109), Expect = 1e-06
Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 3/69 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-- 309
+FVGG+ E++++F+++G V+E ++ D +T +G+GFV+F ++ V I E
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIVESQ 66
Query: 310 IHFHMIKNK 318
I+FH K K
Sbjct: 67 INFHGKKLK 75
>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 = 50.0 bits (119), Expect = 4e-08
Identities = 31/83 (37%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 151 RSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
R+ P DP L V GLS T+ LRE F +G + DV I+ D ++RSRGF F+ F
Sbjct: 3 RANP---DPNCC-LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58
Query: 211 AEPE-TVEKVLKVPIHTLDGKKI 232
+ E + LDG++I
Sbjct: 59 ENVDDAKEAKERANGMELDGRRI 81
Score = 49.3 bits (117), Expect = 8e-08
Identities = 19/49 (38%), Positives = 33/49 (67%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
V G+S T+ +++ FS++G + + ++ DQQ++R RGF FV FEN +
Sbjct: 14 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62
>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 = 49.9 bits (119), Expect = 4e-08
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+FVG L ++ E L FG G + V I++DP T +GF ++ F + VEK L
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL--- 58
Query: 224 IHTLDGKKIDPKHA 237
L+ KK P
Sbjct: 59 --LLNEKKFPPMLP 70
Score = 32.5 bits (74), Expect = 0.046
Identities = 15/54 (27%), Positives = 29/54 (53%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
+FVG + + E + F + G +E ++ D +T +GF +V F++E V+
Sbjct: 2 VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVE 55
>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 = 49.5 bits (118), Expect = 5e-08
Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVG L+ Q + +++ E F +G V D+ +M+D + Q SRG F+ ++ E + +K
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQ-SRGCAFVKYSSKEMAQAAIKA 59
Query: 223 --PIHTLDG 229
++T+ G
Sbjct: 60 LNGVYTMRG 68
Score = 46.8 bits (111), Expect = 5e-07
Identities = 19/52 (36%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K+FVG +++ + +EV+ FS +G+VE+ M+ D+ K+ RG FV + ++E
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKE 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 = 49.3 bits (118), Expect = 6e-08
Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 7/79 (8%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR-SRGFGFITFAEPETVEKVLK 221
+L V + ++ LR+ FG FG + DV I+ +R S+GFGF+TFA ++ +
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEII---FNERGSKGFGFVTFANSADADRA-R 57
Query: 222 VPIH--TLDGKKIDPKHAT 238
+H ++G+KI+ +AT
Sbjct: 58 EKLHGTVVEGRKIEVNNAT 76
Score = 40.5 bits (95), Expect = 6e-05
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 265 EVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKVECK 323
+++ F QFG + + ++ +++ + GFGFVTF N D E +H +++ +K+E
Sbjct: 16 DLRQMFGQFGPILDVEIIFNERGSK--GFGFVTFANSADADRAREKLHGTVVEGRKIEVN 73
Query: 324 KA 325
A
Sbjct: 74 NA 75
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 49.1 bits (118), Expect = 8e-08
Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLI-----MKDPITQRSRGFGFITFAEPETVEK 218
LFV L+++T+ E L+++F G V V I K P S G+GF+ F E +K
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 219 VLKVPIHT-LDGKKID 233
LK T LDG ++
Sbjct: 63 ALKRLQGTVLDGHALE 78
Score = 29.5 bits (67), Expect = 0.67
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVM-----LMDQQTKRHRGFGFVTFENEEVVDH 306
+FV ++ T+ E +K +F + G V + G+GFV F+++E
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62
Query: 307 ICE 309
+
Sbjct: 63 ALK 65
>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 = 48.8 bits (117), Expect = 8e-08
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGA-VTDVLIMKDPITQRSRGFGFITFA 211
A LF+G L + + L + F FG + IM+DP T S+GF FI++
Sbjct: 2 ANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYD 52
Score = 41.1 bits (97), Expect = 4e-05
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 252 IFVGGVSQDTSAEEVKAY--FSQFGKVEETVMLM-DQQTKRHRGFGFVTFENEEVVD 305
+F+G + D +E Y FS FG + +T +M D T +GF F+++++ E D
Sbjct: 4 LFIGNL--DPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASD 58
>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 = 48.8 bits (116), Expect = 1e-07
Identities = 27/71 (38%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
+ LFV ++ T SE LR FG +G + DV + D T+R RGF ++ F + E L
Sbjct: 1 SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL- 59
Query: 222 VPIHTLDGKKI 232
H LD K I
Sbjct: 60 ---HNLDRKWI 67
Score = 41.5 bits (97), Expect = 5e-05
Identities = 21/76 (27%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
+FV ++ DT +E+++ F ++G + + + +D T+R RGF +V FE+ + D + +
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 311 HFHMIKNKKVECKKAQ 326
I +++E + AQ
Sbjct: 63 DRKWICGRQIEIQFAQ 78
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 48.8 bits (117), Expect = 1e-07
Identities = 19/49 (38%), Positives = 31/49 (63%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
LFVG LS QT+ E LRE F +G + + +++D +T S+G+ F+ +
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEH 54
Score = 43.4 bits (103), Expect = 1e-05
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
+FVG +S T+ E ++ FS++G + ++ D T +G+ FV +E+E
Sbjct: 4 LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALR 60
>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 = 1e-07
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L VG L+ + + L+E F +G V DV + D RG+ ++ F PE EK +K
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK-- 58
Query: 224 IHTLDGKKID 233
H +DG +ID
Sbjct: 59 -H-MDGGQID 66
Score = 39.5 bits (93), Expect = 2e-04
Identities = 14/51 (27%), Positives = 32/51 (62%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ VG ++++ + + +K FS +G V++ + +D++ RG+ +V FE+ E
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPE 51
>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 = 48.1 bits (115), Expect = 2e-07
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+FV L L + F FGAVT+V +++D T + +G+GF+T E E
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE--EAY--SA 59
Query: 224 IHTLDGKKIDPK 235
I +L+G ++ +
Sbjct: 60 IASLNGYRLGGR 71
Score = 43.5 bits (103), Expect = 6e-06
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
IFV + D + FS FG V ++ D T + +G+GFVT N EE I +
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63
>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 = 47.6 bits (114), Expect = 2e-07
Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
++VG + + + E + F Q G V + D+ T+ H+G+GFV F +EE D+ +I
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI- 59
Query: 312 FHMIK--NKKVECKK 324
+MIK K + K
Sbjct: 60 MNMIKLYGKPIRVNK 74
Score = 45.3 bits (108), Expect = 1e-06
Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++VG L + + E L E F G V +V I KD +TQ +G+GF+ F E + +K+
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59
>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 = 47.4 bits (113), Expect = 3e-07
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+++VG +S + + ++ FS FG ++ M D T +H+GF FV +E E
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPE 53
Score = 44.0 bits (104), Expect = 5e-06
Identities = 15/52 (28%), Positives = 32/52 (61%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
+++VG +S++ + +R+ F FG + + + DP+T + +GF F+ + PE
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPE 53
>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 = 47.2 bits (113), Expect = 3e-07
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
+F+ + + + +++ F+ FG V + +D+ T + + FGFV+++N E I +
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 311 HFHMIKNK--KVE 321
+ + K KV+
Sbjct: 61 NGFQVGGKRLKVQ 73
Score = 46.1 bits (110), Expect = 6e-07
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LF+ L + + + L + F FG V + D T +S+ FGF+++ PE+ +
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAA---- 56
Query: 224 IHTLDGKKIDPKH 236
I ++G ++ K
Sbjct: 57 IKAMNGFQVGGKR 69
>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 = 47.1 bits (113), Expect = 3e-07
Identities = 19/58 (32%), Positives = 29/58 (50%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
L+VG L + L E F G V + + +D IT+RS G+ ++ F P E+ L
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALD 59
Score = 32.1 bits (74), Expect = 0.062
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 253 FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC-EIH 311
+VG + D + + FS G V + D T+R G+ +V F+N + ++
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62
Query: 312 FHMIKNK 318
F +IK K
Sbjct: 63 FDVIKGK 69
>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 = 47.0 bits (111), Expect = 4e-07
Identities = 18/50 (36%), Positives = 35/50 (70%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
+FVG +S + + E++K+ F+ FGK+ + ++ D T + +G+GFV+F N+
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 53
Score = 47.0 bits (111), Expect = 4e-07
Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK-VLKV 222
+FVG LS + ++E ++ F FG ++D ++KD T +S+G+GF++F E ++ +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 223 PIHTLDGKKIDPKHAT 238
L G++I AT
Sbjct: 64 GGQWLGGRQIRTNWAT 79
>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 = 46.7 bits (111), Expect = 4e-07
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-I 310
I++G + +E+K YFSQFG V+ + ++T + +GF+ F N EV + +
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 311 HFHMIKNKKVECK 323
+ +++ K ++
Sbjct: 62 NNYLLMGKVLQVH 74
Score = 42.5 bits (100), Expect = 1e-05
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V 222
+++G L ++L++YF FG V +V + + T S+ +GFI F PE K +
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 223 PIHTLDGKKI 232
+ L GK +
Sbjct: 62 NNYLLMGKVL 71
>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 = 46.5 bits (111), Expect = 5e-07
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE- 309
KIF+GG+ S ++VK FGK++ ++ D T +G+ F + + V D
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 310 IHFHMIKNKKVECKKA 325
++ + +KK+ ++A
Sbjct: 62 LNGMQLGDKKLTVQRA 77
Score = 37.2 bits (87), Expect = 0.001
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+F+GGL S ++++E FG + ++KD T S+G+ F + +P V
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDP----SVTDQ 57
Query: 223 PIHTLDGKKI 232
I L+G ++
Sbjct: 58 AIAGLNGMQL 67
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 47.6 bits (113), Expect = 5e-07
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V 222
LFV L + + E L +F FG+V L + D T R++G GF+ F + T LK
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63
Query: 223 PIH 225
P
Sbjct: 64 PAA 66
Score = 47.2 bits (112), Expect = 6e-07
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
+FV + D + E + +FS+FG V + ++D+ T R +G GFV F+++ +
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN 57
>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 = 46.5 bits (111), Expect = 5e-07
Identities = 19/67 (28%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+FV L + ++LR+ F G +TDV ++K+ +S+G+ ++ F E+V++ LK+
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEALKLD 60
Query: 224 IHTLDGK 230
+ G+
Sbjct: 61 RELIKGR 67
Score = 41.5 bits (98), Expect = 3e-05
Identities = 14/54 (25%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
+FV + +E++ FS+ G++ + ++ + + + +G+ +V FENEE V
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQ 54
>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 = 46.6 bits (111), Expect = 5e-07
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 174 SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
+ E+LR F G + I++D IT +S G+GF+ + + +K I+TL+G +I
Sbjct: 13 TQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKA----INTLNGFEIR 68
Query: 234 PKH 236
K
Sbjct: 69 NKR 71
Score = 38.5 bits (90), Expect = 4e-04
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
QD + EE+++ F G +E ++ D+ T + G+GFV + +E
Sbjct: 10 QDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDEN 53
>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 = 46.1 bits (110), Expect = 7e-07
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGA--VTDVLIMKDPITQRSRGFGFITFAEPETVEKVL- 220
L+VG L+W T+ E L G V + + +S+GF ++ FA V
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 221 KVPIHTLDGKK 231
K+ +GKK
Sbjct: 61 KLEGREFNGKK 71
>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 = 46.0 bits (110), Expect = 7e-07
Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF-AEPETVEKVLKV 222
LFVGGLS + L E F FG V+DV I+K RGF +I ++K
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61
Score = 42.9 bits (102), Expect = 1e-05
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FVGG+S + +++ FS+FG V + ++ + RGF ++ E
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSE 52
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 46.1 bits (109), Expect = 8e-07
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 166 VGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE-TVEKVLKVPI 224
V GLS T+ LRE F +G + V ++ D T RSRGF F+ F + + E +
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63
Query: 225 HTLDGKKIDPKHATPK 240
LDG++I ++ K
Sbjct: 64 MELDGRRIRVDYSITK 79
Score = 42.3 bits (99), Expect = 2e-05
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE----NEEVVDH 306
V G+S T+ +++ FS++G + ++ DQ+T R RGF FV FE ++E ++H
Sbjct: 4 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60
>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 = 46.2 bits (110), Expect = 8e-07
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
LFVG L + + E L E F G + V I KDP + + F F+TF +V
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFKHEVSV 55
Score = 39.6 bits (93), Expect = 2e-04
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
+RT +FVG + + E + F Q G +E + D K + F FVTF++E V +
Sbjct: 1 DRT--LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKP-KSFAFVTFKHEVSVPY 57
Query: 307 ICEI 310
++
Sbjct: 58 AIQL 61
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 45.7 bits (109), Expect = 1e-06
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 6/70 (8%)
Query: 164 LFVGGLS-WQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
L++G L W + + F G VT V I+++ T +S G+GF+ FA E E+ L
Sbjct: 2 LWMGDLEPWMDEAY-IYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQAL-- 58
Query: 223 PIHTLDGKKI 232
+L+GK I
Sbjct: 59 --QSLNGKPI 66
Score = 29.9 bits (68), Expect = 0.51
Identities = 12/56 (21%), Positives = 28/56 (50%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
+++G + + + F++ G+V ++ ++QT + G+GFV F E +
Sbjct: 2 LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQA 57
>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 = 46.0 bits (109), Expect = 1e-06
Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+K+FVG +S+ + +V+ F+ FG +EE +L DQ + RG FVTF + +
Sbjct: 2 RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQS-RGCAFVTFASRQ 53
Score = 41.7 bits (98), Expect = 3e-05
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVG LS + + +R F FG++ + +++D Q SRG F+TFA + +K
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQ-SRGCAFVTFASRQCALNAIKA 61
Query: 223 PIH--TLDG 229
H T++G
Sbjct: 62 MHHSQTMEG 70
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 49.6 bits (118), Expect = 1e-06
Identities = 36/162 (22%), Positives = 68/162 (41%), Gaps = 4/162 (2%)
Query: 142 NGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR 201
N +S SG S + + L V L + +L F G + IM+D T
Sbjct: 88 NSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGY 147
Query: 202 SRGFGFITFAEPETVEKVLKVPIH-TLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQD 260
S G+ F+ F ++ +K T+ K++ +A P + ++V + +
Sbjct: 148 SFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESI---KDTNLYVTNLPRT 204
Query: 261 TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ +++ F ++G++ + +L D+ T RG FV F E
Sbjct: 205 ITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKRE 246
Score = 36.9 bits (85), Expect = 0.013
Identities = 17/67 (25%), Positives = 32/67 (47%)
Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP 213
P G+ L+V L + ++L FG +G + I++D +T RG F+ F +
Sbjct: 186 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKR 245
Query: 214 ETVEKVL 220
E ++ +
Sbjct: 246 EEAQEAI 252
>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 = 45.3 bits (108), Expect = 1e-06
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 10/75 (13%)
Query: 251 KIFVGGVSQD-TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-IC 308
++FVG ++ D S E+++ FS++GK+ + H+G+GFV F+NEE +
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53
Query: 309 EIHFHMIKNKKVECK 323
+ I +K++
Sbjct: 54 GENGREIAGQKLDIN 68
Score = 29.9 bits (68), Expect = 0.31
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 10/74 (13%)
Query: 162 AKLFVGGL-SWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK-V 219
+++FVG L + + S E L E F +G + + + K G+GF+ F E V
Sbjct: 1 SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK--------GYGFVQFDNEEDARAAV 52
Query: 220 LKVPIHTLDGKKID 233
+ G+K+D
Sbjct: 53 AGENGREIAGQKLD 66
>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 = 45.5 bits (107), Expect = 2e-06
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
+ + L V L + E+L+ FG G + +++D IT +S G+GF+ + +P+ E
Sbjct: 1 EDSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 60
Query: 218 KVLKVPIHTLDGKKIDPK 235
K I+TL+G ++ K
Sbjct: 61 KA----INTLNGLRLQTK 74
Score = 33.2 bits (75), Expect = 0.032
Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF-ENEEVVDHICEI 310
+ V + Q+ + EE+K+ F G++E ++ D+ T + G+GFV + + ++ I +
Sbjct: 7 LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66
Query: 311 HFHMIKNKKVECKKAQP 327
+ ++ K ++ A+P
Sbjct: 67 NGLRLQTKTIKVSYARP 83
>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 = 45.5 bits (108), Expect = 2e-06
Identities = 17/48 (35%), Positives = 31/48 (64%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
K+FVG + ++ ++++ F QFGK+ E +L D+ T H+G F+T+
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 54
Score = 42.4 bits (100), Expect = 2e-05
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 158 DPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
D + KLFVG + + LR F FG + ++ ++KD T +G F+T+ E+
Sbjct: 2 DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61
Query: 218 K 218
K
Sbjct: 62 K 62
>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 = 45.1 bits (106), Expect = 2e-06
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
+ L V L + E+ R FG G + +++D IT +S G+GF+ + +P+ EK
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 220 LKVPIHTLDGKKIDPK 235
I+TL+G ++ K
Sbjct: 61 ----INTLNGLRLQTK 72
Score = 32.4 bits (73), Expect = 0.065
Identities = 17/77 (22%), Positives = 41/77 (53%), Gaps = 1/77 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF-ENEEVVDHICEI 310
+ V + Q+ + EE ++ F G++E ++ D+ T + G+GFV + + ++ I +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 311 HFHMIKNKKVECKKAQP 327
+ ++ K ++ A+P
Sbjct: 65 NGLRLQTKTIKVSYARP 81
>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 = 44.9 bits (107), Expect = 2e-06
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
LFV L+ T+ E L F FG + +++D T S + FI F E E+
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60
Score = 39.9 bits (94), Expect = 1e-04
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 261 TSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHM 314
T+ E+++ FS+FGK++ ++ D++T + F+ FE +E CE +F M
Sbjct: 15 TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKED----CEEAYFKM 65
>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 = 44.5 bits (105), Expect = 2e-06
Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 9/68 (13%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
K+FVG + + + +E+++ F Q+GKV E ++ + +GFV +++ D I
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53
Query: 310 IHFHMIKN 317
+H + +
Sbjct: 54 LHHYKLHG 61
Score = 34.1 bits (78), Expect = 0.010
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
KLFVG L + + +++R F +G V + I+K+ +GF+
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFV 39
>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 = 44.6 bits (106), Expect = 2e-06
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
++V G+S T A ++K FS++GKV ++ + ++ R FGFVT + E C H
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAK-CIQH 60
Query: 312 FH 313
H
Sbjct: 61 LH 62
Score = 31.9 bits (73), Expect = 0.067
Identities = 19/55 (34%), Positives = 29/55 (52%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
L+V GLS T + L++ F +G V I+ + + +R FGF+T A E K
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAK 56
>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 = 44.7 bits (105), Expect = 2e-06
Identities = 17/50 (34%), Positives = 35/50 (70%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
+FVG +S + + +++KA F+ FG++ + ++ D T + +G+GFV+F N+
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 53
Score = 43.5 bits (102), Expect = 6e-06
Identities = 17/47 (36%), Positives = 33/47 (70%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
+FVG LS + +++ ++ F FG ++D ++KD T +S+G+GF++F
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50
>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 = 44.2 bits (105), Expect = 3e-06
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L VG L + + E+ RE FGAV ++ T S+G+GF+ +A + K K
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA-K-- 58
Query: 224 IHTLDGKKIDPKHA 237
+ LDGK+I +
Sbjct: 59 -NQLDGKQIGGRKL 71
Score = 36.1 bits (84), Expect = 0.003
Identities = 13/51 (25%), Positives = 27/51 (52%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+ VG + + + E+ + S FG VE ++ + T +G+GFV + ++
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKA 52
>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 = 44.7 bits (105), Expect = 3e-06
Identities = 20/47 (42%), Positives = 30/47 (63%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
+FV LS + L + FG FGAVT+V +++D T + +GFGF+T
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTM 50
Score = 33.5 bits (76), Expect = 0.031
Identities = 17/49 (34%), Positives = 24/49 (48%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
IFV +S + + F FG V ++ D T + +GFGFVT N
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTN 52
>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 = 44.1 bits (105), Expect = 3e-06
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++VG +S T+ E++ FS+ G ++ +M +D+ TK GF FV + E
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTRE 51
Score = 42.1 bits (100), Expect = 2e-05
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L+VG LS+ T+ E++ E F G + +++ D T+ GF F+ + E E +K
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKY- 59
Query: 224 IHTLDGKKID 233
L+G K+D
Sbjct: 60 ---LNGTKLD 66
>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 = 43.9 bits (104), Expect = 4e-06
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP-ETVEKV 219
+FV L ++ +KL+E F + G V I +D +SRG G + F P E V+ +
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHPIEAVQAI 56
Score = 33.9 bits (78), Expect = 0.013
Identities = 24/100 (24%), Positives = 39/100 (39%), Gaps = 28/100 (28%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
IFV + +++K F GKV + D++ + RG G V FE
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFE------------ 47
Query: 312 FHMIKNKKVECKKAQPKEAVQA-NLLVGKRVILGPLGLRM 350
P EAVQA ++ G+ + P+ ++M
Sbjct: 48 --------------HPIEAVQAISMFNGQMLFDRPMRVKM 73
>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 = 43.6 bits (103), Expect = 5e-06
Identities = 23/45 (51%), Positives = 29/45 (64%), Gaps = 4/45 (8%)
Query: 176 EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
E + EYFG FG V DV I P Q+ R FGF+TF ETV+++L
Sbjct: 14 EDVSEYFGQFGPVLDVRI---PYQQK-RMFGFVTFENAETVKRIL 54
Score = 41.7 bits (98), Expect = 3e-05
Identities = 27/61 (44%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 264 EEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI-CEIHFHMIKNKKVEC 322
E+V YF QFG V + V + QQ R FGFVTFEN E V I + + H I +V
Sbjct: 14 EDVSEYFGQFGPVLD-VRIPYQQ---KRMFGFVTFENAETVKRILSKGNPHFICGSRVRV 69
Query: 323 K 323
K
Sbjct: 70 K 70
>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 = 43.8 bits (104), Expect = 6e-06
Identities = 13/50 (26%), Positives = 34/50 (68%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
I++GG+ + + ++ FSQ+G++ + ++ D++T + +GF F+ +E++
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQ 61
Score = 40.3 bits (95), Expect = 1e-04
Identities = 14/52 (26%), Positives = 32/52 (61%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
SA +++GGL ++ + + F +G + D+ +++D T +S+GF F+ + +
Sbjct: 9 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYED 60
>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 = 43.7 bits (103), Expect = 6e-06
Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L+VG L + + + L++ F + G V +V I+ D + +GF+ + + E L+
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQ-- 57
Query: 224 IHTLDGKKI 232
TL+G++I
Sbjct: 58 --TLNGRQI 64
>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 = 43.4 bits (103), Expect = 6e-06
Identities = 15/51 (29%), Positives = 34/51 (66%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+++ G+ +T+ E+++ FGK+ T ++D++T + +G+GFV F++ E
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPE 53
Score = 35.3 bits (82), Expect = 0.005
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
+++ GL T+ E L + FG + + D T + +G+GF+ F PE K ++
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
>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 = 43.5 bits (103), Expect = 6e-06
Identities = 22/79 (27%), Positives = 31/79 (39%), Gaps = 4/79 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV- 222
++V L + E L+ F +G V V + + T +GF FI F PE +K K
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 223 ---PIHTLDGKKIDPKHAT 238
P D PK
Sbjct: 62 NNPPETATDKPGKFPKTVA 80
Score = 41.2 bits (97), Expect = 4e-05
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 4/78 (5%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE----VVDHI 307
++V + ++ + E +KA FS++G V + + T +GF F+ FE E H+
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 308 CEIHFHMIKNKKVECKKA 325
K
Sbjct: 62 NNPPETATDKPGKFPKTV 79
>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 = 43.0 bits (102), Expect = 7e-06
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 9/71 (12%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHICE 309
K+FVG + T++EE++A F ++G V E ++ + +GFV E EE D I
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52
Query: 310 IHFHMIKNKKV 320
++ + K++
Sbjct: 53 LNGYEFMGKRI 63
Score = 41.4 bits (98), Expect = 3e-05
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 9/71 (12%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
KLFVG L T+SE+LR F +G VT+ ++K+ +GF+ E E E +K
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKA 52
Query: 222 VPIHTLDGKKI 232
+ + GK+I
Sbjct: 53 LNGYEFMGKRI 63
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 43.0 bits (102), Expect = 8e-06
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 9/70 (12%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K++VG L + + +L + F +G + V + ++P GF F+ F +P E
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDA--- 52
Query: 223 PIHTLDGKKI 232
+ LDG++I
Sbjct: 53 -VRALDGRRI 61
Score = 35.7 bits (83), Expect = 0.003
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 5/52 (9%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K++VG + + E++ F ++G + +V + + GF FV FE+
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPL-RSVWV----ARNPPGFAFVEFEDPR 47
>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 = 43.4 bits (102), Expect = 8e-06
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFV GLS T+ E L+E F G++ I+ D T S+GFGF+ F+ E K K
Sbjct: 3 LFVKGLSEDTTEETLKESFD--GSIA-ARIVTDRDTGSSKGFGFVDFSSEEDA-KAAKEA 58
Query: 224 IH--TLDGKKIDPKHATPK 240
+ +DG K+ A PK
Sbjct: 59 MEDGEIDGNKVTLDFAKPK 77
Score = 40.7 bits (95), Expect = 7e-05
Identities = 21/53 (39%), Positives = 32/53 (60%), Gaps = 3/53 (5%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K +FV G+S+DT+ E +K F G + ++ D+ T +GFGFV F +EE
Sbjct: 1 KTLFVKGLSEDTTEETLKESFD--GSIAARIV-TDRDTGSSKGFGFVDFSSEE 50
>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 = 43.0 bits (102), Expect = 8e-06
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 12/71 (16%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L+V L T+ E+LRE F +G V V +KD + F+ F E + K
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKA---- 51
Query: 224 IHTLDGKKIDP 234
+ ++GK+++
Sbjct: 52 MEEMNGKELEG 62
Score = 37.2 bits (87), Expect = 9e-04
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHIC 308
K ++V + T+ E+++ FS++G+VE + D + FV FE ++ V +
Sbjct: 2 KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAME 53
Query: 309 EIHFHMIKNKKVECKKAQP 327
E++ ++ +E A+P
Sbjct: 54 EMNGKELEGSPIEVSLAKP 72
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a transcription
coactivator of LEF-1 and AML-1 for the TCRalpha enhancer
function. In addition, THOC4 specifically binds to
rhesus (RH) promoter in erythroid, and might be a novel
transcription cofactor for erythroid-specific genes.
