RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9171
(118 letters)
>gnl|CDD|241132 cd12688, RRM1_PTBP1_like, RNA recognition motif 1 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM1 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and functions at several aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTBP2
is highly homologous to PTB and is perhaps specific to
the vertebrates. Unlike PTB, PTBP2 is enriched in the
brain and in some neural cell lines. It binds more
stably to the downstream control sequence (DCS) RNA
than PTB does but is a weaker repressor of splicing in
vitro. PTBP2 also greatly enhances the binding of two
other proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. PTBP2 also contains four
RRMs. ROD1 coding protein Rod1 is a mammalian PTB
homolog of a regulator of differentiation in the
fission yeast Schizosaccharomyces pombe, where the nrd1
gene encodes an RNA binding protein and negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 81
Score = 85.9 bits (213), Expect = 2e-23
Identities = 33/46 (71%), Positives = 39/46 (84%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAE 76
RV+HIRNIPN+ TEAEII LG+PFG+VTNVL+LKGKNQ L + E
Sbjct: 1 RVLHIRNIPNDATEAEIIALGLPFGKVTNVLMLKGKNQAFLEMADE 46
>gnl|CDD|241223 cd12779, RRM1_ROD1, RNA recognition motif 1 in vertebrate
regulator of differentiation 1 (Rod1). This subgroup
corresponds to the RRM1 of ROD1 coding protein Rod1, 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 that negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It might play a role controlling
differentiation in mammals. Rod1 contains four repeats
of RNA recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and
does have RNA binding activities. .
Length = 90
Score = 73.2 bits (179), Expect = 2e-18
Identities = 32/48 (66%), Positives = 42/48 (87%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAE 76
PSRV+H+R IPN+VTEAEII LG+PFG+VTN+L+LKGK+Q L + +E
Sbjct: 4 PSRVLHLRKIPNDVTEAEIISLGLPFGKVTNLLMLKGKSQAFLEMASE 51
>gnl|CDD|241222 cd12778, RRM1_PTBP2, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM1 of PTBP2, also known
as neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein
(PTB) and perhaps specific to the vertebrates. Unlike
PTB, PTBP2 is enriched in the brain and in some neural
cell lines. It binds more stably to the downstream
control sequence (DCS) RNA than PTB does but is a
weaker repressor of splicing in vitro. PTBP2 also
greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 82
Score = 70.1 bits (171), Expect = 3e-17
Identities = 31/47 (65%), Positives = 38/47 (80%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAE 76
SRV+HIR +P EVTE E+I LG+PFG+VTN+L+LKGKNQ L L E
Sbjct: 1 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATE 47
>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 = 69.5 bits (171), Expect = 4e-17
Identities = 24/43 (55%), Positives = 37/43 (86%)
Query: 32 VIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
V+H+RN+P +VTE+++I L PFG+VTNVL+L+GKNQ L+ ++
Sbjct: 1 VLHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMD 43
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract
binding protein ) and hnRNP-L. These proteins contain
four RNA recognition motifs (rrm: pfam00067).
Length = 481
Score = 74.5 bits (183), Expect = 6e-17
Identities = 23/49 (46%), Positives = 34/49 (69%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAEI 77
PS V+H+RN+P +V EA+++ IPFG V+ V++L GK Q L+ E E
Sbjct: 1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEE 49
Score = 25.9 bits (57), Expect = 6.2
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 27 FKPSRVIHIRNIPNEVTEAEIIHL 50
PS +H+ NIP V+E ++ L
Sbjct: 391 QPPSATLHLSNIPLSVSEEDLKEL 414
>gnl|CDD|241221 cd12777, RRM1_PTBP1, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM1 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there
is an unusual and conserved interdomain interaction
between RRM3 and RRM4. It is widely held that only RRMs
3 and 4 are involved in RNA binding and RRM2 mediates
PTB homodimer formation. However, new evidence shows
that the RRMs 1 and 2 also contribute substantially to
RNA binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 81
Score = 67.7 bits (165), Expect = 3e-16
Identities = 30/46 (65%), Positives = 39/46 (84%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAE 76
RVIH+R +PN+VTEAE+I LG+PFG+VTN+L+LKGKNQ L + E
Sbjct: 1 RVIHVRKLPNDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMNTE 46
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show
significant sequence similarity to polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 48.8 bits (116), Expect = 7e-09
Identities = 19/40 (47%), Positives = 27/40 (67%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
PS+V+H+RN+P E TE E+I L PFG++ N G N+
Sbjct: 1 PSKVLHLRNLPWECTEEELIELCKPFGKIVNTKCNVGANR 40
>gnl|CDD|241129 cd12685, RRM_RBM20, RNA recognition motif of vertebrate
RNA-binding protein 20 (RBM20). This subfamily
corresponds to the RRM of RBM20, an alternative
splicing regulator associated with dilated
cardiomyopathy (DCM). It contains only one copy of
RNA-recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 46.2 bits (109), Expect = 6e-08
Identities = 21/44 (47%), Positives = 32/44 (72%), Gaps = 1/44 (2%)
Query: 31 RVIHIRNIPN-EVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHL 73
RV+HI N+P TE ++I+LG+PFG+VTN +++K NQ L +
Sbjct: 1 RVVHICNLPEGSCTENDVINLGLPFGKVTNYILMKSTNQAFLEM 44
Score = 36.2 bits (83), Expect = 4e-04
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 74 EAEIIHLGIPFGRVTNVLVLKGKNQVSLISGY 105
E ++I+LG+PFG+VTN +++K NQ L Y
Sbjct: 15 ENDVINLGLPFGKVTNYILMKSTNQAFLEMAY 46
>gnl|CDD|241131 cd12687, RRM1_PTBPH3, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 3
(PTBPH3). This subfamily corresponds to the RRM1 of
PTBPH3. Although its biological roles remain unclear,
PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. Like PTB, PTBPH3 contains four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 75
Score = 45.7 bits (108), Expect = 9e-08
Identities = 18/44 (40%), Positives = 34/44 (77%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
+V+H+RN+ +E++E +++ L PFG VT +++L+ KNQ LL ++
Sbjct: 1 KVLHVRNVGHEISENDLLQLVQPFGVVTKLVMLRAKNQALLQMQ 44
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 80
Score = 42.7 bits (101), Expect = 1e-06
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
PS V+H+R +P+ VTEA+++ FG ++ V ++ K Q L+ E
Sbjct: 1 PSPVVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQALVEFE 46
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of
nuclear proteins consisting of Matrin 3 (MATR3),
nuclear protein 220 (NP220) and similar proteins. MATR3
is a highly conserved inner nuclear matrix protein that
has been implicated in various biological processes.