SKAR shows high sequence homology with THOC4 and
possesses one RRM as well. SKAR is widely expressed and
localizes to the nucleus. It may be a critical player in
the function of S6K1 in cell and organism growth control
by binding the activated, hyperphosphorylated form of
S6K1 but not S6K2. Furthermore, SKAR functions as a
protein partner of the p50 subunit of DNA polymerase
delta. In addition, SKAR may have particular importance
in pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 43.0 bits (102), Expect = 9e-06
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
+L V L + + E L E FG G V V I D + RS G + F + E E+ +K
Sbjct: 1 TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59
Query: 222 VPIHTLDGKKIDPKH 236
+G +D +
Sbjct: 60 ----QFNGVLLDGQP 70
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 42.9 bits (101), Expect = 1e-05
Identities = 19/69 (27%), Positives = 38/69 (55%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
++VG + + ++E+L +F G+V V I+ D + +GF +I F++ E+V L +
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61
Query: 224 IHTLDGKKI 232
G++I
Sbjct: 62 ESLFRGRQI 70
Score = 39.8 bits (93), Expect = 1e-04
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++VG V +AEE++A+F G V +L D+ + +GF ++ F ++E V
Sbjct: 2 VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 55
>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 = 43.1 bits (101), Expect = 1e-05
Identities = 22/57 (38%), Positives = 30/57 (52%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
LFV ++ T E LR FG +G + DV + D T+R RGF +I F + E L
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDAL 59
Score = 38.1 bits (88), Expect = 7e-04
Identities = 19/76 (25%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
+FV V+ T E+++ F ++G + + + +D T+R RGF ++ FE+ + D + +
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 311 HFHMIKNKKVECKKAQ 326
+ + +++E + AQ
Sbjct: 63 NRKWVCGRQIEIQFAQ 78
>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 = 42.6 bits (100), Expect = 1e-05
Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 2/71 (2%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
+IF+G + +D +E+ + GK+ E M+MD +RG+ FVTF N +E + I +
Sbjct: 3 EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQ 61
Query: 310 IHFHMIKNKKV 320
++ + I+N ++
Sbjct: 62 LNNYEIRNGRL 72
>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 = 42.7 bits (101), Expect = 1e-05
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
++V L + ++ L + F +G V V I+KD T++S+G FI F + E K
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKC---- 59
Query: 224 IHTLDGKKI 232
+ L+ K++
Sbjct: 60 VKALNNKEL 68
Score = 31.9 bits (73), Expect = 0.077
Identities = 10/29 (34%), Positives = 21/29 (72%)
Query: 270 FSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
FS++GKV + ++ D++T++ +G F+ F
Sbjct: 22 FSKYGKVVKVTIVKDKETRKSKGVAFILF 50
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 41.7 bits (99), Expect = 1e-05
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 9/58 (15%)
Query: 178 LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK 235
L + F FG V + ++K GF F+ F+ E EK + L+G +
Sbjct: 1 LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKA----VQYLNGVLFGGR 49
Score = 40.2 bits (95), Expect = 6e-05
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 266 VKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHM--IKNKKVECK 323
+ FS FG VE+ +L K+ GF FV F EE + + + + + +
Sbjct: 1 LYKLFSPFGNVEKIKLL-----KKKPGFAFVEFSTEEAAEKAVQ-YLNGVLFGGRPLRVD 54
Query: 324 KA 325
+
Sbjct: 55 YS 56
>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 = 42.2 bits (99), Expect = 2e-05
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 9/73 (12%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
++LFVG L + E++R+ F +G ++ I KD +GFGFI E T+ ++ K
Sbjct: 2 SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRL-ETRTLAEIAK 54
Query: 222 VPIHT--LDGKKI 232
+ L GK++
Sbjct: 55 AELDNMPLRGKQL 67
Score = 41.4 bits (97), Expect = 3e-05
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++FVG + D + EE++ F ++GK E + D +GFGF+ E + +
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAE 51
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 42.5 bits (100), Expect = 2e-05
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 164 LFVGGLSWQTSSEKLREYF-GMFGAVTDVLIMKDPITQRSRGFGFITFAE 212
+FVG LS + + L F F + IM DP+T SRG+GF+ F++
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSD 53
Score = 36.0 bits (83), Expect = 0.003
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYF-SQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
IFVG +S + + ++ + F S+F + ++ D T RG+GFV F +E
Sbjct: 4 IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDE 54
>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 = 42.4 bits (99), Expect = 2e-05
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+F+ L L + FG FGAVT+V +++D T + +GFGF+T E +
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEA----AMA 59
Query: 224 IHTLDGKKIDPK 235
I +L+G ++ K
Sbjct: 60 IASLNGYRLGDK 71
Score = 36.6 bits (84), Expect = 0.002
Identities = 18/51 (35%), Positives = 25/51 (49%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
IF+ + QD + F FG V ++ D T + +GFGFVT N E
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYE 54
>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 = 42.4 bits (99), Expect = 2e-05
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
+ L V L + E+ + FG G + +++D IT +S G+GF+ + +P +K
Sbjct: 2 SKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61
Query: 220 LKVPIHTLDGKKIDPK 235
I+TL+G K+ K
Sbjct: 62 ----INTLNGLKLQTK 73
Score = 33.2 bits (75), Expect = 0.032
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
+ V + Q+ + EE K+ F G++E ++ D+ T + G+GFV + + D I +
Sbjct: 6 LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65
Query: 311 HFHMIKNKKVECKKAQP 327
+ ++ K ++ A+P
Sbjct: 66 NGLKLQTKTIKVSYARP 82
>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 = 41.9 bits (99), Expect = 2e-05
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 164 LFVGGLSWQTSSEKLREYF-GMFGAVTDVLIMKDPITQRSRGFGFITFA 211
+FVG L+ + L+E F + +V ++ DP+T RS+G+GF+ F
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFG 52
Score = 36.1 bits (84), Expect = 0.003
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQ-FGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
IFVG ++ D + ++ F + V ++MD T R +G+GFV F +E+
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDED 55
>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 = 41.8 bits (99), Expect = 3e-05
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
++VG + + EE++ FS FG +EE + D+ G+ FV F+ E I +
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAV 56
Query: 311 HFHMIKNKKVEC 322
+ I + V+C
Sbjct: 57 NGTSINGQTVKC 68
Score = 38.0 bits (89), Expect = 5e-04
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 6/48 (12%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
++VG L + E+L+ F FGA+ +V + KD +G+ F+ F
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFD 44
>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 = 41.6 bits (98), Expect = 3e-05
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L V L + +++R F G + +++D +T +S G+GF+ + +PE EK
Sbjct: 4 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA---- 59
Query: 224 IHTLDGKKIDPK 235
I+TL+G ++ K
Sbjct: 60 INTLNGLRLQNK 71
Score = 38.9 bits (91), Expect = 3e-04
Identities = 13/44 (29%), Positives = 28/44 (63%)
Query: 259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
Q+ + +E+++ FS G++E ++ D+ T + G+GFV + + E
Sbjct: 11 QNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPE 54
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. hnRNP M functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 41.5 bits (98), Expect = 3e-05
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-KV 222
+FV L + + + L++ F G V + D RS+GFG + F PE ++ +
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPEDAQRAIEMF 59
Query: 223 PIHTLDGKKID 233
+ L+G++++
Sbjct: 60 NGYDLEGRELE 70
Score = 37.2 bits (87), Expect = 0.001
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
IFV + + +++K F + G V + D R +GFG V FE+ E E+
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEM 58
>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 = 41.9 bits (99), Expect = 3e-05
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 7/75 (9%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM---KDPITQRSRGFGFITFAEPETVE 217
+ L+VG L+ + + E L + FG FG + V IM + +R+R GF+ F E
Sbjct: 1 TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60
Query: 218 KVLKVPIHTLDGKKI 232
+ L LDGK +
Sbjct: 61 RALD----ELDGKDV 71
Score = 35.3 bits (82), Expect = 0.007
Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM----DQQTKRHRGFGFVTFEN 300
T ++VG ++ + E + F +FG + +V +M +++ +R+R GFV F N
Sbjct: 1 TTNLYVGNLNPKVTEEVLCQEFGRFGPL-ASVKIMWPRTEEERRRNRNCGFVAFMN 55
>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 = 41.5 bits (98), Expect = 3e-05
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 17/82 (20%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
+LFVG L + E+ +E F +G V++V + K+ +GFGFI EK
Sbjct: 2 CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKA-- 53
Query: 222 VPIHTLDGKKIDPKHATPKNRP 243
LDG K R
Sbjct: 54 --KAELDGIMR-------KGRQ 66
Score = 40.3 bits (95), Expect = 6e-05
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 6/50 (12%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
++FVG + D + EE K FS++G+V E + + +GFGF+ +
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDT 46
>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 = 41.9 bits (98), Expect = 3e-05
Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
P S +LFVG L +L+E+F FG V ++ I + + FGF+ F + E V++
Sbjct: 3 PDSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62
Query: 219 VL 220
+L
Sbjct: 63 IL 64
Score = 35.3 bits (81), Expect = 0.007
Identities = 19/59 (32%), Positives = 29/59 (49%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
+ ++FVG + D E+K +F FG V E + + FGFV F++ E V I
Sbjct: 5 SHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRI 63
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. Also included in this subfamily is the
sex-lethal protein (SXL) from Drosophila melanogaster.
SXL governs sexual differentiation and X chromosome
dosage compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 41.5 bits (97), Expect = 3e-05
Identities = 20/60 (33%), Positives = 33/60 (55%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
A L+V GL + ++L + F +G + I++D +T SRG GFI F + E+ +K
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Score = 38.8 bits (90), Expect = 3e-04
Identities = 16/51 (31%), Positives = 31/51 (60%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++V G+ + + +E++ FSQ+G++ + +L DQ T RG GF+ F+
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRI 53
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 45.5 bits (108), Expect = 4e-05
Identities = 18/104 (17%), Positives = 23/104 (22%), Gaps = 4/104 (3%)
Query: 1 METMALGGAPDHHEQFNGLIPTMNGLVQIPHHPGLV----HLNGPPPPPHQLVKLNGAPQ 56
P + Q P Q P L P ++ P
Sbjct: 191 FPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPG 250
Query: 57 VNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVL 100
++ P Q QP Q Q QPP P
Sbjct: 251 LSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNA 294
Score = 41.7 bits (98), Expect = 7e-04
Identities = 16/82 (19%), Positives = 18/82 (21%), Gaps = 2/82 (2%)
Query: 24 NGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAP--QVNTSPPQNAILHQQPTPQPQQQQQQ 81
+ PPPP Q + P PPQN PQ Q
Sbjct: 238 QQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLP 297
Query: 82 PPQPQPRDLQPNSNNQLVLVNG 103
PPQ
Sbjct: 298 PPQQPQLLPLVQQPQGQQRGPQ 319
Score = 38.2 bits (89), Expect = 0.008
Identities = 16/71 (22%), Positives = 20/71 (28%)
Query: 27 VQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQ 86
Q P PPP + + P Q P QQ Q Q PQ
Sbjct: 260 PQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQ 319
Query: 87 PRDLQPNSNNQ 97
R+ + Q
Sbjct: 320 FREQLVQLSQQ 330
Score = 34.4 bits (79), Expect = 0.13
Identities = 17/73 (23%), Positives = 22/73 (30%), Gaps = 4/73 (5%)
Query: 27 VQIPHHPGLVHLNGPPPPPHQLVKLNG----APQVNTSPPQNAILHQQPTPQPQQQQQQP 82
+P GPP P + Q P + QP PQ QQ P
Sbjct: 182 QGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPP 241
Query: 83 PQPQPRDLQPNSN 95
P QP+ +
Sbjct: 242 PLQQPQFPGLSQQ 254
Score = 32.8 bits (75), Expect = 0.36
Identities = 14/69 (20%), Positives = 17/69 (24%), Gaps = 6/69 (8%)
Query: 27 VQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQ 86
Q P + P P Q N PPQ L QQ+ + Q
Sbjct: 270 PQPQAQPPPQNQPTPHPGLPQ--GQNAPLP----PPQQPQLLPLVQQPQGQQRGPQFREQ 323
Query: 87 PRDLQPNSN 95
L
Sbjct: 324 LVQLSQQQR 332
Score = 32.0 bits (73), Expect = 0.64
Identities = 11/60 (18%), Positives = 12/60 (20%)
Query: 38 LNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQ 97
L P P Q A Q P QP Q P +
Sbjct: 163 LQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPA 222
Score = 32.0 bits (73), Expect = 0.69
Identities = 18/66 (27%), Positives = 22/66 (33%), Gaps = 5/66 (7%)
Query: 21 PTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQ 80
P N P P + PPP QL+ L PQ PQ + QQQ
Sbjct: 277 PPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQ-----FREQLVQLSQQQ 331
Query: 81 QPPQPQ 86
+ Q
Sbjct: 332 REALSQ 337
Score = 29.7 bits (67), Expect = 3.5
Identities = 14/80 (17%), Positives = 16/80 (20%), Gaps = 8/80 (10%)
Query: 24 NGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQ----PQQQQ 79
P L PP G P+ P Q P+ Q
Sbjct: 166 RQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPE----QPPGYPQPPQGHPEQVQPQQFLP 221
Query: 80 QQPPQPQPRDLQPNSNNQLV 99
P L P Q
Sbjct: 222 APSQAPAQPPLPPQLPQQPP 241
Score = 29.0 bits (65), Expect = 6.0
Identities = 12/48 (25%), Positives = 14/48 (29%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPR 88
P P K+ +V Q Q P P Q Q P Q
Sbjct: 143 QPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAA 190
>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 = 41.6 bits (97), Expect = 4e-05
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
+FV L+ L + FG FGAVT+V +++D T + +GFGF+T
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTM 52
Score = 34.3 bits (78), Expect = 0.015
Identities = 17/49 (34%), Positives = 24/49 (48%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
IFV ++ D + F FG V ++ D T + +GFGFVT N
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTN 54
>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 = 41.6 bits (97), Expect = 4e-05
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
+FV LS + L + FG FGAV +V +++D T + +GFGF+T
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTM 52
Score = 36.6 bits (84), Expect = 0.002
Identities = 18/49 (36%), Positives = 25/49 (51%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
IFV +S D+ + F FG V ++ D T + +GFGFVT N
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTN 54
>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 = 41.2 bits (96), Expect = 4e-05
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE----VVD 305
+ ++V G+S T A ++K FS++GKV ++ + ++ R +GFVT E ++
Sbjct: 2 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCIN 61
Query: 306 HI--CEIHFHMI 315
H+ E+H MI
Sbjct: 62 HLHRTELHGRMI 73
Score = 32.8 bits (74), Expect = 0.048
Identities = 16/60 (26%), Positives = 29/60 (48%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
L+V GLS T + L+ F +G V ++ + + +R +GF+T + E K +
Sbjct: 1 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60
>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 = 41.1 bits (96), Expect = 4e-05
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
K+FVG V + + +EV+ F + G V E ++ D++T +G FV + + D
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEAD 55
Score = 38.4 bits (89), Expect = 4e-04
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
KLFVG + + +++R F G V +V I+KD T +G F+ ++ + ++
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRA--- 57
Query: 223 PIHTLDGKKIDPKHATP 239
I L ++ P A+P
Sbjct: 58 -IRALHNQRTLPGGASP 73
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 40.8 bits (95), Expect = 6e-05
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP-ETVEKV 219
+ +FV L ++ +KL+E F M G V I++D +SRG G +TF +P E V+ +
Sbjct: 1 STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDK-DGKSRGIGTVTFEQPIEAVQAI 58
>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 = 40.6 bits (96), Expect = 6e-05
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
+FVG + +D +E+ F + G + E ++MD +RG+ FVT+ N E + ++
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAVKQL 62
Query: 311 HFHMIKNKK 319
H + I+ K
Sbjct: 63 HNYEIRPGK 71
Score = 33.7 bits (78), Expect = 0.022
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
+FVG + ++L F G + ++ +M D +RG+ F+T+ E ++ +K
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTYTNKEAAQRAVK-- 60
Query: 224 IHTLDGKKIDP 234
L +I P
Sbjct: 61 --QLHNYEIRP 69
>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 = 7e-05
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
A L+V GL + ++L F +G + I+ D +T SRG GFI F + E
Sbjct: 1 ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAE---- 56
Query: 222 VPIHTLDGKK 231
I L+G
Sbjct: 57 RAIKALNGTI 66
Score = 36.1 bits (84), Expect = 0.003
Identities = 15/48 (31%), Positives = 30/48 (62%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
++V G+ + + +E++A FS +G++ + +L D T RG GF+ F+
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFD 50
>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 = 40.5 bits (95), Expect = 7e-05
Identities = 24/75 (32%), Positives = 33/75 (44%), Gaps = 9/75 (12%)
Query: 163 KLFVGGLSWQTSSEK----LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
+FV G + L E+F G +T V I D T S+GF +I F + VEK
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60
Query: 219 VLKVPIHTLDGKKID 233
L+ LDG +
Sbjct: 61 ALE-----LDGSDLG 70
Score = 30.8 bits (70), Expect = 0.19
Identities = 14/65 (21%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 251 KIFVGGVSQDTSAEEVKA----YFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH 306
IFV G ++++ +FS G++ + D++T +GF ++ F++ + V+
Sbjct: 1 TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60
Query: 307 ICEIH 311
E+
Sbjct: 61 ALELD 65
>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 = 40.6 bits (95), Expect = 8e-05
Identities = 15/54 (27%), Positives = 32/54 (59%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++VG V ++AEE++A+FS G + +L D+ + +G+ ++ F + V+
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVE 55
Score = 37.2 bits (86), Expect = 0.001
Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
++VG + + +++E+L +F G + V I+ D + +G+ +I FA ++VE + +
Sbjct: 2 VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61
Query: 224 IHTLDGK--KIDPK 235
+ G+ K+ PK
Sbjct: 62 ESSFRGRVIKVLPK 75
>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 = 40.3 bits (95), Expect = 8e-05
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
KL V + ++ + ++LRE F FG V V + K RGF F+ F +
Sbjct: 2 KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQ 52
Score = 38.7 bits (91), Expect = 3e-04
Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 21/94 (22%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
K+ V V + + +E++ FS FG+V+ +V L + HRGF FV F ++
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVK-SVRLPKKFDGSHRGFAFVEFVTKQ------- 52
Query: 310 IHFHMIKNKKVECKKAQPKEAVQANLLVGKRVIL 343
E + A EA+++ L G+ ++L
Sbjct: 53 -----------EAQNA--MEALKSTHLYGRHLVL 73
>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 = 40.3 bits (95), Expect = 8e-05
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
RT +FV ++ + EE++A F QFG + K HRGF V++
Sbjct: 2 RT--LFVRNINSNVEDEELRALFEQFGDIRTLYT----ACK-HRGFIMVSY 45
Score = 30.3 bits (69), Expect = 0.32
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK-V 222
LFV ++ E+LR F FG D+ + + RGF +++ + + + +
Sbjct: 4 LFVRNINSNVEDEELRALFEQFG---DIRTLYTAC--KHRGFIMVSYYDIRAARRAKRAL 58
Query: 223 PIHTLDGKKIDPKHATPK 240
L G+K+D + PK
Sbjct: 59 QGTELGGRKLDIHFSIPK 76
>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 = 40.1 bits (94), Expect = 8e-05
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 9/73 (12%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
+++V DTS ++ FS +G V+E M+ F FV FE+ E +
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52
Query: 310 IHFHMIKNKKVEC 322
+H ++ N +
Sbjct: 53 VHGKVLNNNPLYV 65
Score = 38.2 bits (89), Expect = 3e-04
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
+L+V TS +RE F +GAV +V ++ F F+ F E+ +
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIR 48
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with wild
type of survival motor neuron (SMN) proteins directly,
further providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, and in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; it binds RNA
through its RRM domains. .
Length = 79
Score = 40.3 bits (94), Expect = 9e-05
Identities = 18/60 (30%), Positives = 35/60 (58%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++FVG + ++L F G + D+ +M DP++ ++RG+ FITF E ++ +K+
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62
Score = 38.8 bits (90), Expect = 3e-04
Identities = 15/52 (28%), Positives = 32/52 (61%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++FVG + +D +E+ F + G + + ++MD + ++RG+ F+TF +E
Sbjct: 3 EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKE 54
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 40.5 bits (95), Expect = 9e-05
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG-FGFVTFENEE 302
K F+ GV D +++ YF QFGK + ++ HR GFV FE E
Sbjct: 2 IKSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIV-------NHRAKCGFVRFETRE 49
Score = 28.5 bits (64), Expect = 1.5
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
F+ G+ K+R+YF FG V+ + R++ GF+ F E EK
Sbjct: 5 FFLFGVEDDLPEYKIRDYFEQFGKSKSVI-----VNHRAK-CGFVRFETREAAEKFAA 56
>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 = 40.1 bits (93), Expect = 1e-04
Identities = 17/52 (32%), Positives = 33/52 (63%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
R ++V G+ + + +E++ FSQ+G++ + +L+DQ T RG GF+ F+
Sbjct: 1 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 52
Score = 38.5 bits (89), Expect = 4e-04
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
A L+V GL + ++L + F +G + I+ D +T SRG GFI F + E+ +K
Sbjct: 3 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62
Query: 222 VPIHTLDGKKIDPKHAT 238
L+G+K P A
Sbjct: 63 ----GLNGQK--PSGAA 73
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 39.8 bits (93), Expect = 1e-04
Identities = 25/71 (35%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICE 309
KIFVG V +DTS EE++A F +G V + +M Q F FV E D I E
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAV-LSCAVMRQ-------FAFVHLRGEAAADRAIEE 53
Query: 310 IHFHMIKNKKV 320
++ + +K+
Sbjct: 54 LNGRELHGRKL 64
Score = 33.3 bits (76), Expect = 0.022
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMK 195
K+FVG + TS E+LR F +GAV +M+
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMR 34
>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 = 40.3 bits (94), Expect = 1e-04
Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 9/50 (18%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEE-TVMLMDQQTKRHRG--FGFVTF 298
I+VG + DT+ E++ F FG++EE TV L R G +GF+T+
Sbjct: 5 IYVGKIRPDTTRTELRDRFEVFGEIEECTVNL------RDDGDSYGFITY 48
>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 = 39.5 bits (92), Expect = 1e-04
Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 17/81 (20%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
+LFVG L + E ++ F +G ++V I +D RGFGFI E T+ ++ K
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRL-ESRTLAEIAKA 55
Query: 223 PIHTLDGKKIDPKHATPKNRP 243
LDG + KNRP
Sbjct: 56 ---ELDGTIL-------KNRP 66
Score = 38.4 bits (89), Expect = 3e-04
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++FVG + D + E+ K F ++G+ E + R RGFGF+ E+ + +
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAE 51
>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 = 39.6 bits (92), Expect = 2e-04
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
LFVG L + E L E F G +T V I KD + + FGF+ F E+V
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHSESV 55
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+FVGGL + ++LR FG FG + V I P +G GF+ F E +
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PP---GKGCGFVQFVHRAAAEAAI 54
Score = 31.9 bits (73), Expect = 0.082
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FVGG+ + +E+++ F FG+ ++ + +G GFV F +
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGE------IVYVKIPPGKGCGFVQFVHRA 48
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation factor
64 kDa subunit (CstF64), is the vertebrate conterpart of
yeast mRNA 3'-end-processing protein RNA15. It is
expressed in all somatic tissues and is one of three
cleavage stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. .
Length = 75
Score = 39.4 bits (92), Expect = 2e-04
Identities = 15/51 (29%), Positives = 33/51 (64%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FVG + + + E++K FS+ G V ++ D++T + +G+GF ++++E
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQE 51
Score = 38.6 bits (90), Expect = 3e-04
Identities = 15/52 (28%), Positives = 30/52 (57%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET 215
+FVG + ++ + E+L++ F G V ++ D T + +G+GF + + ET
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQET 52
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 39.2 bits (91), Expect = 2e-04
Identities = 18/60 (30%), Positives = 34/60 (56%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++FVG + ++L F G + D+ +M DP+T +RG+ F+TF E ++ +K+
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62
Score = 37.3 bits (86), Expect = 0.001
Identities = 18/52 (34%), Positives = 31/52 (59%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+IFVG + +D +E+ F + G + + ++MD T +RG+ FVTF +E
Sbjct: 3 EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKE 54
>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 = 38.9 bits (91), Expect = 2e-04
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++ G +VK F G V + ML ++ + F+TFEN E
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQ 51
Score = 37.0 bits (86), Expect = 0.001
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 8/70 (11%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
++ G ++ F G V V + +++ + FITF E +
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTM----LSRTVQPHAFITFENLEAAQLA---- 53
Query: 224 IHTLDGKKID 233
I TL+G +D
Sbjct: 54 IETLNGASVD 63
>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 = 39.1 bits (91), Expect = 2e-04
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE-NEEVVDHICE 309
KIFVG VS +++E++ F +FG+V E + D + FV E EE + I
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEA 53
Query: 310 IHFHMIKNKKV 320
++ +K +++
Sbjct: 54 LNGKEVKGRRI 64
Score = 32.5 bits (74), Expect = 0.045
Identities = 14/34 (41%), Positives = 21/34 (61%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKD 196
K+FVG +S +S++LR F FG V + +KD
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD 35
>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 = 39.1 bits (92), Expect = 2e-04
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++V G +D + ++++ +F +FGKV + + K+ +G FV F+ EE
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKV-NNIRMRRDLDKKFKGSVFVEFKTEEDAK 54
Score = 35.3 bits (82), Expect = 0.005
Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
++V G + + ++E+F FG V ++ + +D ++ +G F+ F E +K L+
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDL-DKKFKGSVFVEFKTEEDAKKFLEKE 60
Query: 224 IHTLDGKKI 232
K++
Sbjct: 61 KLKYKEKEL 69
>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 = 3e-04
Identities = 11/70 (15%), Positives = 29/70 (41%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+ + G+ + E+++ +FS + + ++ R G +V F + E H
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61
Query: 312 FHMIKNKKVE 321
+ + + +E
Sbjct: 62 NNKMGGRYIE 71
Score = 33.7 bits (78), Expect = 0.017
Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 20/91 (21%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTD-VLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
+ + GL + + E +R++F D + I+ D + + G ++ FA PE + L+
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPT-GEAYVEFASPEDARRALR- 59
Query: 223 PIHTLDGKKIDPKHATPKNRPKIGNRTKKIF 253
K+ K+G R ++F
Sbjct: 60 -----------------KHNNKMGGRYIEVF 73
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 39.1 bits (91), Expect = 3e-04
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
P S +LFVG L +L+E+F +G V ++ I + FGF+ F + E V+K
Sbjct: 1 PDSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSG---GKLPNFGFVVFDDSEPVQK 57
Query: 219 VL 220
+L
Sbjct: 58 IL 59
Score = 34.5 bits (79), Expect = 0.012
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHI 307
+ ++FVG + D E+K +F Q+G V E L + FGFV F++ E V I
Sbjct: 3 SHQLFVGNLPHDVDKSELKEFFQQYGNVVE---LRINSGGKLPNFGFVVFDDSEPVQKI 58
>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 = 38.8 bits (91), Expect = 3e-04
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 163 KLFVGGLSWQTSSEKLREYFG-MFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
+L V L + +L+E+F G +TDV +++ +SR FI + E +K
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKAKD 60
Query: 222 V 222
Sbjct: 61 Y 61
Score = 34.2 bits (79), Expect = 0.012
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 5/78 (6%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
++ V + + E+K +FS+ G V L+ + + R F+ ++ EE +
Sbjct: 2 RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEE--EAQKAK 59
Query: 311 -HFH--MIKNKKVECKKA 325
+F+ I K+ + A
Sbjct: 60 DYFNNTYINTSKISVEFA 77
>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 = 39.2 bits (91), Expect = 3e-04
Identities = 26/84 (30%), Positives = 48/84 (57%), Gaps = 5/84 (5%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMK---DPITQRSRGFGFITFAEPETVEK 218
A ++VG SW T+ ++L + G V DV+ +K + +S+G+ + A +V K
Sbjct: 2 AAVYVGNFSWWTTDQQLIQVIRSVG-VKDVVELKFAENRANGQSKGYAEVVVASENSVHK 60
Query: 219 VLK-VPIHTLDGKKIDPKHATPKN 241
+L+ +P L+G+K+D + AT +N
Sbjct: 61 LLELLPGKVLNGEKVDVRPATRQN 84
>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 = 38.8 bits (90), Expect = 3e-04
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF----ENEEVV 304
++V G+ + S +E++ FSQ+G++ + +L+DQ T RG GF+ F E EE +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60
Score = 36.9 bits (85), Expect = 0.002
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
A L+V GL S +++ + F +G + I+ D +T SRG GFI F + E+ +K
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIK 61
Query: 222 VPIHTLDGKK 231
L+G+K
Sbjct: 62 ----GLNGQK 67
>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 = 38.7 bits (91), Expect = 3e-04
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 7/55 (12%)
Query: 252 IFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+++ +++ +E+K A FSQFG V + V +T + RG FV F++ E
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVAS---KTLKMRGQAFVVFKDVE 53
Score = 37.5 bits (88), Expect = 0.001
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 164 LFVGGLSWQTSSEKLR----EYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
L++ L+ + ++L+ F FG V D++ K T + RG F+ F + E+
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATNA 58
Query: 220 LK 221
L+
Sbjct: 59 LR 60
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 38.5 bits (90), Expect = 4e-04
Identities = 13/70 (18%), Positives = 34/70 (48%), Gaps = 12/70 (17%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++++G L ++ + +F +G + ++ + GFGF+ F +P +
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDA--- 49
Query: 223 PIHTLDGKKI 232
++ L+GK++
Sbjct: 50 -VYELNGKEL 58
Score = 36.9 bits (86), Expect = 0.001
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
++++G + +V+ +F +G++ E + GFGFV FE+
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDP 43
>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 = 38.5 bits (89), Expect = 4e-04
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L V L + ++LR F G V +++D + S G+GF+ + + E+
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERA---- 59
Query: 224 IHTLDGKKIDPK 235
I+TL+G ++ K
Sbjct: 60 INTLNGLRLQSK 71
Score = 34.3 bits (78), Expect = 0.012
Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
+ V + Q+ + +E+++ FS G+VE ++ D+ G+GFV + N + + I +
Sbjct: 4 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63
Query: 311 HFHMIKNKKVECKKAQP 327
+ +++K ++ A+P
Sbjct: 64 NGLRLQSKTIKVSYARP 80
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome
proliferator-activated receptor gamma coactivator 1A
(PGC-1alpha) family of regulated coactivators. This
subfamily corresponds to the RRM of PGC-1alpha,
PGC-1beta, and PGC-1-related coactivator (PRC), which
serve as mediators between environmental or endogenous
signals and the transcriptional machinery governing
mitochondrial biogenesis. They play an important
integrative role in the control of respiratory gene
expression through interacting with a number of
transcription factors, such as NRF-1, NRF-2, ERR, CREB
and YY1. All family members are multi-domain proteins
containing the N-terminal activation domain, an LXXLL
coactivator signature, a tetrapeptide motif (DHDY)
responsible for HCF binding, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In contrast to PGC-1alpha
and PRC, PGC-1beta possesses two glutamic/aspartic
acid-rich acidic domains, but lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 89
Score = 38.8 bits (91), Expect = 4e-04
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEE-TVMLMDQQTKRHRGFGFVTFE 299
I+VG + DT+ E++ F FG++EE T+ D +GFVT+
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN----YGFVTYR 49
Score = 35.8 bits (83), Expect = 0.005
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRG--FGFITFAEPETVEKVL 220
++VG + T+ +LR+ F FG + ++ + R G +GF+T+ + +
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHF-----RDDGDNYGFVTYRYACDAFRAI 58
>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 = 39.0 bits (90), Expect = 4e-04
Identities = 17/52 (32%), Positives = 33/52 (63%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
R ++V G+ + + +E++ FSQ+G++ + +L+DQ T RG GF+ F+
Sbjct: 4 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 55
Score = 37.1 bits (85), Expect = 0.002
Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 6/86 (6%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
A L+V GL + ++L + F +G + I+ D +T SRG GFI F + E+ +K
Sbjct: 6 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65
Query: 222 VPIHTLDGKKIDPKHATPKNRPKIGN 247
L+G+K P AT K N
Sbjct: 66 ----GLNGQK--PPGATEPITVKFAN 85
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 38.7 bits (91), Expect = 4e-04
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FVG + + S + ++ + GKV + D T + + FGF FE+ E
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPE 53
Score = 34.9 bits (81), Expect = 0.009
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
+FVG + S + +R+ G V +KDP T + + FGF F +PE + L++
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61
Query: 223 PIHTLDGKKIDPK 235
L+G ++ K
Sbjct: 62 ----LNGLELGGK 70
>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 = 38.9 bits (91), Expect = 4e-04
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP----ETVEKV 219
+ + GLS T+ +++R +F FG + + + DP T +S G +TF +
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEA 60
Query: 220 LKVPIHTLDGKKIDPK 235
K + L+G++I K
Sbjct: 61 AKAAVDGLNGRRIGGK 76
Score = 31.2 bits (71), Expect = 0.18
Identities = 15/48 (31%), Positives = 30/48 (62%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
I + G+S T+ ++++ +F FG++EE+ + +D +T + G VTF
Sbjct: 1 ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFR 48
>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 = 38.5 bits (90), Expect = 4e-04
Identities = 19/47 (40%), Positives = 26/47 (55%)
Query: 174 SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+ E LRE F FG + V I+KD T S+GFG++ F +P L
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59
Score = 37.0 bits (86), Expect = 0.001
Identities = 14/48 (29%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
++FV + + + E+++ F +FG +E ++ D+ T +GFG+V F
Sbjct: 3 RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49
>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 = 38.6 bits (90), Expect = 4e-04
Identities = 18/49 (36%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
KLFVG LS Q + + +R F FG + + I++ P S+G F+ F+
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGN-SKGCAFVKFS 50
Score = 35.1 bits (81), Expect = 0.007
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM--DQQTKRHRGFGFVTFEN 300
+K+FVG +S+ + ++V+ F FG +EE +L D +K G FV F +
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSK---GCAFVKFSS 51
>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 = 41.8 bits (98), Expect = 5e-04
Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 6/91 (6%)
Query: 141 VNGKSSGDSGRSTPTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ 200
N K+ ST D ++++G L ++++E FG + ++KD T
Sbjct: 277 DNAKNVEKLVNSTTVLDSKD--RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATG 334
Query: 201 RSRGFGFITFAEPETVEKVLKVPIHTLDGKK 231
S+G+ F + +P + V I L+GK
Sbjct: 335 LSKGYAFCEYKDPSVTD----VAIAALNGKD 361
Score = 34.9 bits (80), Expect = 0.084
Identities = 11/58 (18%), Positives = 27/58 (46%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
+I++G + +++K FG ++ ++ D T +G+ F +++ V D
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354
>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 = 38.1 bits (88), Expect = 5e-04
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
+K+F+G VS+ + +++ FS FG++EE +L RG FVTF
Sbjct: 2 RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTF 49
Score = 35.4 bits (81), Expect = 0.006
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
KLF+G +S + + +R F FG + + I++ P SRG F+TF + +K
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIK 60
>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 = 38.1 bits (88), Expect = 6e-04
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP-ETVEKV 219
+ +FV L ++ +KL+E F + G V I +D +SRG G +TF +P E V+ +
Sbjct: 1 STIFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDK-DGKSRGMGTVTFEQPIEAVQAI 58
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 37.8 bits (88), Expect = 7e-04
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI-TQRSRGFGFITF 210
K+ V + ++ + ++LRE F FG + V + K T RGFGF+ F
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDF 50
Score = 37.0 bits (86), Expect = 0.001
Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 3/50 (6%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ--QTKRHRGFGFVTF 298
KI V + + + +E++ FS FG+++ TV L + T HRGFGFV F
Sbjct: 2 KILVRNIPFEATVKELRELFSTFGELK-TVRLPKKMTGTGSHRGFGFVDF 50
>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 = 37.8 bits (88), Expect = 8e-04
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 12/69 (17%)
Query: 179 REYFGMFGAVTDV---LIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDG-----K 230
E+ +F AV V I++D T S GFGF+ + E ++ I TL+G K
Sbjct: 15 EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRA----IRTLNGLQLQNK 70
Query: 231 KIDPKHATP 239
+I +A P
Sbjct: 71 RIKVAYARP 79
Score = 31.6 bits (72), Expect = 0.12
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 259 QDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
Q + EE ++ F G V+ ++ D++T GFGFV +++ E
Sbjct: 10 QTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAE 53
>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 = 37.4 bits (87), Expect = 8e-04
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 13/83 (15%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LF+G L T+ LRE F FG + D+ I K + + FI +A+ +V K ++
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQG---GNPAYAFIQYADIASVVKAMR-- 59
Query: 224 IHTLDGKKIDPKHATPKNRPKIG 246
+DG+ + NR K+G
Sbjct: 60 --KMDGEYLG------NNRVKLG 74
Score = 30.1 bits (68), Expect = 0.30
Identities = 7/30 (23%), Positives = 20/30 (66%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEE 278
T+ +F+G + + T+ +++ F +FG++ +
Sbjct: 2 TRTLFIGNLEKTTTYSDLREAFERFGEIID 31
>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 = 37.7 bits (88), Expect = 0.001
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
+VG L T++++L E+F G V V + D TQ +R + F+ FAE +V LK+
Sbjct: 8 YVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE-TQPTR-YAFVEFAEQTSVINALKLNG 65
Query: 225 HTLDGKKIDPKHAT 238
G+ + H+
Sbjct: 66 AMFGGRPLKVNHSN 79
Score = 30.0 bits (68), Expect = 0.41
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ-QTKRHRGFGFVTFENEEVVDH 306
RT I+VG + T+A+++ +FSQ G+V+ M D+ Q R + FV F + V +
Sbjct: 5 RT--IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTR---YAFVEFAEQTSVIN 59
>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 = 36.9 bits (86), Expect = 0.001
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIM--KDPITQRSRGFGFITFAEPETVEKVL 220
+L V L +KLR+ F FG +TDV + KD R FGF+ + E +K L
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKF---RKFGFVGYKTEEEAQKAL 58
Query: 221 K 221
K
Sbjct: 59 K 59
Score = 31.5 bits (72), Expect = 0.095
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++ V + + ++++ F FG + + V L + + R FGFV ++ EE
Sbjct: 2 RLIVKNLPKGIKEDKLRKLFEAFGTITD-VQLKYTKDGKFRKFGFVGYKTEE 52
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 84
Score = 37.0 bits (86), Expect = 0.001
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 11/74 (14%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI------TQRSRGFGFITFAEPETV 216
++++ LS+ +S E L E+ F V+ VLI + R G + F+ PE
Sbjct: 1 RVYISNLSYSSSEEDLEEFLKDFEPVS-VLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59
Query: 217 EKVLKVPIHTLDGK 230
EKV+K L+GK
Sbjct: 60 EKVVK----DLNGK 69
>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 = 36.9 bits (86), Expect = 0.002
Identities = 14/36 (38%), Positives = 23/36 (63%)
Query: 176 EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
+ LRE F FG + D+ ++KD T+ S+G ++ FA
Sbjct: 17 DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFA 52
Score = 34.2 bits (79), Expect = 0.013
Identities = 10/43 (23%), Positives = 26/43 (60%)
Query: 257 VSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
+ + ++++ F+ FG++++ ++ D+QTK +G +V F
Sbjct: 10 CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFA 52
>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 = 37.2 bits (86), Expect = 0.002
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+++G + + E+K FS FG++EE + + +GFVT+ E
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGD---NYGFVTYRYTE 52
>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 = 36.5 bits (85), Expect = 0.002
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 11/73 (15%)
Query: 166 VGGLSWQTSSEKLREYFGMF-----GAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
V GL S +KL YF G VT V +++ G +TFA+ + E+V+
Sbjct: 5 VAGLPETVSDDKLELYFENKRRSGGGDVTRVQYLREK------GSALVTFADFKVAERVV 58
Query: 221 KVPIHTLDGKKID 233
K H L+G ++
Sbjct: 59 KQKKHPLNGTQLS 71
>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 = 37.0 bits (85), Expect = 0.002
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV---- 216
+ +F L+ + L E+F G V DV ++ D ++RS+G ++ F + +V
Sbjct: 1 ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAI 60
Query: 217 ----EKVLKVPI 224
++VL VPI
Sbjct: 61 GLTGQRVLGVPI 72
Score = 31.9 bits (72), Expect = 0.11
Identities = 13/56 (23%), Positives = 29/56 (51%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVV 304
+ +F ++ +++ +FS GKV + M+ D+ ++R +G +V F + V
Sbjct: 1 ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSV 56
>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 = 36.6 bits (85), Expect = 0.002
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
K+FV G+ + EE++ F + G V+ V L+ ++ + +G +V +ENE
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKS-VRLVTNRSGKPKGLAYVEYENE 53
Score = 33.2 bits (76), Expect = 0.030
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS---RGFGFITFA-EPETVEK 218
KLFV GL + + E+L + F G V V + +T RS +G ++ + E +
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRL----VTNRSGKPKGLAYVEYENESSASQA 59
Query: 219 VLKVPIHTLDGKKI 232
VLK+ + K I
Sbjct: 60 VLKMDGTEIKEKTI 73
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 36.5 bits (84), Expect = 0.002
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 12/70 (17%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++F+G L+ + + +F +G + D+ + RGFGF+ F +P +
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDA--- 49
Query: 223 PIHTLDGKKI 232
++ LDGK++
Sbjct: 50 -VYELDGKEL 58
Score = 33.8 bits (77), Expect = 0.018
Identities = 17/77 (22%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICE 309
++F+G ++ ++V+ +F +G++ + + RGFGFV F++ + D + E
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDAVYE 52
Query: 310 IHFHMIKNKKVECKKAQ 326
+ + N++V + A+
Sbjct: 53 LDGKELCNERVTIEHAR 69
>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 = 36.6 bits (85), Expect = 0.002
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
RT I VGG+ S +++K +FS G+V + D+Q F FV F + E
Sbjct: 1 RT--IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAE 51
Score = 36.2 bits (84), Expect = 0.003
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
VGG+ S + L+E+F G VT V + D Q S F F+ FA+ E+ L +
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDR--QHSARFAFVEFADAESALSALNLSG 61
Query: 225 HTLDGKKI 232
L G +
Sbjct: 62 TLLGGHPL 69
>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 = 36.8 bits (86), Expect = 0.002
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 176 EKLREYFGMFGAVTDVLI-MKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP 234
+ LR+ F FG V I M T +++G+ F+ FA PE ++ +K L+G K+D
Sbjct: 22 KVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVK----ALNGYKLDK 77
Query: 235 KH 236
KH
Sbjct: 78 KH 79
Score = 30.2 bits (69), Expect = 0.32
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 270 FSQFGKVEETVMLM----DQQTKRHRGFGFVTFENEE 302
FS+FG + + M +TK G+ FV F E
Sbjct: 28 FSKFGVGKIVGIYMPVDETGKTK---GYAFVEFATPE 61
>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin.
This subfamily corresponds to the RRM1 of ubiquitously
expressed protein nucleolin, also termed protein C23.
Nucleolin is a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines. RRM1,
together with RRM2, binds specifically to RNA stem-loops
containing the sequence (U/G)CCCG(A/G) in the loop. .
Length = 75
Score = 36.7 bits (85), Expect = 0.002
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 16/74 (21%)
Query: 164 LFVGGLSWQTSSEKLR----EYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
LFVG L+ ++L+ E+F AV DV I S+ FG++ F E +EK
Sbjct: 3 LFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRI------GSSKKFGYVDFESAEDLEK 56
Query: 219 VLKVPIHTLDGKKI 232
L+ L GKK+
Sbjct: 57 ALE-----LTGKKL 65
Score = 33.2 bits (76), Expect = 0.025
Identities = 18/75 (24%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQ-FGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
+FVG ++ + +E+K S+ F K + + + D + + FG+V FE+ E ++ E+
Sbjct: 3 LFVGNLNPNKDFDELKTAISEFFSK--KNLAVQDVRIGSSKKFGYVDFESAEDLEKALEL 60
Query: 311 HFHMIKNKKVECKKA 325
+ +++ +KA
Sbjct: 61 TGKKLLGNEIKLEKA 75
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 36.0 bits (84), Expect = 0.002
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 9/54 (16%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVE 217
L+VGGL TS +L F FGA+ + R + +I + E++E
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRI------DYDPGRNYAYIEY---ESIE 45
Score = 30.3 bits (69), Expect = 0.25
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++VGG+ TS E++ F +FG + +D R + ++ +E+ E
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRR----IDYD--PGRNYAYIEYESIE 45
>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 = 36.1 bits (84), Expect = 0.003
Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ---QTKRHRGFGFVTFENEEVVDH- 306
++++G + + + FS++GK+++ L + + RG+ FVTFE +E +
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 307 ICEIHFHMIKNKK 319
+ ++ KK
Sbjct: 61 LKSLNGKTALGKK 73
Score = 34.2 bits (79), Expect = 0.016
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVT--DVLIMKD-PITQRSRGFGFITFAEPETVEKV 219
+L++G L + + L + F +G + D L K P+ + RG+ F+TF E EK
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 220 LKVPIHTLDGKKI 232
LK +L+GK
Sbjct: 61 LK----SLNGKTA 69
>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 = 36.3 bits (84), Expect = 0.003
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR--SRGFGFITF 210
K+FVG + S + LRE F +GAV + +++D S+G F+TF
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52
Score = 32.8 bits (75), Expect = 0.051
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQT--KRHRGFGFVTF 298
K+FVG + + S ++++ F Q+G V + +L D+ + +G FVTF
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52
>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 = 36.0 bits (83), Expect = 0.003
Identities = 15/52 (28%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++FVG + +D +E+ F + GK+ E ++M + + +RG+ FV + +E
Sbjct: 3 EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMM-EFSGENRGYAFVMYTTKE 53
>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 = 36.2 bits (83), Expect = 0.003
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 8/69 (11%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV------- 216
+F L+ + L ++F G V DV I+ D ++RS+G ++ F E ++V
Sbjct: 4 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLT 63
Query: 217 -EKVLKVPI 224
+++L VPI
Sbjct: 64 GQRLLGVPI 72
Score = 30.8 bits (69), Expect = 0.23
Identities = 11/49 (22%), Positives = 27/49 (55%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
+ +F ++ +++ +FS GKV + ++ D+ ++R +G +V F
Sbjct: 2 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 50
>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 = 36.0 bits (83), Expect = 0.003
Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 9/77 (11%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQR-----SRGFGFITFAEPETV 216
A LFV L++ T+++ L + F + P +R S GFGF+ F E
Sbjct: 1 ATLFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQA 60
Query: 217 EKVLKVPIHTLDGKKID 233
+ LK +DG +D
Sbjct: 61 QAALKA----MDGFVLD 73
>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 = 35.7 bits (82), Expect = 0.004
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
++FVG + +D +E+ F G++ E ++MD K +RG+ FV +
Sbjct: 3 EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGK-NRGYAFVMY 49
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 35.8 bits (83), Expect = 0.004
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 187 AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKI 232
V V I+++ +T G+ F+ FA+ T E+ L H L+GK I
Sbjct: 26 TVLSVKIIRNKLTGGPAGYCFVEFADEATAERCL----HKLNGKPI 67
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function in
RNA packaging, stabilization of RNA secondary structure,
or other macromolecular interactions. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 35.5 bits (82), Expect = 0.004
Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 18/86 (20%)
Query: 168 GLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTL 227
GL + + + + ++F V D +++ R G ++ FA PE K L
Sbjct: 8 GLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALL------ 61
Query: 228 DGKKIDPKHATPKNRPKIGNRTKKIF 253
K+R +IGNR ++F
Sbjct: 62 ------------KHREEIGNRYIEVF 75
Score = 28.9 bits (65), Expect = 0.98
Identities = 13/66 (19%), Positives = 30/66 (45%)
Query: 256 GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMI 315
G+ + +++ +F V++ V+++ + R G +V F E+ + H I
Sbjct: 8 GLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKHREEI 67
Query: 316 KNKKVE 321
N+ +E
Sbjct: 68 GNRYIE 73
>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 = 35.4 bits (81), Expect = 0.005
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++FV L + + +KL+E F G V I + +S+G G + F PE+ EK ++
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKACRL 58
Query: 223 PIHT-LDGKKID 233
++G++ID
Sbjct: 59 MNGIKINGREID 70
Score = 30.8 bits (69), Expect = 0.20
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
+IFV + D + +++K FSQ G V + M + + +G G V F++ E + C +
Sbjct: 1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKM--ENGKSKGCGTVRFDSPESAEKACRL 58
>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 = 35.3 bits (81), Expect = 0.005
Identities = 14/53 (26%), Positives = 27/53 (50%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPE 214
L+V L Q + ++LR+ F +G + +++D T RG F+ + + E
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKRE 53
Score = 31.0 bits (70), Expect = 0.16
Identities = 12/51 (23%), Positives = 27/51 (52%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
++V + + + +E++ F +G + + +L D+ T RG FV ++ E
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKRE 53
>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 = 35.8 bits (83), Expect = 0.006
Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 14/85 (16%)
Query: 256 GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMI 315
G+++ TS E++K FSQ G+V+ L + G+V F+ E E
Sbjct: 8 GLNKPTSREDIKEAFSQHGEVKYVDFLEGDKE------GYVRFKTPEAAKKALE------ 55
Query: 316 KNKKVECKKAQPKEAVQANLLVGKR 340
K E K + V LL G+
Sbjct: 56 --KATEAKLKIKEAEVTLELLEGEE 78
>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 = 35.1 bits (81), Expect = 0.006
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
LFVG L + E+LR F +G V DV I + P Q + + F+ F
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGN-AYAFVKFL 51
Score = 33.9 bits (78), Expect = 0.015
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 11/57 (19%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKR-----HRGFGFVTFEN 300
T+ +FVG + + EE++ F ++G VE+ + KR + FV F N
Sbjct: 2 TRTLFVGNLEITITEEELRRAFERYGVVEDVDI------KRPPRGQGNAYAFVKFLN 52
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 34.9 bits (81), Expect = 0.007
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 12/76 (15%)
Query: 243 PKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
P+ GN ++V G + E +K FS FG + M ++ + GFVTFE E
Sbjct: 1 PRKGN---TLYVHGY--GLTEEILKKAFSPFGNIINISM------EKEKNCGFVTFEKME 49
Query: 303 VVDH-ICEIHFHMIKN 317
D I E++ ++
Sbjct: 50 SADRAIAELNGTTVQG 65
Score = 32.6 bits (75), Expect = 0.040
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 12/70 (17%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L+V G + E L++ F FG + ++ + K+ + GF+TF + E+ ++
Sbjct: 7 LYVHGYG--LTEEILKKAFSPFGNIINISMEKE------KNCGFVTFEKMESADRA---- 54
Query: 224 IHTLDGKKID 233
I L+G +
Sbjct: 55 IAELNGTTVQ 64
>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 = 35.1 bits (81), Expect = 0.007
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 12/62 (19%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMD----QQTKRHR---GFGFVTFENEE 302
+K+FVGG+ D +E+ A F +FG + ++D ++K + G+ F+ F+ E
Sbjct: 1 RKVFVGGLPPDIDEDEITASFRRFGPL-----VVDWPHKAESKSYFPPKGYAFLLFQEES 55
Query: 303 VV 304
V
Sbjct: 56 SV 57
Score = 29.3 bits (66), Expect = 0.85
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 10/66 (15%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSR------GFGFITFAEPETV 216
K+FVGGL +++ F FG L++ P S+ G+ F+ F E +V
Sbjct: 2 KVFVGGLPPDIDEDEITASFRRFGP----LVVDWPHKAESKSYFPPKGYAFLLFQEESSV 57
Query: 217 EKVLKV 222
+ ++
Sbjct: 58 QALIDA 63
>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 = 34.8 bits (80), Expect = 0.008
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
+ +F G D E++ F ++G+V+ +D ++ GF FV E+E
Sbjct: 1 RPVFCGNFEYDARQSEIERLFGKYGRVDR----VDMKS----GFAFVYMEDE 44
>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 = 34.6 bits (79), Expect = 0.008
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K++VG L +L F +G + V I ++P GF F+ F +P E ++
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVR- 54
Query: 223 PIHTLDGKKI 232
LDGK I
Sbjct: 55 ---GLDGKVI 61
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 38.1 bits (88), Expect = 0.009
Identities = 29/85 (34%), Positives = 36/85 (42%), Gaps = 16/85 (18%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQ---------QQQQQPPQPQPRD-- 89
P P +Q + APQ PQ + Q QPQ QQ QQP PQP+D
Sbjct: 786 APQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDTL 845
Query: 90 LQPNSNNQLVLVNGKSSGDSGRSTP 114
L P L++ NG S +TP
Sbjct: 846 LHP-----LLMRNGDSRPLHKPTTP 865
Score = 33.1 bits (75), Expect = 0.33
Identities = 18/81 (22%), Positives = 26/81 (32%)
Query: 21 PTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQ 80
P Q P++ P + A + Q + Q T Q +Q Q
Sbjct: 410 PAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQ 469
Query: 81 QPPQPQPRDLQPNSNNQLVLV 101
QP +P QP Q +V
Sbjct: 470 QPAAQEPLYQQPQPVEQQPVV 490
Score = 32.7 bits (74), Expect = 0.44
Identities = 18/45 (40%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 55 PQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLV 99
PQ +P Q QQP PQ Q QQP QP Q Q V
Sbjct: 755 PQQPVAPQQQYQQPQQPVA-PQPQYQQPQQPVAPQPQYQQPQQPV 798
Score = 32.4 bits (73), Expect = 0.60
Identities = 22/86 (25%), Positives = 27/86 (31%), Gaps = 11/86 (12%)
Query: 18 GLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNG--APQVNTSPPQNAILHQQPTPQP 75
+ P + P P Q + APQ PQ + Q QP
Sbjct: 748 IVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQP 807
Query: 76 QQQQ---------QQPPQPQPRDLQP 92
QQ QQP PQP+ QP
Sbjct: 808 QQPVAPQPQYQQPQQPVAPQPQYQQP 833
Score = 30.4 bits (68), Expect = 1.8
Identities = 24/73 (32%), Positives = 26/73 (35%), Gaps = 4/73 (5%)
Query: 30 PHHPGLVHLNGPPPPPHQLVKLNGA---PQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQ 86
PH P + P P Q V PQ +P QQP PQ Q QQP QP
Sbjct: 740 PHEPLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVA-PQPQYQQPQQPV 798
Query: 87 PRDLQPNSNNQLV 99
Q Q V
Sbjct: 799 APQPQYQQPQQPV 811
>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 = 35.1 bits (81), Expect = 0.010
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRH--RGFGFVTFENEEVV 304
K+F+GGV D + + F FG V D + RH +G+ ++ FE+E+ V
Sbjct: 4 KVFLGGVPWDITEAGLINTFKPFGSVSVEWPGKDGKHPRHPPKGYVYLIFESEKSV 59
Score = 33.5 bits (77), Expect = 0.038
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRS--RGFGFITFAEPETVEK 218
S K+F+GG+ W + L F FG+V+ KD R +G+ ++ F ++V+
Sbjct: 2 SCKVFLGGVPWDITEAGLINTFKPFGSVSVEWPGKDGKHPRHPPKGYVYLIFESEKSVKA 61
Query: 219 VLKVPIHTLDG 229
+L+ H
Sbjct: 62 LLQACTHDFLN 72
>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106). This
family of proteins are found in large numbers in the
Trichomonas vaginalis proteome. The function of this
protein is unknown.
Length = 422
Score = 37.3 bits (86), Expect = 0.011
Identities = 17/70 (24%), Positives = 18/70 (25%)
Query: 31 HHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDL 90
H P P Q N A Q P Q + Q QQ P Q
Sbjct: 199 HAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKR 258
Query: 91 QPNSNNQLVL 100
NQ L
Sbjct: 259 SREQGNQEFL 268
Score = 35.8 bits (82), Expect = 0.036
Identities = 19/58 (32%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 37 HLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNS 94
H + P P V+ N A Q P QQP QP Q QQP P P +
Sbjct: 197 HRHAPKPTQQPTVQ-NPAQQPTVQNPAQQP-QQQPQQQPVQPAQQPTPQNPAQQPPQT 252
>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 = 34.3 bits (79), Expect = 0.012
Identities = 13/51 (25%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
+I+VG + D +++ F ++G ++ + L +++ R F FV FE+
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKA-IDLKNRR--RGPPFAFVEFEDP 48
>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 = 34.3 bits (79), Expect = 0.012
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
S +++G L S E+LRE FG + + I+K+ + F+ F KV+
Sbjct: 3 SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFLSIANAIKVV 56
Score = 28.6 bits (64), Expect = 1.5
Identities = 9/52 (17%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
++ +++G + + S EE++ +FG +++ ++ + + FV F +
Sbjct: 3 SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIV------KEKNIAFVHFLS 48
>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 = 34.3 bits (79), Expect = 0.013
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAV-TDVLIMKDPITQRSRGFGFITFA 211
+ + GL + E +R G DV +M+ T SRGF F+ F
Sbjct: 5 IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFM 53
Score = 29.3 bits (66), Expect = 0.65
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLM-DQQTKRHRGFGFVTF 298
I + G+ + E+++ G + V LM + T RGF FV F
Sbjct: 5 IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEF 52
>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 = 34.5 bits (79), Expect = 0.013
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
D + LF+G L + LR F FG +T+V I K P ++ +GF+ F
Sbjct: 3 DQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDI-KRPGRGQTSTYGFLKF 55
>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 = 34.2 bits (79), Expect = 0.014
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 8/54 (14%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVT----DVLIMKDPI-TQRSRGFGFITFA 211
+LFVGG+ + E++ E F VT DV++ + P ++RGF F+ +
Sbjct: 3 RLFVGGIPKTKTKEEILE---EFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYE 53
Score = 31.9 bits (73), Expect = 0.089
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 12/57 (21%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETV-------MLMDQQTKRHRGFGFVTFEN 300
++FVGG+ + + EE+ +F KV E V D ++RGF FV +E+
Sbjct: 3 RLFVGGIPKTKTKEEI---LEEFSKVTEGVVDVIVYRSPDD--KNKNRGFAFVEYES 54
>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 = 33.8 bits (78), Expect = 0.015
Identities = 15/50 (30%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 253 FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
FVG + +T ++ A F V+ ++ D++T + +GF +V FE+ E
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVE 53
Score = 30.0 bits (68), Expect = 0.36
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 165 FVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
FVG L + T L F +V V +++D T + +GF ++ F + E++++ L+
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDG 63
Query: 225 HTLDGKKI 232
D + +
Sbjct: 64 ALFDDRSL 71
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 37.2 bits (86), Expect = 0.016
Identities = 19/52 (36%), Positives = 23/52 (44%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQP 92
P P V+ P V+ S A+ QP PQ Q PPQPQP+ P
Sbjct: 2875 PAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPP 2926
>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a
role in the biomineralisation of teeth. They seem to
regulate formation of crystallites during the secretory
stage of tooth enamel development and are thought to
play a major role in the structural organisation and
mineralisation of developing enamel. The extracellular
matrix of the developing enamel comprises two major
classes of protein: the hydrophobic amelogenins and the
acidic enamelins. Circular dichroism studies of porcine
amelogenin have shown that the protein consists of 3
discrete folding units: the N-terminal region appears to
contain beta-strand structures, while the C-terminal
region displays characteristics of a random coil
conformation. Subsequent studies on the bovine protein
have indicated the amelogenin structure to contain a
repetitive beta-turn segment and a "beta-spiral" between
Gln112 and Leu138, which sequester a (Pro, Leu, Gln)
rich region. The beta-spiral offers a probable site for
interactions with Ca2+ ions. Muatations in the human
amelogenin gene (AMGX) cause X-linked hypoplastic
amelogenesis imperfecta, a disease characterised by
defective enamel. A 9bp deletion in exon 2 of AMGX
results in the loss of codons for Ile5, Leu6, Phe7 and
Ala8, and replacement by a new threonine codon,
disrupting the 16-residue (Met1-Ala16) amelogenin signal
peptide.
Length = 165
Score = 35.5 bits (82), Expect = 0.016
Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 27 VQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQ 86
+Q HH ++ P P L+ + G + +P Q+ HQ PQP QQ QP Q
Sbjct: 52 LQPHHHIPVLPAQQPVVPQQPLMPVPGQHSM--TPTQH---HQPNLPQPAQQPFQPQPLQ 106
Query: 87 PRDLQPNSNNQLVL 100
P Q Q +
Sbjct: 107 PPQPQQPMQPQPPV 120
Score = 32.8 bits (75), Expect = 0.14
Identities = 16/72 (22%), Positives = 19/72 (26%), Gaps = 7/72 (9%)
Query: 28 QIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
+P P + P P H + P Q Q P QQ QP P
Sbjct: 67 VVPQQPLM-----PVPGQHSMTPTQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQPQPPVH 121
Query: 88 --RDLQPNSNNQ 97
L P
Sbjct: 122 PIPPLPPQPPLP 133
Score = 28.2 bits (63), Expect = 4.4
Identities = 14/68 (20%), Positives = 18/68 (26%), Gaps = 9/68 (13%)
Query: 20 IPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQ 79
+P + + HH N P P PQ P + QP P
Sbjct: 76 VPGQHSMTPTQHH----QPNLPQPAQQPF-----QPQPLQPPQPQQPMQPQPPVHPIPPL 126
Query: 80 QQPPQPQP 87
P P
Sbjct: 127 PPQPPLPP 134
>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 = 33.7 bits (77), Expect = 0.018
Identities = 15/49 (30%), Positives = 27/49 (55%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+F+ + Q+ E+ F FG V + +D+ T + + FGFV+F+N
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDN 55
Score = 32.5 bits (74), Expect = 0.059
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 4/77 (5%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
P LF+ L + +L + F FG V + D T +S+ FGF++F P + +
Sbjct: 2 PEGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQA 61
Query: 219 VLKVPIHTLDGKKIDPK 235
I ++G +I K
Sbjct: 62 A----IQAMNGFQIGMK 74
>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 = 36.9 bits (85), Expect = 0.018
Identities = 37/143 (25%), Positives = 69/143 (48%), Gaps = 16/143 (11%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++FVG + ++L F G + ++ +M D + ++RG+ F+TF E ++ +K+
Sbjct: 60 EVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKL 118
Query: 223 PIHTLDGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEE---T 279
L+ +I P R +FVGG+ ++ EE+ +F KV E
Sbjct: 119 ----LNNYEIRPGRLLGVCISVDNCR---LFVGGIPKNKKREEI---LEEFSKVTEGVVD 168
Query: 280 VMLMDQ--QTKRHRGFGFVTFEN 300
V++ K++RGF FV +E+
Sbjct: 169 VIVYHSAADKKKNRGFAFVEYES 191
Score = 36.1 bits (83), Expect = 0.031
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
R ++FVG + +D +E+ F + G + E ++MD + +RG+ FVTF +E
Sbjct: 57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQ-NRGYAFVTFCGKE 110
>gnl|CDD|220603 pfam10152, DUF2360, Predicted coiled-coil domain-containing
protein (DUF2360). This is the conserved 140 amino
acid region of a family of proteins conserved from
nematodes to humans. One C. elegans member is annotated
as a Daf-16-dependent longevity protein 1 but this
could not be confirmed. The function is unknown.
Length = 147
Score = 35.1 bits (81), Expect = 0.018
Identities = 12/55 (21%), Positives = 17/55 (30%), Gaps = 4/55 (7%)
Query: 33 PGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
PGL + PP A PP + +P P + +PP
Sbjct: 48 PGLEDVTVQTTPPPPAS----AITNGGPPPPPPARAEAASPPPPEAPAEPPAEPE 98
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM4 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 68
Score = 33.4 bits (77), Expect = 0.019
Identities = 15/55 (27%), Positives = 28/55 (50%), Gaps = 10/55 (18%)
Query: 178 LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKI 232
L + F FG + DV ++ + +G+ +A+ E+ E+ I TL GK++
Sbjct: 16 LEDVFCRFGGLIDVYLVPG------KNYGYAKYADRESAERA----ITTLHGKEV 60
>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 = 33.6 bits (77), Expect = 0.021
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQ-FGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
K IFVGGV + A E+ + +G V + D + K +G G V F N++
Sbjct: 1 KTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAI 60
Query: 309 EIHF----HMIKNKKVECK 323
F H +K+VE K
Sbjct: 61 SARFVQLQHGDIDKRVEVK 79
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins
is found in bacteria. Proteins in this family are
typically between 115 and 181 amino acids in length.
There are two completely conserved residues (F and G)
that may be functionally important.
Length = 110
Score = 34.3 bits (79), Expect = 0.021
Identities = 15/67 (22%), Positives = 17/67 (25%), Gaps = 5/67 (7%)
Query: 21 PTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQ 80
T Q P HQ + QP P+ QQQ
Sbjct: 6 NTNQYPPQNQQQQPYQQ-----QPYHQQMPPPPYSPPQQQQGHFMPPQPQPYPKQSPQQQ 60
Query: 81 QPPQPQP 87
QPPQ
Sbjct: 61 QPPQFSS 67
Score = 26.6 bits (59), Expect = 9.8
Identities = 14/31 (45%), Positives = 14/31 (45%), Gaps = 2/31 (6%)
Query: 58 NTSPPQNAILHQQPTPQPQQQQQQPPQPQPR 88
N PPQN QQP Q QQ PP P
Sbjct: 8 NQYPPQNQ--QQQPYQQQPYHQQMPPPPYSP 36
>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 = 33.7 bits (78), Expect = 0.022
Identities = 16/71 (22%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN-EEVVDHICEI 310
IFV GV ++ E+V F++FG+++ + +D++T +G+ + +E +E I +
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 311 HFHMIKNKKVE 321
+ + + +
Sbjct: 69 NGKELLGQTIS 79
>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 = 33.5 bits (76), Expect = 0.022
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
++V G+S +T A ++K F ++GKV ++ + ++ + +G VT + V C H
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVAR-CISH 60
Query: 312 FH 313
H
Sbjct: 61 LH 62
Score = 30.0 bits (67), Expect = 0.33
Identities = 14/57 (24%), Positives = 29/57 (50%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
L+V GLS T + L+ FG +G V ++ + + ++ +G +T + V + +
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCI 58
>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 = 33.4 bits (77), Expect = 0.022
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 10/73 (13%)
Query: 255 GGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE----EVVDHICEI 310
GV + TS E++K F +FG+V +D R + G+V F+ E E ++ + E
Sbjct: 7 SGVGEQTSREDLKEAFEEFGEVA----WVDFA--RGQTEGYVRFKEENAAKEALEKLKEA 60
Query: 311 HFHMIKNKKVECK 323
IK +V K
Sbjct: 61 KNLKIKGSEVTVK 73
Score = 29.9 bits (68), Expect = 0.37
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 10/73 (13%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEP----ETVEKV 219
L G+ QTS E L+E F FG V V R + G++ F E E +EK+
Sbjct: 4 LHFSGVGEQTSREDLKEAFEEFGEVAWVDF------ARGQTEGYVRFKEENAAKEALEKL 57
Query: 220 LKVPIHTLDGKKI 232
+ + G ++
Sbjct: 58 KEAKNLKIKGSEV 70
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 33.3 bits (76), Expect = 0.027
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFV L + + ++L+E F AV L S+G +I F EK L+
Sbjct: 6 LFVKNLPYNITVDELKEVFE--DAVDIRLPSGK--DGSSKGIAYIEFKTEAEAEKALE-- 59
Query: 224 IHTLDGKKID 233
G ++D
Sbjct: 60 --EKQGAEVD 67
>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 = 33.7 bits (77), Expect = 0.028
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 5/51 (9%)
Query: 187 AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV-----PIHTLDGKKI 232
+V+++ ++KD TQ++RGF F+ + ++L++ P +DGK I
Sbjct: 30 SVSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTI 80
>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 = 33.4 bits (77), Expect = 0.028
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
L+V L ++ SSE+L + FG +GA+ + I T RG F+ +
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVY 48
Score = 28.7 bits (65), Expect = 0.92
Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN----EEVVDHI 307
++V + S+EE+ F ++G + + + ++T RG FV +E+ + DH+
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHL 61
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation
initiation factor 4B (eIF-4B) and similar proteins.
This subfamily corresponds to the RRM of eIF-4B, a
multi-domain RNA-binding protein that has been primarily
implicated in promoting the binding of 40S ribosomal
subunits to mRNA during translation initiation. It
contains two RNA-binding domains; the N-terminal
well-conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), binds the 18S rRNA of the 40S ribosomal subunit
and the C-terminal basic domain (BD), including two
arginine-rich motifs (ARMs), binds mRNA during
initiation, and is primarily responsible for the
stimulation of the helicase activity of eIF-4A. eIF-4B
also contains a DRYG domain (a region rich in Asp, Arg,
Tyr, and Gly amino acids) in the middle, which is
responsible for both, self-association of eIF-4B and
binding to the p170 subunit of eIF3. Additional research
indicates that eIF-4B can interact with the poly(A)
binding protein (PABP) in mammalian cells, which can
stimulate both, the eIF-4B-mediated activation of the
helicase activity of eIF-4A and binding of poly(A) by
PABP. eIF-4B has also been shown to interact
specifically with the internal ribosome entry sites
(IRES) of several picornaviruses which facilitate
cap-independent translation initiation. .
Length = 77
Score = 33.1 bits (76), Expect = 0.029
Identities = 18/70 (25%), Positives = 40/70 (57%), Gaps = 4/70 (5%)
Query: 165 FVGGLSWQTSSEKLREYF-GMFGAVTDVLIMKDP-ITQRSRGFGFITFAEPETVEKVLKV 222
++G L + + E ++E+F G+ V+ V + ++P R RGFG+ F + +++ + L +
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL--NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSL 62
Query: 223 PIHTLDGKKI 232
+L ++I
Sbjct: 63 NDESLKNRRI 72
Score = 30.8 bits (70), Expect = 0.21
Identities = 14/68 (20%), Positives = 32/68 (47%)
Query: 253 FVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHF 312
++G + D + E++K +F + R RGFG+ FE+ + + ++
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLND 64
Query: 313 HMIKNKKV 320
+KN+++
Sbjct: 65 ESLKNRRI 72
>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 = 33.1 bits (76), Expect = 0.029
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
S L++G LS + + E L+ F +G + + D I RG ++ + + L
Sbjct: 2 STTLWIGHLSKKVTEEDLKNLFEEYGEIQSI----DMIP--PRGCAYVCMETRQDAHRAL 55
Query: 221 -KVPIHTLDGKKI 232
K+ L GKKI
Sbjct: 56 QKLRNVKLAGKKI 68
Score = 30.4 bits (69), Expect = 0.24
Identities = 11/52 (21%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+ +++G +S+ + E++K F ++G+++ M+ RG +V E
Sbjct: 2 STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP------RGCAYVCMET 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 = 33.0 bits (75), Expect = 0.030
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+F+ + Q+ + ++ F FG V + +D+QT + FGFV+++N
Sbjct: 7 LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDN 55
Score = 32.3 bits (73), Expect = 0.058
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 4/77 (5%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
P LF+ L + + L + F FG V + D T S+ FGF+++ P++ +
Sbjct: 2 PEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQ- 60
Query: 219 VLKVPIHTLDGKKIDPK 235
I ++G +I K
Sbjct: 61 ---AAIQAMNGFQIGTK 74
>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 = 33.4 bits (76), Expect = 0.030
Identities = 14/48 (29%), Positives = 31/48 (64%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
+++ G+ + + ++V+ FS+FG++ + +L+DQ T RG F+ F+
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFD 50
Score = 33.1 bits (75), Expect = 0.033
Identities = 16/60 (26%), Positives = 29/60 (48%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
A L++ GL + + + + F FG + + ++ D T SRG FI F + E+ +
Sbjct: 1 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT 60
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 33.0 bits (76), Expect = 0.032
Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
++VGG+ + + ++++ +F QFG++ ++ QQ FVTF E + E
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQC------AFVTFTTREAAEKAAERL 57
Query: 312 FH--MIKNKKV 320
F+ +I +++
Sbjct: 58 FNKLIINGRRL 68
Score = 31.5 bits (72), Expect = 0.11
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
L+VGGL + + + LR++F FG + + ++ + F+TF E EK
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVVP------RQQCAFVTFTTREAAEK 52
>gnl|CDD|235585 PRK05733, PRK05733, single-stranded DNA-binding protein;
Provisional.
Length = 172
Score = 34.5 bits (79), Expect = 0.041
Identities = 22/70 (31%), Positives = 25/70 (35%), Gaps = 14/70 (20%)
Query: 23 MNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQP 82
M G +Q+ L G P Q G N S P+ Q PQ QQQ
Sbjct: 104 MQGTMQL--------LGGRPQGDDQ--GGQGGGNYNQSAPR----QQAQRPQQAAQQQSR 149
Query: 83 PQPQPRDLQP 92
P PQ QP
Sbjct: 150 PAPQQPAPQP 159
Score = 27.6 bits (61), Expect = 7.7
Identities = 15/48 (31%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 51 LNGAPQVNTSPPQNAILHQQPTPQPQQQ-QQQPPQPQPRDLQPNSNNQ 97
L G PQ + Q + Q P+ Q Q QQ Q Q R Q
Sbjct: 111 LGGRPQGDDQGGQGGGNYNQSAPRQQAQRPQQAAQQQSRPAPQQPAPQ 158
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B") a unique protein that comprises the U2 snRNP.
It was initially identified as binding to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA. In addition, the
nuclear transport of U2B" is independent of U2 snRNA
binding. U2B" contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also contains a nuclear
localization signal (NLS) in the central domain.
However, nuclear import of U2B'' does not depend on this
NLS. The N-terminal RRM is sufficient to direct U2B" to
the nucleus. .
Length = 91
Score = 33.1 bits (75), Expect = 0.043
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 252 IFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
I++ ++ EE+K A FSQFG V + V L +T + RG FV F+
Sbjct: 4 IYINNLNDKIKKEELKRSLYALFSQFGHVVDIVAL---KTMKMRGQAFVIFK 52
Score = 28.1 bits (62), Expect = 2.6
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 178 LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
L F FG V D++ +K T + RG F+ F E + L+
Sbjct: 22 LYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELSSATNALR 62
>gnl|CDD|215544 PLN03029, PLN03029, type-a response regulator protein; Provisional.
Length = 222
Score = 35.0 bits (80), Expect = 0.044
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 56 QVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKS 105
Q + + + + QP QQ Q PQPQ + QPN+N + + G S
Sbjct: 158 QEKQEKLEESEIQSEKQEQPSQQPQSQPQPQQQPQQPNNNKRKAMEEGLS 207
>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 = 32.5 bits (75), Expect = 0.044
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 270 FSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE-IHFHMIKNKKV 320
FS FG + + D+ +G+GFV FE EE E ++ ++ +KKV
Sbjct: 23 FSAFGNILSCKVATDENGGS-KGYGFVHFETEEAAVRAIEKVNGMLLNDKKV 73
Score = 31.4 bits (72), Expect = 0.11
Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 20/78 (25%)
Query: 178 LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPKHA 237
L + F FG + + D S+G+GF+ F E + I ++G ++
Sbjct: 19 LYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRA----IEKVNGMLLN---- 69
Query: 238 TPKNRPKIGNRTKKIFVG 255
KK+FVG
Sbjct: 70 -----------DKKVFVG 76
>gnl|CDD|220883 pfam10824, DUF2580, Protein of unknown function (DUF2580). This
family of proteins with unknown function appears to be
mainly found in actinobacteria.
Length = 100
Score = 33.1 bits (76), Expect = 0.046
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 350 MAAPAPITPAT--QLAALQSQAQAQVQAAAAAVAAQNAAAVANYGKIF 395
M P + PA +LAA +A AQ+ +A AA A AA A +G I
Sbjct: 1 MTDPLHVDPAHLRELAAKHDEAAAQIASAVAAAAGVAAAVAATHGPIC 48
>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 32.7 bits (74), Expect = 0.048
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 169 LSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV-PIHTL 227
+ WQ + +RE G VT V + KD +SRG G + F + E V+K L+V + L
Sbjct: 11 MKWQAIKDLMRE---KVGEVTYVELFKDA-EGKSRGCGVVEFKDEEFVKKALEVMNKYDL 66
Query: 228 DGKKIDPK 235
+G+ ++ K
Sbjct: 67 NGRPLNIK 74
>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 = 32.3 bits (73), Expect = 0.049
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
++ GGV+ + + ++ FS FG++ E + D +G+ FV F + E H I +
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56
Query: 311 HFHMIKNKKVEC 322
+ I+ V+C
Sbjct: 57 NGTTIEGHVVKC 68
Score = 27.7 bits (61), Expect = 2.8
Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET-VEKVLKV 222
++ GG++ + + +R+ F FG + +V + D +G+ F+ F E+ ++ V
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSV 56
Query: 223 PIHTLDG 229
T++G
Sbjct: 57 NGTTIEG 63
>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 = 32.6 bits (75), Expect = 0.055
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 19/76 (25%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVE-----------------ETVMLMDQQTKRH 290
RT +FVG + T +++K F QFG +E + K+
Sbjct: 1 RT--VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKD 58
Query: 291 RGFGFVTFENEEVVDH 306
+V F+ EE +
Sbjct: 59 NVNAYVVFKEEESAEK 74
Score = 27.6 bits (62), Expect = 4.1
Identities = 21/86 (24%), Positives = 33/86 (38%), Gaps = 17/86 (19%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDV-----------------LIMKDPITQRSRGFG 206
+FVG L T + L++ F FG + V I K ++
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62
Query: 207 FITFAEPETVEKVLKVPIHTLDGKKI 232
++ F E E+ EK LK+ +G I
Sbjct: 63 YVVFKEEESAEKALKLNGTEFEGHHI 88
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 87
Score = 32.7 bits (74), Expect = 0.056
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 189 TDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV-----PIHTLDGKKIDPKHA 237
++V ++KD TQ +RGF FI + ++L++ P ++DGK I+ + A
Sbjct: 32 SNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLSIDGKTINVEFA 85
>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 = 32.5 bits (74), Expect = 0.058
Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
K+ V L ++ + + +R F +G + V + K Q +RGF F+ F+ + +
Sbjct: 2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKK-FDQSARGFAFVEFSTAKEALNAMNA 60
Query: 223 PIHT 226
T
Sbjct: 61 LKDT 64
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 32.6 bits (75), Expect = 0.067
Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 161 SAKLFVGGL-SWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
S LFV L LR+ F G T + P Q RGF F+ +A E E+
Sbjct: 2 SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQ-PRGFAFVEYATAEDAEEA 60
>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 = 32.3 bits (73), Expect = 0.072
Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 5/92 (5%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
P A LF+ L + + L + F FG V + D T S+ FGF+++ P + +
Sbjct: 5 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 64
Query: 219 VLKVPIHTLDGKKIDPKHATPK-NRPKIGNRT 249
I ++G +I K + R K ++
Sbjct: 65 A----IQAMNGFQIGMKRLKVQLKRSKNDSKP 92
Score = 31.2 bits (70), Expect = 0.18
Identities = 16/57 (28%), Positives = 30/57 (52%)
Query: 244 KIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
K G +F+ + Q+ +++ F FG V + +D+QT + FGFV+++N
Sbjct: 2 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDN 58
>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 = 32.3 bits (73), Expect = 0.072
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 159 PTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEK 218
P K++VG L + +L FG +G + V + ++P GF F+ F +P
Sbjct: 2 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAAD 56
Query: 219 VLKVPIHTLDGKKI 232
++ LDG+ +
Sbjct: 57 AVR----ELDGRTL 66
>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 = 31.9 bits (73), Expect = 0.074
Identities = 10/31 (32%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 247 NRTKKIFVGGVSQDTSAEEVKAYFSQFGKVE 277
R +++ V G + +E+ A+F+QFG++E
Sbjct: 3 RRPRQLSVTGF-TEEDKDELLAHFAQFGEIE 32
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. The family
also includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 31.9 bits (73), Expect = 0.075
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE 299
V +S S E ++ FSQFG+VE V+++D + R G G V F
Sbjct: 4 VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEFS 48
Score = 27.3 bits (61), Expect = 4.0
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFA 211
L V LS S+E L + F FG V +++ D RS G G + F+
Sbjct: 2 LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFS 48
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein (SXL).
SNF contains two RNA recognition motifs (RRMs); it can
self-associate through RRM1, and each RRM can recognize
poly(U) RNA binding independently. .
Length = 78
Score = 32.2 bits (73), Expect = 0.076
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 252 IFVGGVSQDTSAEEVK----AYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
I++ +++ EE+K A FSQFG++ + V L +T + RG FV F++
Sbjct: 2 IYINNLNEKVKKEELKKSLYAIFSQFGQILDIVAL---KTLKMRGQAFVVFKD 51
>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 = 31.9 bits (73), Expect = 0.084
Identities = 13/62 (20%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIH 311
+++ + ++++ +G+V T +L D + + RG GF E+ E + I
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQS-RGVGFARMESREKCEDIIS-K 60
Query: 312 FH 313
F+
Sbjct: 61 FN 62
Score = 30.0 bits (68), Expect = 0.39
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 178 LREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDP 234
L +G V I++D Q SRG GF E E + I +GK +
Sbjct: 17 LETMLKPYGQVISTRILRDSKGQ-SRGVGFARMESREKCEDI----ISKFNGKYLKG 68
>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 = 32.2 bits (73), Expect = 0.089
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 187 AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV-----PIHTLDGKKI 232
AV ++ ++KD TQ++RGF F+ + ++L++ P +DGK I
Sbjct: 30 AVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTI 80
>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 = 32.1 bits (72), Expect = 0.097
Identities = 15/64 (23%), Positives = 30/64 (46%)
Query: 157 DDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
D + L++ GL T+ + L + +G + + D T + +G+GF+ F P
Sbjct: 3 DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAA 62
Query: 217 EKVL 220
+K +
Sbjct: 63 QKAV 66
Score = 30.6 bits (68), Expect = 0.31
Identities = 12/49 (24%), Positives = 31/49 (63%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+++ G+ +T+ +++ +GK+ T ++D+ T + +G+GFV F++
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS 58
>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 = 31.4 bits (72), Expect = 0.11
Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQF-GKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K +F+ + ++T+ E ++ F+QF G E V L+ + RG FV FE EE
Sbjct: 3 KILFLQNLPEETTKEMLEMLFNQFPGFKE--VRLVPR-----RGIAFVEFETEE 49
>gnl|CDD|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional.
Length = 256
Score = 33.9 bits (78), Expect = 0.11
Identities = 14/56 (25%), Positives = 17/56 (30%), Gaps = 3/56 (5%)
Query: 39 NGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQ--QPPQPQPRDLQP 92
N P + + Q P QP P+Q QP P P QP
Sbjct: 108 NEQTPQVPR-STVQIQQQAQQQQPPATTAQPQPVTPPRQTTAPVQPQTPAPVRTQP 162
Score = 29.2 bits (66), Expect = 3.6
Identities = 14/57 (24%), Positives = 14/57 (24%), Gaps = 4/57 (7%)
Query: 44 PPHQL--VKLNGAPQVNTSPPQNAILHQQPTPQPQQQ-QQQPPQPQPRDLQPNSNNQ 97
P QL V N I Q QP Q P PR Q
Sbjct: 98 QPTQLSEVPYNEQTPQ-VPRSTVQIQQQAQQQQPPATTAQPQPVTPPRQTTAPVQPQ 153
>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 = 31.5 bits (72), Expect = 0.11
Identities = 13/69 (18%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
L+VG L + + L E F G + ++++ + + F+ + + + L+
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH---GNDPYAFVEYYDHRSAAAALQ-- 55
Query: 224 IHTLDGKKI 232
T++G+ I
Sbjct: 56 --TMNGRLI 62
>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 = 31.5 bits (71), Expect = 0.12
Identities = 14/70 (20%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++++G LS+Q + +F +G + +V + G+GF+ F + +
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDA--- 49
Query: 223 PIHTLDGKKI 232
++ L+GK +
Sbjct: 50 -VYELNGKDL 58
Score = 28.8 bits (64), Expect = 1.1
Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++++G +S +V+ +F +GK+ E + G+GFV F++ D
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDAD 47
>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 = 31.6 bits (71), Expect = 0.12
Identities = 14/60 (23%), Positives = 28/60 (46%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
L++ GL T+ + L + +G + + D T + +G+GF+ F P +K +
Sbjct: 1 KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60
Score = 30.9 bits (69), Expect = 0.19
Identities = 12/49 (24%), Positives = 30/49 (61%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+++ G+ T+ +++ +GK+ T ++D+ T + +G+GFV F++
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS 52
>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 = 31.5 bits (71), Expect = 0.12
Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 9/79 (11%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE-VVDHIC 308
K +FV ++ + E ++ FS+FGK+E + K+ + + FV FE + V +
Sbjct: 2 KVLFVRNLATTVTEEILEKSFSEFGKLE--------RVKKLKDYAFVHFEERDAAVRAMD 53
Query: 309 EIHFHMIKNKKVECKKAQP 327
E++ I+ +++E A+P
Sbjct: 54 EMNGKEIEGEEIEIVLAKP 72
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. Moreover, hnRNP M is able to
interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. hnRNP M
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 31.2 bits (71), Expect = 0.12
Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 3/76 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYF-SQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICE 309
++F+ + D +++K F + G+V + D++ K RG G V F+++E V E
Sbjct: 1 RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGK-SRGCGVVEFKDKESVQKALE 59
Query: 310 -IHFHMIKNKKVECKK 324
++ + +K +K+ K+
Sbjct: 60 TMNRYELKGRKLVVKE 75
Score = 30.5 bits (69), Expect = 0.26
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 169 LSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL-KVPIHTL 227
L WQ + RE G VT V + KD +SRG G + F + E+V+K L + + L
Sbjct: 11 LKWQDLKDLFRE---KVGEVTYVELFKDE-EGKSRGCGVVEFKDKESVQKALETMNRYEL 66
Query: 228 DGKKI 232
G+K+
Sbjct: 67 KGRKL 71
>gnl|CDD|240990 cd12546, RRM_RBM43, RNA recognition motif in vertebrate RNA-binding
protein 43 (RBM43). This subgroup corresponds to the
RRM of RBM43, a putative RNA-binding protein containing
one RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although its biological function remains unclear, RBM43
shows high sequence homology to poly [ADP-ribose]
polymerase 10 (PARP-10), which is a novel oncoprotein
c-Myc-interacting protein with poly(ADP-ribose)
polymerase activity. .
Length = 77
Score = 31.5 bits (72), Expect = 0.12
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 256 GVSQDTSAEEVKAYF----SQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
GV +++ +F + G VE R +G +VTFE EE ++ + +
Sbjct: 11 GVFDGALKDKLTIHFQRRKNGGGDVENVTY-----PTRTKGVAYVTFEEEEDAENVLKKK 65
Query: 311 HFHMIKNKKVEC 322
H K+ V+
Sbjct: 66 HVLQDKSLGVKL 77
Score = 26.1 bits (58), Expect = 7.7
Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 10/73 (13%)
Query: 168 GLSWQTSSEKLREYF----GMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
G+ +KL +F G V +V P + + +TF E E E VLK
Sbjct: 11 GVFDGALKDKLTIHFQRRKNGGGDVENVTY---PTRTKGVAY--VTFEEEEDAENVLKKK 65
Query: 224 IHTLDGKKIDPKH 236
H L K + K
Sbjct: 66 -HVLQDKSLGVKL 77
>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 = 31.0 bits (70), Expect = 0.13
Identities = 13/55 (23%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++++G +S ++++ +F +GK+ E + G+GFV FE+ D
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDAD 47
Score = 31.0 bits (70), Expect = 0.15
Identities = 13/70 (18%), Positives = 35/70 (50%), Gaps = 12/70 (17%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKV 222
++++G LS+ + ++ +FG +G + ++ + G+GF+ F + +
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDA--- 49
Query: 223 PIHTLDGKKI 232
++ L+GK +
Sbjct: 50 -VYELNGKDL 58
>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421). This
family represents a conserved region approximately 350
residues long within a number of plant proteins of
unknown function.
Length = 357
Score = 33.8 bits (77), Expect = 0.13
Identities = 20/48 (41%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPR 88
P PPP Q + PQ PQ +Q P QPQ QQ PPQ Q
Sbjct: 128 PQPPPAQQPQAQ-QPQPPPQVPQQQ-QYQSPPQQPQYQQNPPPQAQSA 173
Score = 33.0 bits (75), Expect = 0.25
Identities = 20/68 (29%), Positives = 22/68 (32%), Gaps = 3/68 (4%)
Query: 28 QIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
Q+P P P P PP QQP P PQ QQQ Q P
Sbjct: 101 QLPPQQVQSVPQQPTPQQ---EPYYPPPSQPQPPPAQQPQAQQPQPPPQVPQQQQYQSPP 157
Query: 88 RDLQPNSN 95
+ Q N
Sbjct: 158 QQPQYQQN 165
Score = 30.3 bits (68), Expect = 1.8
Identities = 17/56 (30%), Positives = 19/56 (33%), Gaps = 2/56 (3%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNN 96
P P Q V+ + Q QP P P QQ Q QPQP P
Sbjct: 99 PSQLPPQQVQ-SVPQQPTPQQEPYYPPPSQPQPPPAQQPQ-AQQPQPPPQVPQQQQ 152
Score = 30.3 bits (68), Expect = 1.8
Identities = 19/65 (29%), Positives = 22/65 (33%), Gaps = 3/65 (4%)
Query: 33 PGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQP 92
P P P Q + AP + P Q Q PQ QQ+P P P QP
Sbjct: 74 PPAPAPQSPQPDQQQQ---SQAPPSHQYPSQLPPQQVQSVPQQPTPQQEPYYPPPSQPQP 130
Query: 93 NSNNQ 97
Q
Sbjct: 131 PPAQQ 135
Score = 28.0 bits (62), Expect = 9.1
Identities = 11/37 (29%), Positives = 14/37 (37%)
Query: 56 QVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQP 92
+ +P Q A P Q PP P P+ QP
Sbjct: 48 KQPPAPEQVAKHELADAPLQQVNAALPPAPAPQSPQP 84
>gnl|CDD|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage
factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar
proteins. This subgroup corresponds to the RRM of
CFIm68. 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. The family includes CFIm68, also
termed cleavage and polyadenylation specificity factor
subunit 6 (CPSF6), or cleavage and polyadenylation
specificity factor 68 kDa subunit (CPSF68), or protein
HPBRII-4/7. CFIm68 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 CFIm68 mediates the interaction
with CFIm25. It also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 77
Score = 31.2 bits (71), Expect = 0.16
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMK---DPITQRSRGFGFITFAEPETVEKVL 220
L+VG L+W T+ + L E G V D+L +K + +S+GF I + K++
Sbjct: 2 LYVGNLTWWTTDQDLTEAIQSIG-VNDLLEIKFFENRANGQSKGFALIVLGSESSSRKLM 60
Query: 221 -KVPIHTLDGKK 231
K+P L G+
Sbjct: 61 DKLPKKELHGQN 72
>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 = 31.5 bits (72), Expect = 0.17
Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 15/61 (24%)
Query: 176 EKLREYFGMFGAVTDVLIMKDP-------------ITQRSRGF--GFITFAEPETVEKVL 220
E L+ F G V V + + P + +GF ++ F +P ++ + L
Sbjct: 15 ESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVAYVVFKKPSSLSRAL 74
Query: 221 K 221
K
Sbjct: 75 K 75
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 30.7 bits (69), Expect = 0.17
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 6/55 (10%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVD 305
++FVG + D + +E K F+++G+ E + + +GFGF+ E+ + +
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAE 51
Score = 30.3 bits (68), Expect = 0.30
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFI 208
+LFVG L + ++ ++ F +G +V I K +GFGFI
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFINK------GKGFGFI 42
>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 = 30.7 bits (69), Expect = 0.18
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 9/52 (17%)
Query: 251 KIFVGGV-SQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
++F+G + + +V+A FS++GK+ + H+GF FV + NE
Sbjct: 3 RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNE 46
>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 = 0.19
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQF--GKVEETVM----LMDQQTKRHRGFGFVTFENEE 302
+K+++V +S+ + E++ F +F EE M LM R +G FVTF +EE
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLM--TEGRMKGQAFVTFPSEE 58
Query: 303 V 303
+
Sbjct: 59 I 59
Score = 30.6 bits (70), Expect = 0.22
Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 8/67 (11%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPI------TQRSRGFGFITFAEPE 214
S +L+V LS + + E L FG F V K+ R +G F+TF E
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEE 58
Query: 215 TVEKVLK 221
K L
Sbjct: 59 IATKALN 65
>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 = 30.9 bits (70), Expect = 0.19
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+I+VG + D ++++ F ++G + + +D + +R F FV FE+
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRD----IDLKNRRGPPFAFVEFED 46
>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 = 31.1 bits (70), Expect = 0.19
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFG--KVEETV------MLMDQQTKRHRGFGFVTFEN 300
IFV G+ +D + E V YF Q G K + + D++T + +G V+F++
Sbjct: 5 IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 61
>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 = 31.1 bits (71), Expect = 0.19
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 271 SQFGKVEETVMLMDQQTKRHRGFGFVTFEN----EEVVDHI 307
++G+VEE + +T +H G V F++ + V+ +
Sbjct: 24 KKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKL 64
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 30.8 bits (70), Expect = 0.21
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 193 IMKDPITQRSRGFGFITFAEPETV 216
+ +DP T +S+GF ++T++ P +
Sbjct: 31 LKRDPYTGKSKGFAYVTYSNPASA 54
>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 = 30.8 bits (70), Expect = 0.21
Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 18/86 (20%)
Query: 168 GLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTL 227
GL + S E++ ++F V + + + RS G ++ FA E+ E+ L
Sbjct: 7 GLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERALG------ 60
Query: 228 DGKKIDPKHATPKNRPKIGNRTKKIF 253
K++ KIG+R +IF
Sbjct: 61 ------------KHKEKIGHRYIEIF 74
Score = 30.0 bits (68), Expect = 0.37
Identities = 16/66 (24%), Positives = 27/66 (40%)
Query: 256 GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMI 315
G+ S EE+ +FS V + L R G +V F ++E + H I
Sbjct: 7 GLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERALGKHKEKI 66
Query: 316 KNKKVE 321
++ +E
Sbjct: 67 GHRYIE 72
>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 = 30.6 bits (70), Expect = 0.21
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 176 EKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPI 224
KL E+F FG + + I + + + + F+ E +K + P
Sbjct: 17 TKLNEHFSKFGTIVN--IQVNYNPESA----LVQFSTSEEAKKAYRSPE 59
>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 = 31.5 bits (71), Expect = 0.23
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFG 274
+K+FVGG+ D + ++ F +FG
Sbjct: 1 RKVFVGGLPWDITEADILNSFRRFG 25
Score = 28.4 bits (63), Expect = 2.7
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFG 186
K+FVGGL W + + F FG
Sbjct: 2 KVFVGGLPWDITEADILNSFRRFG 25
>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 = 30.7 bits (70), Expect = 0.24
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 249 TKKIFV--GGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
T+ + V GG+ S EE+ F ++G VE+ VM + + FV++ + E
Sbjct: 1 TQHLVVANGGLGNGVSREELLRVFEKYGTVEDLVMP------PGKPYCFVSYSSIE 50
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 30.4 bits (68), Expect = 0.24
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKD 196
KL VG +S ++++LR F +G V + I+KD
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD 35
Score = 28.8 bits (64), Expect = 0.86
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 9/58 (15%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE-NEEVVDHI 307
K+ VG +S + +E++A F ++G V E ++ D + FV E E+ V+ I
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAI 51
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 30.6 bits (69), Expect = 0.26
Identities = 15/51 (29%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
I++ +S S+ E+K F FG++EE +L+ + ++ +GF+T+ + E
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGEK---YGFITYRHSE 52
>gnl|CDD|218774 pfam05843, Suf, Suppressor of forked protein (Suf). This family
consists of several eukaryotic suppressor of forked
(Suf) like proteins. The Drosophila melanogaster
Suppressor of forked [Su(f)] protein shares homology
with the yeast RNA14 protein and the 77-kDa subunit of
human cleavage stimulation factor, which are proteins
involved in mRNA 3' end formation. This suggests a role
for Su(f) in mRNA 3' end formation in Drosophila. The
su(f) gene produces three transcripts; two of them are
polyadenylated at the end of the transcription unit, and
one is a truncated transcript, polyadenylated in intron
4. It is thought that su(f) plays a role in the
regulation of poly(A) site utilisation and an important
role of the GU-rich sequence for this regulation to
occur.
Length = 271
Score = 32.6 bits (75), Expect = 0.26
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 9/52 (17%)
Query: 39 NGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDL 90
+ P +L + +P N PQQQQQ P P P ++
Sbjct: 196 SKKPDKSRRLDQQRRSPSTNP---------APQASGPQQQQQGQPAPLPPEI 238
>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 = 30.8 bits (70), Expect = 0.26
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 10/64 (15%)
Query: 242 RPKIGNRTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
RP G +T +FVGG+ ++ + E ++ F Q G++ + + +K++ F + F E
Sbjct: 2 RP-PGCKT--VFVGGLPENATEEIIREVFEQCGEI-----IAIRMSKKN--FCHIRFAEE 51
Query: 302 EVVD 305
VD
Sbjct: 52 FAVD 55
Score = 30.1 bits (68), Expect = 0.40
Identities = 18/57 (31%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
+FVGGL + E +RE F G + I + F I FAE V+K +
Sbjct: 9 VFVGGLPENATEEIIREVFEQCGEIIA-------IRMSKKNFCHIRFAEEFAVDKAI 58
>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 = 30.7 bits (69), Expect = 0.27
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 154 PTGDDPTSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITF 210
P D + LF+G L S +LR F +G + +V+I K P + + F+ F
Sbjct: 1 PEDDQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVI-KRPARGQGGAYAFLKF 56
Score = 29.9 bits (67), Expect = 0.58
Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG--FGFVTFEN 300
T+ +F+G + + S E++ F ++G +EE V+ ++ R +G + F+ F+N
Sbjct: 8 TRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVI---KRPARGQGGAYAFLKFQN 58
>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 = 30.3 bits (68), Expect = 0.28
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETV 216
LFVG L + + E + E F G V V I KD + + F F+ F +V
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSV 55
>gnl|CDD|184358 PRK13874, PRK13874, conjugal transfer protein TrbJ; Provisional.
Length = 230
Score = 32.6 bits (75), Expect = 0.28
Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 7/36 (19%)
Query: 361 QLAALQSQAQAQVQA-------AAAAVAAQNAAAVA 389
QL ALQ+Q A +QA A A AA+ AAA
Sbjct: 183 QLLALQAQQLADLQALMAAQGRAQALEAARQAAAEE 218
>gnl|CDD|184697 PRK14475, PRK14475, F0F1 ATP synthase subunit B; Provisional.
Length = 167
Score = 31.8 bits (72), Expect = 0.34
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 361 QLAALQSQAQAQVQAAAAAVAAQNAAAV 388
++A ++QA A V+AAA +AAQ A V
Sbjct: 114 KIAQAEAQAAADVKAAAVDLAAQAAETV 141
>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 = 0.36
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 6/52 (11%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
++ +++G + + E+++ FSQ+G++E L R + FV F N
Sbjct: 3 SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYL------REKNCAFVNFTN 48
>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 = 30.1 bits (68), Expect = 0.37
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVT--------DVLIMKDPITQRSRGFGFITFAEPET 215
+FV L T+ + L E+FG G + + + KD T +G +T+ +P
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 216 VE 217
Sbjct: 61 AS 62
>gnl|CDD|178307 PLN02705, PLN02705, beta-amylase.
Length = 681
Score = 32.6 bits (74), Expect = 0.40
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 1/37 (2%)
Query: 52 NGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPR 88
T+ Q+ L P P P + + QPQ R
Sbjct: 4 LNNTITTTTGSQDPNLDPIPQPDPFPNRNR-NQPQSR 39
>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 = 29.9 bits (68), Expect = 0.40
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 9/66 (13%)
Query: 174 SSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKID 233
S ++LR+ F +G V+DV+ ++ + +G + FA + E ++ G +
Sbjct: 17 SEDELRKIFSKYGDVSDVV-----VSSKKKGSAIVEFASKKAAEAAVENEC----GLPSN 67
Query: 234 PKHATP 239
P +
Sbjct: 68 PLLVSW 73
>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 = 30.2 bits (67), Expect = 0.42
Identities = 12/49 (24%), Positives = 30/49 (61%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN 300
+++ G+ T+ +++ +GK+ T ++D+ T + +G+GFV F++
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDS 55
Score = 28.6 bits (63), Expect = 1.4
Identities = 14/61 (22%), Positives = 29/61 (47%)
Query: 160 TSAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKV 219
+ L++ GL T+ + L + +G + + D T + +G+GF+ F P +K
Sbjct: 3 SKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKA 62
Query: 220 L 220
+
Sbjct: 63 V 63
>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 = 30.1 bits (67), Expect = 0.42
Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ--QTKRHRGFGFVTFENEE 302
++FVG + + + E++ FS+ + V+L Q K++RGF F+ +E+ +
Sbjct: 4 RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKNRGFCFLEYEDHK 57
>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM1 of the majority of family members that include
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), heterogeneous
nuclear ribonucleoprotein L (hnRNP-L), heterogeneous
nuclear ribonucleoprotein L-like (hnRNP-LL),
polypyrimidine tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTBP2
is highly homologous to PTB and is perhaps specific to
the vertebrates. Unlike PTB, PTBP2 is enriched in the
brain and in some neural cell lines. It binds more
stably to the downstream control sequence (DCS) RNA than
PTB does but is a weaker repressor of splicing in vitro.
PTBP2 also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. The family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. In
addition, this family also includes RNA-binding motif
protein 20 (RBM20) that is an alternative splicing
regulator associated with dilated cardiomyopathy (DCM)
and contains only one RRM. .
Length = 74
Score = 29.9 bits (68), Expect = 0.43
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 6/52 (11%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEV 303
+ + + D + ++ A S FGKV ++L R + V ++ E
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLL------RGKNQALVEMDSVES 47
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 82
Score = 30.0 bits (68), Expect = 0.44
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 164 LFVGGLSWQTSSEKLREYFGM-FGAVTDVLIMKDPITQRSRGFGFITFAE 212
LFVG L+ +L E+F + + ++ D SRG+GF+ F++
Sbjct: 4 LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSD 52
Score = 28.8 bits (65), Expect = 1.1
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQ-FGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
+FVG ++ D ++ +FS+ + + +++DQ RG+GFV F +E
Sbjct: 4 LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNS-RGYGFVRFSDES 54
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM2 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli.Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. It shows high sequence
homology to ESRPs and contains three RRMs as well. It
also has an N-terminal domain with unknown function and
a C-terminal domain particularly rich in alanine,
glutamine, and serine. .
Length = 80
Score = 30.0 bits (68), Expect = 0.45
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 3/69 (4%)
Query: 256 GVSQDTSAEEVKAYFSQFGKV---EETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHF 312
G+ +A ++ A+F V + ++ + R G FV FE EE H
Sbjct: 8 GLPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRALGKHK 67
Query: 313 HMIKNKKVE 321
+ ++ +E
Sbjct: 68 ENLGSRYIE 76
>gnl|CDD|238058 cd00110, LamG, Laminin G domain; Laminin G-like domains are usually
Ca++ mediated receptors that can have binding sites for
steroids, beta1 integrins, heparin, sulfatides,
fibulin-1, and alpha-dystroglycans. Proteins that
contain LamG domains serve a variety of purposes
including signal transduction via cell-surface steroid
receptors, adhesion, migration and differentiation
through mediation of cell adhesion molecules.
Length = 151
Score = 31.2 bits (71), Expect = 0.51
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 129 LNVVREAHQLVL-VNGKSSGDSGRSTPTGDDPTSAKLFVGGL--SWQTSSEKLREYF 182
++V R + L V+G+ +SG + L++GGL ++ + F
Sbjct: 85 VSVERNGRSVTLSVDGERVVESGSPGGSALLNLDGPLYLGGLPEDLKSPGLPVSPGF 141
Score = 28.5 bits (64), Expect = 3.9
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 94 SNNQLVL-VNGKSSGDSGRSTPTGDDPTSAKLFVGGLNVVREAHQLVLVNG 143
+ + L V+G+ +SG + L++GGL ++ L + G
Sbjct: 90 NGRSVTLSVDGERVVESGSPGGSALLNLDGPLYLGGLPEDLKSPGLPVSPG 140
>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 = 30.1 bits (68), Expect = 0.51
Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 14/63 (22%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFG----------KVEETVMLMDQQTKRHRGFGFVTFE 299
K +++ + DT+ E++++F+Q+G +E + + GF F+
Sbjct: 1 KVLYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSK----DSISGFAVFQ 56
Query: 300 NEE 302
+ E
Sbjct: 57 SHE 59
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 31.9 bits (73), Expect = 0.53
Identities = 17/54 (31%), Positives = 18/54 (33%), Gaps = 2/54 (3%)
Query: 40 GPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQ-QQQQPPQPQPRDLQP 92
PP H APQ P +QP QP Q PQP QP
Sbjct: 111 AQVPPQHAPRPAQPAPQPVQQPAY-QPQPEQPLQQPVSPQVAPAPQPVHSAPQP 163
Score = 31.5 bits (72), Expect = 0.64
Identities = 14/52 (26%), Positives = 17/52 (32%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQP 92
P P Q + PQ P Q A Q Q +Q QP + P
Sbjct: 101 PRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAP 152
Score = 31.2 bits (71), Expect = 0.88
Identities = 14/86 (16%), Positives = 20/86 (23%), Gaps = 8/86 (9%)
Query: 34 GLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPN 93
G V ++ P + A Q QP QQ + PQ +P
Sbjct: 64 GEVRVHRVNHAPANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAP-RP- 121
Query: 94 SNNQLVLVNGKSSGDSGRSTPTGDDP 119
P + P
Sbjct: 122 ------AQPAPQPVQQPAYQPQPEQP 141
Score = 31.2 bits (71), Expect = 0.88
Identities = 13/57 (22%), Positives = 16/57 (28%)
Query: 31 HHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
P P +Q Q + A PQP QQ QP +P
Sbjct: 119 PRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVA 175
Score = 28.8 bits (65), Expect = 5.0
Identities = 12/45 (26%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 43 PPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
P P Q ++ P P +H P P Q Q P P
Sbjct: 136 PQPEQPLQ---QPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAP 177
Score = 28.8 bits (65), Expect = 5.7
Identities = 14/53 (26%), Positives = 18/53 (33%), Gaps = 1/53 (1%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAIL-HQQPTPQPQQQQQQPPQPQPRDLQP 92
P P Q V+ P Q + P PQP QP Q + +P
Sbjct: 121 PAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEP 173
>gnl|CDD|235999 PRK07353, PRK07353, F0F1 ATP synthase subunit B'; Validated.
Length = 140
Score = 30.7 bits (70), Expect = 0.53
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 359 ATQLAALQSQAQAQVQAAAAAVAAQNAAAVA 389
A LA Q++AQA + A + Q AA+A
Sbjct: 89 AEALAEAQAEAQASKEKARREIEQQKQAALA 119
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 29.5 bits (66), Expect = 0.54
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK- 221
++FV L + + + L++ F G V I + +S+G G + F PE E+ +
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERACRM 58
Query: 222 VPIHTLDGKKID 233
+ + L+G++ID
Sbjct: 59 MNGYKLNGREID 70
Score = 29.2 bits (65), Expect = 0.83
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEI 310
+IFV + D + + +K F++ G V + M + + +G G V FE+ EV + C +
Sbjct: 1 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVRFESPEVAERACRM 58
>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 = 29.3 bits (66), Expect = 0.55
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
++VG + D EV+ F ++G + + + + R G+ F+ FE+
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDA 48
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 29.6 bits (66), Expect = 0.57
Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
V +S S E ++ FSQFG VE V+++D + R G GFV F +
Sbjct: 4 VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDR-GRPTGKGFVEFAAK 50
Score = 28.8 bits (64), Expect = 1.0
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
L V LS S+E L + F FG V +++ D R G GF+ FA K L+
Sbjct: 2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDD-RGRPTGKGFVEFAAKPAARKALE 58
>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 = 30.0 bits (68), Expect = 0.60
Identities = 16/71 (22%), Positives = 25/71 (35%), Gaps = 2/71 (2%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
+I V G TS + +K YFS FG++ E D T G + +
Sbjct: 2 PVEIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYG--SPGKPD 59
Query: 309 EIHFHMIKNKK 319
+K +
Sbjct: 60 RAAKAALKAVR 70
>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 = 29.2 bits (65), Expect = 0.62
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF-ENEEVVDHIC 308
K +FV ++ + E ++ F QFGK+E + K+ + + F+ F E + V +
Sbjct: 2 KVLFVRNLANTVTEEILEKAFGQFGKLE--------RVKKLKDYAFIHFDERDGAVKAME 53
Query: 309 EIHFHMIKNKKVECKKAQP 327
E++ ++ + +E A+P
Sbjct: 54 EMNGKELEGENIEIVFAKP 72
Score = 28.4 bits (63), Expect = 1.2
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 12/73 (16%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVP 223
LFV L+ + E L + FG FG + V +KD + FI F E + K ++
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAME-- 53
Query: 224 IHTLDGKKIDPKH 236
++GK+++ ++
Sbjct: 54 --EMNGKELEGEN 64
>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 = 29.4 bits (66), Expect = 0.64
Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFE-NEEVVDHICEI 310
++VG + T+ ++ F FG + E D RGF FV + +E+ I ++
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56
Query: 311 HFHMIKNKKVEC 322
+ + + C
Sbjct: 57 QGFPVHGRPLRC 68
>gnl|CDD|115882 pfam07255, Benyvirus_14KDa, Benyvirus 14KDa protein. This family
consists of several Benyvirus specific 14KDa proteins of
around 125 residues in length. Members of this family
contain 9 conserved cysteine residues. The function of
this family is unknown.
Length = 126
Score = 30.4 bits (68), Expect = 0.64
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 7/37 (18%)
Query: 295 FVTF----ENEEVVDHICEIHFHM--IK-NKKVECKK 324
FV + ++E + C +HFHM +K +K++CK
Sbjct: 43 FVEYRGKGDDECSLKDTCRLHFHMKCVKCCRKLKCKA 79
>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 = 29.5 bits (67), Expect = 0.65
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 283 MDQQTKRHRGFGFVTFENEEVVDHICEIHFH 313
+D + K + G+ F+ F N E + + F+
Sbjct: 35 IDFKNKCNVGYAFINFVNPEYAEKFYKA-FN 64
Score = 29.5 bits (67), Expect = 0.73
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 9/65 (13%)
Query: 173 TSSEKLREYF---GMFGAVTDVLIM-KDPITQRSRGFGFITFAEPETVEKVLKVPIHTLD 228
+ E L + G GA D L + D + + G+ FI F PE EK K +
Sbjct: 10 YTQEMLLQLLDEHGKGGAY-DFLYLPIDFKNKCNVGYAFINFVNPEYAEKFYKA----FN 64
Query: 229 GKKID 233
GKK
Sbjct: 65 GKKWK 69
>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 = 29.7 bits (66), Expect = 0.70
Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQ--QTKRHRGFGFVTFENEE 302
++FVG + ++ + E + FS+ + V+L Q K++RGF F+ +E+ +
Sbjct: 4 RLFVGSIPKNKTKENILEEFSKVTEGLVDVILYHQPDDKKKNRGFCFLEYEDHK 57
>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 = 29.4 bits (66), Expect = 0.72
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 11/80 (13%)
Query: 164 LFVGGLSWQTSSEKLREYF--GMFGAVTDVLI----MKDPITQRS-----RGFGFITFAE 212
+++G LS+ T+ E LR++F +TD I M D +R +GF ++ F
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60
Query: 213 PETVEKVLKVPIHTLDGKKI 232
E + + + L+G+K+
Sbjct: 61 QEATKAAIALSEKILNGRKL 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 = 29.0 bits (65), Expect = 0.73
Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRG---FGFVTFEN 300
+I+VG + D ++++ F ++G++ + + K RG F FV FE+
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDI------ELKNRRGLVPFAFVRFED 47
>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 = 29.1 bits (66), Expect = 0.77
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 162 AKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
KL V L + S + ++E F FGA+ + D + RS G + F K +K
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMK 59
Query: 222 ----VPIHTLDGK 230
VP LDG+
Sbjct: 60 QYNGVP---LDGR 69
>gnl|CDD|182937 PRK11061, PRK11061, fused phosphoenolpyruvate-protein
phosphotransferase PtsP/GAF domain; Provisional.
Length = 748
Score = 31.9 bits (73), Expect = 0.77
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 356 ITPATQLAALQSQAQAQV------QAAAAAVAAQNAAAVA 389
+T ATQLAA+ SQ+Q Q A+ A A+A
Sbjct: 144 VTLATQLAAILSQSQLTALFGQYRQTRIRALPASPGVAIA 183
>gnl|CDD|233366 TIGR01348, PDHac_trf_long, pyruvate dehydrogenase complex
dihydrolipoamide acetyltransferase, long form. This
model describes a subset of pyruvate dehydrogenase
complex dihydrolipoamide acetyltransferase specifically
close by both phylogenetic and per cent identity (UPGMA)
trees. Members of this set include two or three copies
of the lipoyl-binding domain. E. coli AceF is a member
of this model, while mitochondrial and some other
bacterial forms belong to a separate model [Energy
metabolism, Pyruvate dehydrogenase].
Length = 546
Score = 31.8 bits (72), Expect = 0.78
Identities = 13/37 (35%), Positives = 16/37 (43%)
Query: 351 AAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAA 387
PA+ A QS A Q + AAA AA+ A
Sbjct: 195 TPATAPAPASAQPAAQSPAATQPEPAAAPAAAKAQAP 231
>gnl|CDD|217298 pfam02948, Amelogenin, Amelogenin. Amelogenins play a role in
biomineralisation. They seem to regulate the formation
of crystallites during the secretory stage of tooth
enamel development. thought to play a major role in the
structural organisation and mineralisation of developing
enamel. They are found in the extracellular matrix.
Mutations in X-chromosomal amelogenin can cause
Amelogenesis imperfecta.
Length = 174
Score = 30.7 bits (69), Expect = 0.82
Identities = 24/91 (26%), Positives = 31/91 (34%), Gaps = 10/91 (10%)
Query: 9 APDHHEQFNGLIPTMNGLVQIPHHPGLV----HLNGPPPPPHQLVKLNGAPQVNTSPPQN 64
+P +Q P PHH L+ P P H +V + G Q + PP
Sbjct: 54 SPQMPQQQQSAHPK-----LTPHHQLLILPPQQPMMPVPGHHPMVPMTGQ-QPHLQPPAQ 107
Query: 65 AILHQQPTPQPQQQQQQPPQPQPRDLQPNSN 95
L PQ QQ QP + QP
Sbjct: 108 HPLQPTYGQNPQPQQPTHTQPPVQPQQPADP 138
>gnl|CDD|151621 pfam11179, DUF2967, Protein of unknown function (DUF2967). This
family of proteins with unknown function appears to be
restricted to Drosophila.
Length = 284
Score = 31.1 bits (69), Expect = 0.94
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 56 QVNTSPP--QNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRST 113
++N++PP ++A Q Q+ Q P PQ L P+S SS SG S
Sbjct: 163 KINSAPPTMKDANFFGSSGKQKQRPSQNIPPPQQHQLSPSSQAAAQQRKYSSSSSSGSSD 222
Query: 114 PTGDDPTSA 122
D T+A
Sbjct: 223 RCLRDATAA 231
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 31.4 bits (72), Expect = 1.0
Identities = 12/49 (24%), Positives = 12/49 (24%), Gaps = 7/49 (14%)
Query: 348 LRM-------AAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVA 389
LRM P P P A S AA A A
Sbjct: 354 LRMLAFHPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPP 402
Score = 29.4 bits (67), Expect = 3.4
Identities = 10/53 (18%), Positives = 13/53 (24%)
Query: 42 PPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNS 94
P P Q + Q +P Q P P P + S
Sbjct: 368 PEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTS 420
Score = 29.1 bits (66), Expect = 4.4
Identities = 14/58 (24%), Positives = 18/58 (31%), Gaps = 3/58 (5%)
Query: 33 PGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDL 90
P + + P Q AP +PPQ + P PQQ P L
Sbjct: 368 PEVPPQSAAPAASAQA---TAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQL 422
Score = 28.7 bits (65), Expect = 7.0
Identities = 15/82 (18%), Positives = 22/82 (26%), Gaps = 1/82 (1%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVL 100
P P A T+ P A+ Q P P Q L ++ L
Sbjct: 366 PEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAA 425
Query: 101 VNGKSSGDSGRSTPTGDDPTSA 122
G + +P +A
Sbjct: 426 RQQLQR-AQGATKAKKSEPAAA 446
>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 = 29.1 bits (66), Expect = 1.0
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 274 GKVEETVMLMDQQ------TKRHRGFGFVTFENEE 302
K+++ ++ D + + +G+GFV F N E
Sbjct: 34 PKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHE 68
Score = 28.7 bits (65), Expect = 1.5
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 15/75 (20%)
Query: 163 KLFVGGLSWQTSSEKLRE----YFGMF-----GAVTDVLIMKD-----PITQ-RSRGFGF 207
+L + L +KL+E + V IM+D P + +S+G+GF
Sbjct: 2 RLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGF 61
Query: 208 ITFAEPETVEKVLKV 222
+ F E K L+
Sbjct: 62 VEFTNHEHALKALRA 76
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I. All proteins in this family for
which functions are known are DNA polymerases Many also
have an exonuclease motif. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 887
Score = 31.2 bits (71), Expect = 1.0
Identities = 8/42 (19%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 256 GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVT 297
G+S+ + E ++ YF+++ V++ + ++ ++ G+V
Sbjct: 737 GISRKEAKEFIERYFARYPGVKDYIENTVEEARKK---GYVE 775
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 28.7 bits (64), Expect = 1.1
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 7/61 (11%)
Query: 161 SAKLFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQ-RSRGFGFITFAEPETVEKV 219
S L V LS+ S + L+E F ++ P R +G+ F+ F E ++
Sbjct: 1 SKVLVVNNLSYSASEDSLQEVF------EKATSIRIPQNNGRPKGYAFVEFESAEDAKEA 54
Query: 220 L 220
L
Sbjct: 55 L 55
>gnl|CDD|237000 PRK11855, PRK11855, dihydrolipoamide acetyltransferase; Reviewed.
Length = 547
Score = 31.3 bits (72), Expect = 1.1
Identities = 17/39 (43%), Positives = 18/39 (46%)
Query: 351 AAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVA 389
AA AP A AA + A A A A A AA AAA
Sbjct: 195 AAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAP 233
Score = 29.0 bits (66), Expect = 5.2
Identities = 17/50 (34%), Positives = 20/50 (40%)
Query: 341 VILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVAN 390
V++ AA A A AA + AAAA AA AAA A
Sbjct: 190 VVIEVAAAAPAAAAAPAAAAPAAAAAAAPAPAPAAAAAPAAAAPAAAAAP 239
>gnl|CDD|221084 pfam11336, DUF3138, Protein of unknown function (DUF3138). This
family of proteins with unknown function appear to be
restricted to Proteobacteria.
Length = 514
Score = 31.0 bits (70), Expect = 1.2
Identities = 22/51 (43%), Positives = 29/51 (56%), Gaps = 8/51 (15%)
Query: 341 VILGPL-GLRMAAPAPITPATQLAALQSQA---QAQVQAAAAAVAAQNAAA 387
+I G L G AA + A+Q+ ALQ+Q Q QV AA+AA+ AAA
Sbjct: 9 LIAGALPGAAAAA----SDASQIKALQAQLTALQQQVNELRAALAAKPAAA 55
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM3
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 73
Score = 28.4 bits (63), Expect = 1.2
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDH-ICEI 310
++ GG++ + + ++ FS FG++ E + + +G+ F+ F E H I +
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSV 56
Query: 311 HFHMIKNKKVEC 322
+ I+ V+C
Sbjct: 57 NGTTIEGHVVKC 68
Score = 28.1 bits (62), Expect = 2.1
Identities = 14/67 (20%), Positives = 35/67 (52%), Gaps = 7/67 (10%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPET-VEKVLKV 222
++ GG++ + + +R+ F FG + ++ + + +G+ FI F+ E+ ++ V
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSV 56
Query: 223 PIHTLDG 229
T++G
Sbjct: 57 NGTTIEG 63
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 28.8 bits (65), Expect = 1.2
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 3/61 (4%)
Query: 270 FSQFGKVEETVMLMDQQTKRHR--GFGFVTFENEEVVDHICEI-HFHMIKNKKVECKKAQ 326
F Q K + + + K + F FVTF +EE EI K + + + A+
Sbjct: 19 FKQLKKFLKKQLFKPHKIKLLKRQDFAFVTFRSEEERQKALEILDGFKWKGRVLSARLAK 78
Query: 327 P 327
P
Sbjct: 79 P 79
>gnl|CDD|216447 pfam01346, FKBP_N, Domain amino terminal to FKBP-type
peptidyl-prolyl isomerase. This family is only found at
the amino terminus of pfam00254. This domain is of
unknown function.
Length = 124
Score = 29.5 bits (67), Expect = 1.2
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 360 TQLAALQSQAQAQVQAAAAAVAAQNAAA 387
L A Q + QA+ QA A A +N AA
Sbjct: 72 KALQAFQKKLQAKQQAKAEKKAEENKAA 99
>gnl|CDD|239745 cd03776, MATH_TRAF6, Tumor Necrosis Factor Receptor
(TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily,
TRAF domain, C-terminal MATH subdomain; composed of
proteins with similarity to human TRAF6, including the
Drosophila protein DTRAF2. TRAF molecules serve as
adapter proteins that link TNFRs and downstream kinase
cascades resulting in the activation of transcription
factors and the regulation of cell survival,
proliferation and stress responses. TRAF6 is the most
divergent in its TRAF domain among the mammalian TRAFs.
In addition to mediating TNFR family signaling, it is
also an essential signaling molecule of the
interleukin-1/Toll-like receptor superfamily. Whereas
other TRAF molecules display similar and overlapping
TNFR-binding specificities, TRAF6 binds completely
different sites on receptors such as CD40 and RANK.
TRAF6 serves as a molecular bridge between innate and
adaptive immunity and plays a central role in
osteoimmunology. DTRAF2, as an activator of nuclear
factor-kappaB, plays a pivotal role in Drosophila
development and innate immunity. TRAF6 contains a RING
finger domain, five zinc finger domains, and a TRAF
domain. The TRAF domain can be divided into a more
divergent N-terminal alpha helical region (TRAF-N), and
a highly conserved C-terminal MATH subdomain (TRAF-C)
with an eight-stranded beta-sandwich structure. TRAF-N
mediates trimerization while TRAF-C interacts with
receptors.
Length = 147
Score = 30.0 bits (68), Expect = 1.2
Identities = 10/30 (33%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 190 DVLIMKDPITQRS-RGFGFITFAEPETVEK 218
++L + P T R+ +GFG++ FA E + +
Sbjct: 102 ELLAFQRPTTDRNPKGFGYVEFAHIEDLLQ 131
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 30.9 bits (70), Expect = 1.3
Identities = 13/82 (15%), Positives = 21/82 (25%), Gaps = 6/82 (7%)
Query: 39 NGPPPPPHQLVKLNGAPQV--NTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNS-- 94
P P A Q Q+ P P P P +Q
Sbjct: 59 VAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALPAGPAGPTIQTEPGQ 118
Query: 95 --NNQLVLVNGKSSGDSGRSTP 114
Q+ ++ ++ +S P
Sbjct: 119 LYPVQVPVMVTQNPANSPLDQP 140
Score = 30.9 bits (70), Expect = 1.3
Identities = 20/94 (21%), Positives = 28/94 (29%), Gaps = 9/94 (9%)
Query: 15 QFNGLIPTMNGLVQIPHHPGLVHLNGPPP---------PPHQLVKLNGAPQVNTSPPQNA 65
I T G + P +V N QL + GAP P Q
Sbjct: 107 PAGPTIQTEPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQ 166
Query: 66 ILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLV 99
+ Q QQQ PQ D + ++ +
Sbjct: 167 SAQKNDESQLQQQPNGETPPQQTDGAGDDESEAL 200
Score = 30.5 bits (69), Expect = 1.7
Identities = 9/84 (10%), Positives = 15/84 (17%)
Query: 39 NGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQL 98
+ P P + +L L Q P P +
Sbjct: 50 DPSPQAPPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALPAGPAG 109
Query: 99 VLVNGKSSGDSGRSTPTGDDPTSA 122
+ + P A
Sbjct: 110 PTIQTEPGQLYPVQVPVMVTQNPA 133
Score = 28.6 bits (64), Expect = 6.7
Identities = 18/96 (18%), Positives = 29/96 (30%), Gaps = 8/96 (8%)
Query: 61 PPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSG--RSTPTGDD 118
P A PQP Q Q L Q G + + + P G
Sbjct: 51 PSPQAPPPVAQLPQPLPQPPPTQALQA--LPAGDQQQHNTPTGSPAANPPATFALPAGPA 108
Query: 119 PTSAKLFVGGLNVVREAHQLVLVNGKSSGDSGRSTP 154
+ + G L V Q+ ++ ++ +S P
Sbjct: 109 GPTIQTEPGQLYPV----QVPVMVTQNPANSPLDQP 140
Score = 27.8 bits (62), Expect = 9.9
Identities = 34/161 (21%), Positives = 43/161 (26%), Gaps = 9/161 (5%)
Query: 8 GAPDHHEQFNGLIPTMNGLVQ--IPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNA 65
P N +P P + P QL P + T P N+
Sbjct: 80 AGDQQQHNTPTGSPAANPPATFALPAGPAGPTIQ---TEPGQLYP-VQVPVMVTQNPANS 135
Query: 66 ILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLVNGKSSG--DSGRSTPTGDDPTSAK 123
L QP Q QQ Q P Q S Q N +S TP +
Sbjct: 136 PL-DQPAQQRALQQLQQRYGAPASGQLPSQQQSAQKNDESQLQQQPNGETPPQQTDGAGD 194
Query: 124 LFVGGLNVVREAHQLVLVNGKSSGDSGRSTPTGDDPTSAKL 164
L +REA + K + G AK
Sbjct: 195 DESEALVRLREADGTLEQRIKGAEGGGAMKVLKQPKKQAKS 235
>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 = 28.8 bits (64), Expect = 1.4
Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 24/100 (24%)
Query: 168 GLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTL 227
GL + S E++ ++F V + + + RS G F+ FA E EK LK
Sbjct: 8 GLPFGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALK------ 61
Query: 228 DGKKIDPKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEVK 267
K++ +IG+R +IF +S EV+
Sbjct: 62 ------------KHKERIGHRYIEIF------KSSRAEVR 83
>gnl|CDD|236544 PRK09506, mrcB, bifunctional glycosyl transferase/transpeptidase;
Reviewed.
Length = 830
Score = 30.9 bits (70), Expect = 1.4
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 57 VNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSN 95
V T PQ ++ Q Q Q QQ PQ QP + Q +S+
Sbjct: 782 VWTDDPQ-SLCQQSEMQQQPSQPQQQPQQQPAE-QKDSD 818
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 30.8 bits (70), Expect = 1.5
Identities = 27/107 (25%), Positives = 40/107 (37%), Gaps = 6/107 (5%)
Query: 62 PQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLV-LVNGKSSGDSGRSTPTGDDPT 120
Q A+ + + +Q + + Q + L +L ++ G S G S G DP
Sbjct: 103 IQQAVQSETQELTKEIEQLKSERQQLQGLIDQLQRRLAGVLTGPSGGGSDLPVGLGLDPG 162
Query: 121 SAKLFVGGLNVV----REAHQLVLVNGKSSGDSGRSTPTGDDPTSAK 163
F GG VV ++A NG S S S PT D +
Sbjct: 163 GGAQFEGGGGVVWVEPQDA-LPTDRNGNSGAPSKFSFPTSFDNALDR 208
>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 = 28.1 bits (62), Expect = 1.6
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF-ENEEVVDHICEI 310
++VG +S+D + + FSQ G + M+MD T + + FV F E+ + +
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59
Query: 311 HFHMIKNKKVE 321
+ I K+V+
Sbjct: 60 NGRKIMGKEVK 70
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM2 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 28.4 bits (63), Expect = 1.8
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
L V L S+E L E F MFG V +++ D R G G + FA + K L
Sbjct: 2 LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDD-RGRPTGKGIVEFAGKPSARKAL 57
Score = 28.0 bits (62), Expect = 2.0
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENE 301
V + Q S E ++ FS FG+VE V+++D + R G G V F +
Sbjct: 4 VKNLPQFVSNELLEEAFSMFGQVERAVVIVDDR-GRPTGKGIVEFAGK 50
>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 = 28.4 bits (63), Expect = 1.9
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 272 QFGKVEETVMLMDQQTKRHRGFGFVTFEN----EEVVDHI 307
+FG+VEE +L+ +T++H G V F + ++ V H+
Sbjct: 25 KFGEVEEVEILLHPKTRKHLGLARVLFTSTRGAKDTVKHL 64
>gnl|CDD|241504 cd13350, PH-GRAM1_TBC1D8B, TBC1 domain family member 8B (TBC1D8B)
Pleckstrin Homology-Glucosyltransferases, Rab-like
GTPase activators and Myotubularins (PH-GRAM) domain,
repeat 1. TBC1D8B may act as a GTPase-activating
protein for Rab family protein(s). TBC1D8B contains an
N-terminal PH-GRAM domain and a C-terminal
Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This
cd contains the first repeat of the PH-GRAM domain. The
GRAM domain is found in glucosyltransferases,
myotubularins and other putative membrane-associated
proteins. The GRAM domain is part of a larger motif with
a pleckstrin homology (PH) domain fold.
Length = 135
Score = 29.0 bits (65), Expect = 2.0
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 269 YFSQFGKVEETVMLMDQQTKR--HRGFGFVTFENEEVV 304
YFS F + ET +LM+Q R F TFEN+ V+
Sbjct: 98 YFSMFLHINETFLLMEQLANYAVRRLFDKETFENDPVL 135
>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 = 28.2 bits (63), Expect = 2.2
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 2/57 (3%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL 220
++V + Q + E+L F G V D + DP F FI F + E L
Sbjct: 5 VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDP--NSVLRFAFIEFTDEEGARAAL 59
Score = 27.4 bits (61), Expect = 3.1
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 248 RTKKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
RT ++V + Q + E++ A FS G+V + + D + F F+ F +EE
Sbjct: 3 RT--VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLR--FAFIEFTDEE 53
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 30.1 bits (68), Expect = 2.2
Identities = 11/55 (20%), Positives = 12/55 (21%), Gaps = 2/55 (3%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQ-QQPPQPQPRDLQPNS 94
P P AP V +P P P PP S
Sbjct: 392 PTPAAPAAPPPAAAPPV-PPAAPARPAAARPAPAPAPPAAAAPPARSADPAAAAS 445
>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 = 28.1 bits (62), Expect = 2.2
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYFSQF--GKVEETVMLMDQQTKRHRGFGFVTFEN 300
++FVGG+ + EE+ A + G ++ V ++RGF FV +E+
Sbjct: 4 RLFVGGIPKTKKREEILAEMKKVTDGVLDVIVYPSAADKAKNRGFAFVEYES 55
>gnl|CDD|241185 cd12741, RRM2_Fusilli, RNA recognition motif 2 in Drosophila
RNA-binding protein Fusilli and similar proteins. This
subgroup corresponds to the RRM2 of RNA-binding protein
Fusilli which is encoded by Drosophila fusilli (fus)
gene. Loss of Fusilli activity causes lethality during
embryogenesis in flies. Drosophila Fusilli can regulate
endogenous fibroblast growth factor receptor 2 (FGFR2)
splicing and functions as a splicing factor. Fusilli
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), an N-terminal domain with
unknown function and a C-terminal domain particularly
rich in alanine, glutamine, and serine. .
Length = 100
Score = 28.3 bits (63), Expect = 2.3
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 7/73 (9%)
Query: 256 GVSQDTSAEEVKAYFSQFGKV-------EETVMLMDQQTKRHRGFGFVTFENEEVVDHIC 308
G+ D +A++V +F+ E V+ + + R G FV F EE
Sbjct: 24 GLPYDCTAKQVLEFFTTGDTPPCHVLDGNEGVLFVKKPDGRATGDAFVLFATEEDAPKAL 83
Query: 309 EIHFHMIKNKKVE 321
H I ++ +E
Sbjct: 84 GKHRESIGSRYIE 96
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 28.0 bits (63), Expect = 2.3
Identities = 5/25 (20%), Positives = 12/25 (48%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKV 276
I++ G+ D + + + F G +
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGII 25
>gnl|CDD|183140 PRK11447, PRK11447, cellulose synthase subunit BcsC; Provisional.
Length = 1157
Score = 30.1 bits (68), Expect = 2.3
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 349 RMAAPAPITPATQLA----ALQSQAQAQV--QAAAAAVAAQNAAAVANYGKIF 395
R++ AP + A + + L + Q QA A + A+A+Y K+F
Sbjct: 87 RLSQLAPDSNAYRSSRTTMLLSTPEGRQALQQARLLATTGRTEEALASYDKLF 139
>gnl|CDD|234683 PRK00191, tatA, twin arginine translocase protein A; Provisional.
Length = 84
Score = 28.0 bits (62), Expect = 2.5
Identities = 11/30 (36%), Positives = 12/30 (40%)
Query: 69 QQPTPQPQQQQQQPPQPQPRDLQPNSNNQL 98
QQ PQ Q Q PQP Q Q+
Sbjct: 55 QQQQPQQQIAPNQIEAPQPNFQQHYQGQQV 84
Score = 27.2 bits (60), Expect = 5.0
Identities = 11/31 (35%), Positives = 12/31 (38%), Gaps = 1/31 (3%)
Query: 55 PQVNTSPPQNAILHQQ-PTPQPQQQQQQPPQ 84
P+ PQ I Q PQP QQ Q
Sbjct: 52 PEQQQQQPQQQIAPNQIEAPQPNFQQHYQGQ 82
>gnl|CDD|236154 PRK08119, PRK08119, flagellar motor switch protein; Validated.
Length = 382
Score = 29.8 bits (68), Expect = 2.7
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 43 PPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQP-QPRDLQP 92
+ + +P + Q A +Q Q Q+Q+P + QP ++QP
Sbjct: 231 EEEVEEEEAQASPAAEPATAQAAPAPKQEQQQAPPQRQEPEKEAQPVNVQP 281
Score = 29.4 bits (67), Expect = 2.9
Identities = 10/53 (18%), Positives = 14/53 (26%), Gaps = 1/53 (1%)
Query: 40 GPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQP 92
Q +P Q P Q +++ QP QP Q
Sbjct: 235 EEEEAQASPAAEPATAQAAPAPKQEQQ-QAPPQRQEPEKEAQPVNVQPAQFQS 286
Score = 28.3 bits (64), Expect = 8.4
Identities = 15/49 (30%), Positives = 18/49 (36%), Gaps = 4/49 (8%)
Query: 53 GAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQLVLV 101
+ SP Q Q+QQQ PPQ Q +P Q V V
Sbjct: 235 EEEEAQASPAAEPATAQAAPAPKQEQQQAPPQRQ----EPEKEAQPVNV 279
>gnl|CDD|234994 PRK01973, PRK01973, septum formation inhibitor; Reviewed.
Length = 271
Score = 29.7 bits (67), Expect = 2.7
Identities = 14/41 (34%), Positives = 14/41 (34%), Gaps = 2/41 (4%)
Query: 349 RMAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVA 389
AA PA AA A A AAAA A A
Sbjct: 118 AAAAAEAAAPAAAAAAEA--AAAAPAAAAAPEPPPAPAPEA 156
>gnl|CDD|222449 pfam13908, Shisa, Wnt and FGF inhibitory regulator. Shisa is a
transcription factor-type molecule that physically
interacts with immature forms of the Wnt receptor
Frizzled and the FGF receptor within the endoplasmic
reticulum to inhibit their post-translational maturation
and trafficking to the cell surface.
Length = 177
Score = 29.0 bits (65), Expect = 2.7
Identities = 14/55 (25%), Positives = 18/55 (32%), Gaps = 1/55 (1%)
Query: 44 PPHQLVKLNGAPQVNTSPPQNAILHQQPT-PQPQQQQQQPPQPQPRDLQPNSNNQ 97
P + V + P P+ P PQ Q P PQP P + Q
Sbjct: 108 RPQRPVMTRATSTTVQTTPLPQPPSTAPSYPGPQYQGYHPMPPQPGMPAPPYSLQ 162
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response element
(IGFRE). Moreover, PSF functions as a transcriptional
repressor interacting with Sin3A and mediating silencing
through the recruitment of histone deacetylases (HDACs)
to the DNA binding domain (DBD) of nuclear hormone
receptors. PSF is an essential pre-mRNA splicing factor
and is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. PSF
forms a heterodimer with the nuclear protein p54nrb,
also known as non-POU domain-containing octamer-binding
protein (NonO). The PSF/p54nrb complex displays a
variety of functions, such as DNA recombination and RNA
synthesis, processing, and transport. PSF contains two
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which are responsible for interactions with
RNA and for the localization of the protein in speckles.
It also contains an N-terminal region rich in proline,
glycine, and glutamine residues, which may play a role
in interactions recruiting other molecules. .
Length = 80
Score = 27.8 bits (61), Expect = 2.8
Identities = 20/58 (34%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 164 LFVGGLSWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
L V LS S+E L E F FG V +++ D RS G G + FA K +
Sbjct: 2 LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDD-RGRSTGKGIVEFASKPAARKAFE 58
Score = 27.4 bits (60), Expect = 3.3
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 254 VGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTF 298
V +S S E ++ FSQFG VE V+++D + R G G V F
Sbjct: 4 VRNLSPYVSNELLEEAFSQFGPVERAVVIVDDR-GRSTGKGIVEF 47
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 27.4 bits (61), Expect = 2.8
Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 251 KIFVGGVSQDTSAEEVKAYF-SQFGKVEETVMLMDQQTKRHRGFGFVTFENEE 302
K+ V + +D + +++ YF SQ G + + V+L + + G +TF+
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPI-KRVLLSYNEGGKSTGIANITFKRAG 52
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 29.9 bits (68), Expect = 2.9
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 69 QQPTPQPQQQQQQPPQPQPRDLQP 92
QP Q QQ Q Q Q + Q
Sbjct: 634 GQPGQQGQQGQGQQQGQQGQGGQG 657
Score = 29.5 bits (67), Expect = 3.5
Identities = 9/23 (39%), Positives = 9/23 (39%)
Query: 69 QQPTPQPQQQQQQPPQPQPRDLQ 91
QQ Q Q QQ Q Q L
Sbjct: 641 QQGQGQQQGQQGQGGQGGQGSLA 663
Score = 28.3 bits (64), Expect = 7.9
Identities = 10/31 (32%), Positives = 12/31 (38%)
Query: 67 LHQQPTPQPQQQQQQPPQPQPRDLQPNSNNQ 97
L +Q Q +QQ Q Q QP Q
Sbjct: 611 LQEQFNAQRGEQQGQQGQGGQGQGQPGQQGQ 641
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 30.0 bits (68), Expect = 3.0
Identities = 13/48 (27%), Positives = 14/48 (29%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPR 88
P P N SPP A QP P P + P P
Sbjct: 436 APAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPA 483
>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 = 27.7 bits (61), Expect = 3.0
Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 16/84 (19%)
Query: 163 KLFVGGLSWQTSSEKLREYFGMFG-AVTDVLIMKDPITQRSRGFGFITFAEPETVEKVL- 220
KL++G LS ++E LR+ FG +T +++K G+ F+ + + + +
Sbjct: 3 KLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKS-------GYAFVDYPDQNWAIRAIE 55
Query: 221 ----KVPIHTLDGKKIDPKHATPK 240
KV +H GK ++ ++ PK
Sbjct: 56 TLSGKVELH---GKVMEVDYSVPK 76
>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 = 27.2 bits (60), Expect = 3.1
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFEN----EEVVDHI 307
I+V G ++ + E ++ F Q +E + D + + + F+ F +DHI
Sbjct: 1 IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60
>gnl|CDD|184363 PRK13879, PRK13879, conjugal transfer protein TrbJ; Provisional.
Length = 253
Score = 29.3 bits (66), Expect = 3.2
Identities = 16/33 (48%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 359 ATQLAALQSQAQ-AQVQAAAAAVAAQNAAAVAN 390
A L LQS AQ AQ Q A A Q A+ AN
Sbjct: 171 ARTLQRLQSAAQGAQGQMQAIQYANQLASQQAN 203
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM1 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 87
Score = 27.7 bits (61), Expect = 3.2
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 249 TKKIFVGGVSQDTSAEEVKAYFSQF-GKVEETVMLMDQQTKRHRGFGFVTF 298
+K I + G+ + + +++ F G V LM ++T RGF FV F
Sbjct: 5 SKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEF 55
>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 = 27.4 bits (61), Expect = 3.4
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 252 IFVGGVSQDTSAEEVKAYFSQFGKVEETVML 282
++VG + ++ E + +F ++G+VE +L
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKIL 32
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 29.3 bits (66), Expect = 3.4
Identities = 12/65 (18%), Positives = 15/65 (23%), Gaps = 5/65 (7%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAI--LHQQPTPQPQQQQQQP---PQPQPRDLQPNSN 95
PP P P + + P P QQ P P P
Sbjct: 212 LPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTPPSASATPAPI 271
Query: 96 NQLVL 100
+ L
Sbjct: 272 GGITL 276
Score = 28.1 bits (63), Expect = 8.3
Identities = 11/72 (15%), Positives = 15/72 (20%), Gaps = 11/72 (15%)
Query: 21 PTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQ 80
P+ P P PPP P PP + T +P
Sbjct: 216 PSSFQSDTPPPSPESPTNPSPPPGPAA-----------PPPPPVQQVPPLSTAKPTPPSA 264
Query: 81 QPPQPQPRDLQP 92
+
Sbjct: 265 SATPAPIGGITL 276
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 29.6 bits (66), Expect = 3.5
Identities = 19/89 (21%), Positives = 22/89 (24%), Gaps = 5/89 (5%)
Query: 5 ALGGAPDHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQN 64
L P P PG V P + A Q +
Sbjct: 291 MLPNQMQQMPGGGQGGPGQPMGPP-PQRPGAV----PQGGQAVQQGVMSAGQQQLKQMKL 345
Query: 65 AILHQQPTPQPQQQQQQPPQPQPRDLQPN 93
+ Q Q QQQQQ P Q N
Sbjct: 346 RNMRGQQQTQQQQQQQGGNHPAAHQQQMN 374
>gnl|CDD|219324 pfam07183, DUF1403, Protein of unknown function (DUF1403). This
family consists of several hypothetical bacterial
proteins of around 320 residues in length. Members of
this family are mainly found in Rhizobium and
Agrobacterium species. The function of this family is
unknown.
Length = 308
Score = 29.3 bits (66), Expect = 3.6
Identities = 16/44 (36%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 339 KRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAA 382
R + LGL A A + P A Q+ A V AAA AA
Sbjct: 119 LRALADLLGLADDALAAL-PDQVDALAQAGRGAPVLAAAELAAA 161
>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 = 27.7 bits (61), Expect = 3.7
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 272 QFGKVEETVMLMDQQTKRHRGFGFVTFE 299
++G+VEE +L + + K+H G V F
Sbjct: 25 KYGEVEEVEILYNPKNKKHLGIAKVVFA 52
>gnl|CDD|165527 PHA03269, PHA03269, envelope glycoprotein C; Provisional.
Length = 566
Score = 29.3 bits (65), Expect = 3.7
Identities = 20/73 (27%), Positives = 27/73 (36%), Gaps = 4/73 (5%)
Query: 17 NGLIPTMNGLVQIP--HHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAI--LHQQPT 72
N +I +N + IP H P P PHQ P V + + L Q PT
Sbjct: 16 NLIIANLNTNIPIPELHTSAATQKPDPAPAPHQAASRAPDPAVAPTSAASRKPDLAQAPT 75
Query: 73 PQPQQQQQQPPQP 85
P ++ P P
Sbjct: 76 PAASEKFDPAPAP 88
>gnl|CDD|221198 pfam11740, KfrA_N, Plasmid replication region DNA-binding N-term.
The broad host-range plasmid RK2 is able to replicate in
and be inherited in a stable manner in diverse
Gram-negative bacterial species. It encodes a number of
co-ordinately regulated operons including a central
control korF1 operon that represses the kfrA operon. The
KfrA polypeptide is a site-specific DNA-binding protein
whose operator overlaps the kfrA promoter. The
N-terminus, containing an helix-turn-helix motif, is
essential for function. Downstream from this family is
an extended coiled-coil domain containing a heptad
repeat segment which is probably responsible for
formation of multimers, and may provide an example of a
bridge to host structures required for plasmid
partitioning.
Length = 120
Score = 28.0 bits (63), Expect = 3.9
Identities = 14/44 (31%), Positives = 17/44 (38%)
Query: 346 LGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVA 389
L +A AP P AL A +AA + AAA A
Sbjct: 48 LRAALAPAAPELPDALSEALAELVAALWEAAQEEAEERLAAARA 91
Score = 27.3 bits (61), Expect = 6.9
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 361 QLAALQSQAQAQVQAAAAAVAAQNAAA 387
+LAA ++ A+A+ A +A A A
Sbjct: 85 RLAAARAAAEAERAELEAELAEAAAEA 111
>gnl|CDD|199823 cd10498, MH2_SMAD_4, C-terminal Mad Homology 2 (MH2) domain in
SMAD4. The MH2 domain is located at the C-terminus of
the SMAD (small mothers against decapentaplegic) family
of proteins, which are signal transducers and
transcriptional modulators that mediate multiple
signaling pathways. The MH2 domain is responsible for
type I receptor interaction, phosphorylation-triggered
homo- and hetero-oligomerization, and transactivation.
It is negatively regulated by the N-terminal MH1 domain.
SMAD4, which belongs to the Dwarfin family of proteins,
is involved in many cell functions such as
differentiation, apoptosis, gastrulation, embryonic
development and the cell cycle. SMAD4 binds receptor
regulated SMADs (R-SMADs) such as SMAD1 or SMAD2, and
forms an oligomeric complex that binds to DNA and serves
as a transcription factor. SMAD4 is often mutated in
several cancers, such as multiploid colorectal cancer,
cervical cancer and pancreatic carcinoma, as well as in
juvenile polyposis syndrome.
Length = 222
Score = 29.0 bits (65), Expect = 4.1
Identities = 14/25 (56%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 368 QAQAQVQAAAAAVAAQNAAAVANYG 392
Q Q Q A AA AAQ AAAVA
Sbjct: 127 QMQQQAATAQAAAAAQ-AAAVAGNI 150
>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 = 27.5 bits (62), Expect = 4.1
Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 19/92 (20%)
Query: 250 KKIFVGGVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHR------------GFGFVT 297
++V G+ D + EE FS+ G ++E D +T + + G
Sbjct: 2 TNVYVSGLPLDITVEEFVEVFSKCGIIKE-----DPETGKPKIKLYRDENGNLKGDALCC 56
Query: 298 FENEEVVDHICEI--HFHMIKNKKVECKKAQP 327
+ EE V+ ++ + + K++ ++A+
Sbjct: 57 YLKEESVELAIQLLDGTEIGRGYKMKVERAKF 88
>gnl|CDD|218146 pfam04554, Extensin_2, Extensin-like region.
Length = 57
Score = 26.7 bits (59), Expect = 4.2
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 30 PHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTP 73
P P + PPPP V + P V SPP +++ P P
Sbjct: 15 PPPP--YYYKSPPPPVKSPVYKSPPPPVYKSPPPPKYVYKSPPP 56
>gnl|CDD|241180 cd12736, RRM1_ESRP1, RNA recognition motif 1 in epithelial splicing
regulatory protein 1 (ESRP1) and similar proteins. This
subgroup corresponds to the RRM1 of ESRP1, also termed
RNA-binding motif protein 35A (RBM35A), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (p120-Catenin) and
ENAH (hMena) splicing. It enhances epithelial-specific
exons of CD44 and ENAH, silences mesenchymal exons of
CTNND1, or both within FGFR2. Additional research
indicated that ESRP1 functions as a tumor suppressor in
colon cancer cells. It may be involved in
posttranscriptional regulation of various genes by
exerting a differential effect on protein translation
via 5' untranslated regions (UTRs) of mRNAs. ESRP1
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 85
Score = 27.3 bits (60), Expect = 4.2
Identities = 17/70 (24%), Positives = 29/70 (41%)
Query: 256 GVSQDTSAEEVKAYFSQFGKVEETVMLMDQQTKRHRGFGFVTFENEEVVDHICEIHFHMI 315
G+ +S +++ +F + L R G V F +EE D + H H +
Sbjct: 11 GLPWQSSDQDIARFFKGLNIAKGGAALCLNAQGRRNGEALVRFVSEEHRDLALQRHKHHM 70
Query: 316 KNKKVECKKA 325
N+ +E KA
Sbjct: 71 GNRYIEVYKA 80
>gnl|CDD|224256 COG1337, COG1337, CRISPR system related protein, RAMP superfamily
[Defense mechanisms].
Length = 249
Score = 28.9 bits (65), Expect = 4.3
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 291 RGFGFVTFENEEVVDHICEIHFHMIKNKKVECKKAQPKEAV 331
RG+G V FE +VV E + +N+ E Q E +
Sbjct: 202 RGYGKVKFEIGKVVSRPDEYY-GGNENEPAEKDLKQEVEEL 241
>gnl|CDD|225468 COG2916, Hns, DNA-binding protein H-NS [General function prediction
only].
Length = 128
Score = 27.8 bits (62), Expect = 4.5
Identities = 11/47 (23%), Positives = 17/47 (36%)
Query: 350 MAAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGKIFE 396
MA + ++ + Q + Q AA A+ YG I E
Sbjct: 11 MARETYLELLEEMLEKEEQVVQERQEEEAAAIAEIEERQEKYGTIRE 57
>gnl|CDD|227361 COG5028, COG5028, Vesicle coat complex COPII, subunit
SEC24/subunit SFB2/subunit SFB3 [Intracellular
trafficking and secretion].
Length = 861
Score = 29.4 bits (66), Expect = 4.6
Identities = 12/57 (21%), Positives = 15/57 (26%), Gaps = 8/57 (14%)
Query: 28 QIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQ 84
Q H G P N S Q + P QQ ++Q Q
Sbjct: 13 QSQVHTGAASSKKSARPH--------RAYANFSAGQMGMPPYTTPPLQQQSRRQIDQ 61
>gnl|CDD|106978 PHA00670, PHA00670, hypothetical protein.
Length = 540
Score = 29.0 bits (65), Expect = 4.6
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 351 AAPAPITPATQLAALQS----QAQAQVQAAAAAVAAQNAAA 387
P I P Q+ +++ Q QA QAA A AA A A
Sbjct: 488 VPPTLIVPKEQVQSIRKQRAQQQQAAQQAAIAEAAANAAKA 528
>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 = 26.6 bits (59), Expect = 5.0
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 9/60 (15%)
Query: 163 KLFVGGL-SWQTSSEKLREYFGMFGAVTDVLIMKDPITQRSRGFGFITFAEPETVEKVLK 221
+LF+G L + + S E L F +G + +++ +GF+ F PE+ +
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVL--------KNAYGFVQFDSPESCANAIN 52
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 28.9 bits (65), Expect = 5.1
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 351 AAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVA 389
PA A AA +QA A A AAA AA +A A
Sbjct: 379 KTPARPEAAAPAAAPVAQA-AAAPAPAAAPAAAASAPAA 416
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 27.2 bits (61), Expect = 5.2
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 364 ALQSQAQAQVQAAAAAVAAQNAAAVA 389
A++ A A V AAAAA AA AAA
Sbjct: 53 AIKKAAAAPVAAAAAAAAAAAAAAAE 78
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 29.0 bits (65), Expect = 5.4
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 360 TQLAALQSQAQAQVQAAAAAVAAQNAAA 387
T+L LQ +A + QA A+AA+ A
Sbjct: 250 TRLDELQQEASRRQQALQQALAAEEKAQ 277
>gnl|CDD|236999 PRK11854, aceF, pyruvate dehydrogenase dihydrolipoyltransacetylase;
Validated.
Length = 633
Score = 28.8 bits (65), Expect = 5.5
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 351 AAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAA 387
AAPA PA Q AA + A A+ +A AAA AA+
Sbjct: 283 AAPAAA-PAKQEAAAPAPAAAKAEAPAAAPAAKAEGK 318
>gnl|CDD|235238 PRK04171, PRK04171, ribosome biogenesis protein; Provisional.
Length = 222
Score = 28.3 bits (64), Expect = 5.7
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 10/41 (24%)
Query: 217 EKVLKVPIHTLDGK--KIDPKHATPKNRPKIGNRTKKIFVG 255
E L+V IHT D K ++P+ PKN NR FVG
Sbjct: 79 EGKLRVYIHTRDDKVIYVNPETRLPKNY----NR----FVG 111
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 29.0 bits (65), Expect = 5.7
Identities = 8/55 (14%), Positives = 15/55 (27%)
Query: 41 PPPPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSN 95
P P + +P +++ Q + P P + P S
Sbjct: 388 AAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPST 442
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 26.8 bits (60), Expect = 5.7
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 362 LAALQSQAQAQVQAAAAAVAAQNAAAVA 389
+A ++ A AAAAA AA AAA A
Sbjct: 39 IANGSAKLSAAAAAAAAAAAAAAAAAAA 66
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 29.0 bits (65), Expect = 5.7
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 43 PPPHQLVKLNGAPQVNTSPPQNAILHQQPTPQPQQQQQ---QPPQPQPR 88
P QL + PQ+ +S Q + QP P + +Q PQ +
Sbjct: 365 PAFTQLRLESCPPQIKSSNSQQTVSSPQPQPVAKLEQGSLLTAASPQTK 413
>gnl|CDD|147144 pfam04834, Adeno_E3_14_5, Early E3 14.5 kDa protein. The E3B
14.5 kDa was first identified in Human adenovirus type
5. It is an integral membrane protein oriented with its
C terminus in the cytoplasm. It functions to
down-regulate the epidermal growth factor receptor and
prevent tumour necrosis factor cytolysis. It achieves
this through the interaction with E3 10.4 kDa protein.
Length = 97
Score = 27.0 bits (60), Expect = 6.1
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 61 PPQNAILHQQPTPQPQQQQQQPP 83
P I QQP P P+ Q + P
Sbjct: 63 PDPQHIPLQQPPPPPEPQPRAPS 85
>gnl|CDD|221818 pfam12868, DUF3824, Domain of unknwon function (DUF3824). This is
a repeating domain found in fungal proteins. It is
proline-rich, and the function is not known.
Length = 135
Score = 27.5 bits (61), Expect = 6.1
Identities = 17/56 (30%), Positives = 21/56 (37%), Gaps = 3/56 (5%)
Query: 41 PPPPPHQLVKLNGAPQVNTS---PPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPN 93
PPP + P N + PP A+ Q P P Q P P+PR N
Sbjct: 79 PPPGSTPVPPPGPQPGYNPADYPPPPGAVPPPQNYPYPPGPGQDPYAPRPRRADEN 134
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 28.9 bits (64), Expect = 6.3
Identities = 24/89 (26%), Positives = 30/89 (33%), Gaps = 5/89 (5%)
Query: 11 DHHEQFNGLIPTMNGLVQIPHHPGLVHLNGPPPPPHQLVKLNGAPQVNTSPPQ-----NA 65
D Q L P +Q+P L PP P Q V G+P PQ
Sbjct: 165 DSSAQQQLLQPQGPPSIQVPPGAALAPSAPPPTPSAQAVPPQGSPIAAQPAPQPQQPSPL 224
Query: 66 ILHQQPTPQPQQQQQQPPQPQPRDLQPNS 94
L P+ PQ+ P QP+ S
Sbjct: 225 SLISAPSLHPQRLPSPHPPLQPQTASQQS 253
>gnl|CDD|221300 pfam11898, DUF3418, Domain of unknown function (DUF3418). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria. This domain is typically
between 582 to 594 amino acids in length. This domain is
found associated with pfam07717, pfam00271, pfam04408.
Length = 586
Score = 28.6 bits (65), Expect = 6.6
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 362 LAALQSQAQAQVQAAAAAVAA 382
LAAL+++ + + A AA A
Sbjct: 279 LAALKARLGGKAREAFAAAAD 299
>gnl|CDD|184256 PRK13700, PRK13700, conjugal transfer protein TraD; Provisional.
Length = 732
Score = 28.8 bits (64), Expect = 6.9
Identities = 13/35 (37%), Positives = 13/35 (37%), Gaps = 5/35 (14%)
Query: 53 GAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
G PQ Q PQ QQ QQP QP
Sbjct: 613 GEDVTQAEQPQ-----QPQQPQQPQQPQQPQQPVS 642
Score = 28.4 bits (63), Expect = 9.4
Identities = 23/64 (35%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 55 PQVNTSPPQNAILHQQPTPQPQQ--QQQQPPQPQPRDLQPNSNNQLVLVNGKSSGDSGRS 112
P V + + QPQQ Q QQP QPQ QP S +N K S D+G +
Sbjct: 605 PDVPEVASGEDVTQAEQPQQPQQPQQPQQPQQPQ----QPVSPV----INDKKS-DAGVN 655
Query: 113 TPTG 116
P G
Sbjct: 656 VPAG 659
>gnl|CDD|240356 PTZ00315, PTZ00315, 2'-phosphotransferase; Provisional.
Length = 582
Score = 28.7 bits (64), Expect = 7.1
Identities = 11/70 (15%), Positives = 18/70 (25%), Gaps = 5/70 (7%)
Query: 31 HHPGLVHLNGPPPPPHQLVKLNGAPQVN---TSPPQNAILHQQPTPQPQQQQQQPPQPQP 87
H P L P L +GA Q + P + + Q P+
Sbjct: 271 HAPTEASLPALDALPSTL--ADGAAQHSRDCREPGRRHARTEGDARASDTVNNQQSMPER 328
Query: 88 RDLQPNSNNQ 97
+ +
Sbjct: 329 KHRSAYRHED 338
>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional.
Length = 584
Score = 28.5 bits (64), Expect = 7.3
Identities = 21/67 (31%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 325 AQPKEAVQANLL--VGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAAVAA 382
A+ E A L + + L L LR A PI AA V A+AA
Sbjct: 146 AEEDERAPAALADRLAFHLDLDGLALRDAREIPIDADDIAAA--RARLPAVGPPPEAIAA 203
Query: 383 QNAAAVA 389
AAA A
Sbjct: 204 LCAAAAA 210
>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 = 26.6 bits (58), Expect = 7.3
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 190 DVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLD--GKKIDPKHATPK 240
+V +M++ + +SRGF F+ F + + ++ H+L G+K+ ++ PK
Sbjct: 32 EVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLMILGQKVSMHYSDPK 84
>gnl|CDD|220944 pfam11018, Cuticle_3, Pupal cuticle protein C1. Insect cuticles
are composite structures whose mechanical properties are
optimised for biological function. The major components
are the chitin filament system and the cuticular
proteins, and the cuticle's properties are determined
largely by the interactions between these two sets of
molecules. The proteins can be ordered by species.
Length = 164
Score = 27.6 bits (61), Expect = 7.5
Identities = 16/43 (37%), Positives = 17/43 (39%)
Query: 351 AAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVANYGK 393
AA AP+ A AA A AA A A AA A K
Sbjct: 66 AAAAPVYAAHAYAAPAVHYAAAAHYAAPAYAKYAYAAPAVTAK 108
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 28.5 bits (64), Expect = 7.6
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 53 GAPQVNTSPPQNAILHQQPTPQPQQQ-QQQPPQPQPRDLQPNSNNQ 97
+ S + + QQ T QPQ Q + Q P Q +S Q
Sbjct: 734 SESVEDASNSELQAVEQQATHQPQVQAEAQSPASTTALTQTSSEVQ 779
>gnl|CDD|217591 pfam03492, Methyltransf_7, SAM dependent carboxyl
methyltransferase. This family of plant
methyltransferases contains enzymes that act on a
variety of substrates including salicylic acid, jasmonic
acid and 7-Methylxanthine. Caffeine is synthesised
through sequential three-step methylation of xanthine
derivatives at positions 7-N, 3-N, and 1-N. The protein
7-methylxanthine methyltransferase (designated as
CaMXMT) catalyzes the second step to produce
theobromine.
Length = 331
Score = 28.4 bits (64), Expect = 7.7
Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 234 PKHATPKNRPKIGNRTKKIFVGGVSQDTSAEEV-KAYFSQFGK 275
PK K P N+ I++ G S EEV KAY QF K
Sbjct: 121 PKGLEDKESPAW-NK-GNIYISG----ASPEEVYKAYLDQFKK 157
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 28.8 bits (64), Expect = 7.8
Identities = 19/64 (29%), Positives = 25/64 (39%), Gaps = 9/64 (14%)
Query: 51 LNGAPQVNTSPPQNAILHQQPTPQPQQQQQQPPQPQPR-DLQPNSNNQLVLVNGKSSGDS 109
+ P N PP P P + Q PP P P +++ S QL +V G G S
Sbjct: 1 MASLPPGNPPPPP-------PPPGFEPPSQPPPPPPPGVNVKKRSRKQLSIV-GDILGHS 52
Query: 110 GRST 113
G
Sbjct: 53 GNPI 56
>gnl|CDD|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed.
Length = 1228
Score = 28.3 bits (64), Expect = 8.2
Identities = 18/39 (46%), Positives = 19/39 (48%)
Query: 351 AAPAPITPATQLAALQSQAQAQVQAAAAAVAAQNAAAVA 389
AAPAP PA A + A AAAA A AAA A
Sbjct: 68 AAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAA 106
>gnl|CDD|221416 pfam12090, Spt20, Spt20 family. This presumed domain is found in
the Spt20 proteins from both human and yeast. The Spt20
protein is part of the SAGA complex which is a large
cmplex mediating histone deacetylation. Yeast Spt20 has
been shown to play a role in structural integrity of the
SAGA complex as as no intact SAGA could be purified in
spt20 deletion strains.
Length = 191
Score = 27.8 bits (62), Expect = 8.6
Identities = 11/38 (28%), Positives = 16/38 (42%)
Query: 58 NTSPPQNAILHQQPTPQPQQQQQQPPQPQPRDLQPNSN 95
NT P Q+ Q + + Q ++ P Q Q D Q
Sbjct: 84 NTVPQQSQQQAQAQSQEQQDKENSPAQNQQADGQKQKP 121
>gnl|CDD|213932 TIGR04319, SerAla_Lrha_rpt, surface protein repeat Ser-Ala-175.
This serine and alanine-rich surface protein repeat,
about 175 amino acids long, occurs up to nine times in
surface proteins of some Lactobacillus strains,
particularly in Lactobacillus rhamnosus. Members
proteins have the N-terminal variant signal sequence
described by TIGR03715 and C-terminal LPXTG signals for
surface attachment by sortase.
Length = 175
Score = 27.5 bits (61), Expect = 8.7
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 351 AAPAPITPATQLAALQSQAQAQVQAAAA----AVAAQNAAAVANYGKI 394
+A A + A+ LA S A +AA+ A+AA N A ++Y
Sbjct: 48 SASADASAASSLATKVSSANKAASSAASQANSALAAGNLDAASSYANQ 95
>gnl|CDD|221789 pfam12818, Tegument_dsDNA, dsDNA viral tegument protein. This is a
family of tegument proteins from double-stranded DNA
herpesvirus and related viral species.
Length = 282
Score = 28.1 bits (63), Expect = 9.0
Identities = 15/48 (31%), Positives = 23/48 (47%)
Query: 332 QANLLVGKRVILGPLGLRMAAPAPITPATQLAALQSQAQAQVQAAAAA 379
++LL G R LGL + P+P+ P + Q +A + QA A
Sbjct: 25 HSSLLPGGRTQASALGLYVTTPSPVGPLSHAVHRQIRAALKAQAECLA 72
>gnl|CDD|221266 pfam11851, DUF3371, Domain of unknown function (DUF3371). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 125 to 142 amino acids in length.
Length = 131
Score = 27.0 bits (60), Expect = 9.4
Identities = 6/26 (23%), Positives = 6/26 (23%)
Query: 62 PQNAILHQQPTPQPQQQQQQPPQPQP 87
Q L PQ P P
Sbjct: 27 KQEPQLEDNQCPQDLYPHSSQPDLPP 52
>gnl|CDD|165431 PHA03160, PHA03160, hypothetical protein; Provisional.
Length = 499
Score = 28.1 bits (62), Expect = 9.5
Identities = 17/70 (24%), Positives = 25/70 (35%), Gaps = 3/70 (4%)
Query: 53 GAPQVNTSPPQNAILHQQPTPQPQQQQQQP---PQPQPRDLQPNSNNQLVLVNGKSSGDS 109
GAP+ + QQ QP QQ P P P +QP Q ++ +
Sbjct: 404 GAPKNDHHLLPPLACSQQLPMQPLHVQQAPMQAPHVAPPPMQPPHVQQPRVLPSTDGASN 463
Query: 110 GRSTPTGDDP 119
P+ +P
Sbjct: 464 EAPKPSAQEP 473
>gnl|CDD|112412 pfam03594, BenE, Benzoate membrane transport protein.
Length = 378
Score = 28.1 bits (63), Expect = 9.6
Identities = 25/75 (33%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 322 CKKAQPKEAVQANLLVGKRV--ILG-----PLGLRMAAPAPITPATQLAALQSQAQAQVQ 374
++ P+ AV A LLVG +LG PL L +A P ITP A S A +
Sbjct: 158 ARRFAPRYAVLAVLLVGVAAAALLGQVHPAPLPLELARPQWITPEFSWQATLSLA---LP 214
Query: 375 AAAAAVAAQNAAAVA 389
A+ +QN +A
Sbjct: 215 LYLVAMTSQNLPGIA 229
>gnl|CDD|182322 PRK10234, PRK10234, DNA-binding transcriptional activator GutM;
Provisional.
Length = 118
Score = 26.9 bits (60), Expect = 9.9
Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 10/48 (20%)
Query: 188 VTDVLIMKDPITQRSRGFGFITFAEPETVEKVLKVPIHTLDGKKIDPK 235
V D L MK G FA P+ + + + + L I P
Sbjct: 65 VVDTLFMK----------GLTVFARPQKIPALTGLHLGDLQPDVIFPH 102
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
0.315 0.132 0.386
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,318,357
Number of extensions: 1969114
Number of successful extensions: 5560
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4514
Number of HSP's successfully gapped: 921
Length of query: 398
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 299
Effective length of database: 6,546,556
Effective search space: 1957420244
Effective search space used: 1957420244
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: 42 (22.0 bits)
S2: 60 (27.1 bits)