NP220 is a large nucleoplasmic DNA-binding protein that
binds to cytidine-rich sequences, such as CCCCC (G/C),
in double-stranded DNA (dsDNA). Both, Matrin 3 and
NP220, contain two RNA recognition motif (RRM), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a Cys2-His2 zinc
finger-like motif at the C-terminal region. .
Length = 76
Score = 40.3 bits (95), Expect = 9e-06
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 31 RVIHIRNIPN-EVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
RV+ + N+P TEAE++ L PFG+V + + L +N+ + +E
Sbjct: 1 RVVRLSNLPEGGYTEAELLKLAEPFGKVDHYIFLPNRNKAFIEME 45
Score = 26.1 bits (58), Expect = 2.3
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 74 EAEIIHLGIPFGRVTNVLVLKGKNQVSL 101
EAE++ L PFG+V + + L +N+ +
Sbjct: 15 EAELLKLAEPFGKVDHYIFLPNRNKAFI 42
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3
(PTBPH3). This subfamily corresponds to the RRM4 of
PTBPH3. Although its biological roles remain unclear,
PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. Like PTB, PTBPH3 contains four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 79
Score = 38.6 bits (90), Expect = 5e-05
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 2/50 (4%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK--GKNQLLLHLEAE 76
P+++IH+ N+P++VTE ++I+ G + NV V + GK Q L+ E
Sbjct: 6 PTKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNGKKQALVEFATE 55
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 34.8 bits (81), Expect = 0.001
Identities = 11/35 (31%), Positives = 23/35 (65%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+++RN+P VTE ++ P+G+V V +++ K+
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD 35
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 34.1 bits (79), Expect = 0.002
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 32 VIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ + N+P + TE E+ L FG+V +V +++ K
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKE 36
>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 = 34.1 bits (79), Expect = 0.002
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+++ N+P+ +TE E+ PFG + V V K K
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKG 37
>gnl|CDD|241224 cd12780, RRM1_hnRNPL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM1 of hnRNP-L, 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-L shows significant sequence homology
to polypyrimidine tract-binding protein (PTB or hnRNP
I). Both, hnRNP-L and PTB, are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 33.8 bits (77), Expect = 0.003
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
S V+H+R + + V EA+++ FG ++ V+V+ K Q L+ E
Sbjct: 1 ASPVVHVRGLIDGVVEADLVEALQEFGTISYVVVMPKKRQALVEFE 46
>gnl|CDD|241159 cd12715, RRM2_MATR3, RNA recognition motif 2 in vertebrate
matrin-3. This subgroup corresponds to the RRM2 of
Matrin 3 (MATR3 or P130), a highly conserved inner
nuclear matrix protein with a bipartite nuclear
localization signal (NLS), two zinc finger domains
predicted to bind DNA, and two RNA recognition motifs
(RRM), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that are known to interact
with RNA. MATR3 has been implicated in various
biological processes. It is involved in RNA processing
by interacting with other nuclear proteins to anchor
hyperedited RNAs to the nuclear matrix. It plays a role
in mRNA stabilization through maintaining the stability
of certain mRNA species. Besides, it modulates the
activity of proximal promoters by binding to highly
repetitive sequences of matrix/scaffold attachment
region (MAR/SAR). The phosphorylation of MATR3 is
assumed to cause neuronal death. It is phosphorylated
by the protein kinase ATM, which activates the cellular
response to double strand breaks in the DNA. Its
phosphorylation by protein kinase A (PKA) is
responsible for the activation of the
N-methyl-d-aspartic acid (NMDA) receptor. Furthermore,
MATR3 has been identified as both a Ca2+-dependent
CaM-binding protein and a downstream substrate of
caspases. Additional research indicates that matrin 3
also binds Rev/Rev responsive element (RRE)-containing
viral RNA and functions as a cofactor that mediates the
post-transcriptional regulation of HIV-1. .
Length = 80
Score = 33.3 bits (76), Expect = 0.005
Identities = 14/45 (31%), Positives = 31/45 (68%), Gaps = 1/45 (2%)
Query: 31 RVIHIRNIPN-EVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
RVIH+ N+P+ +++ ++ L P+G++ N ++++ KNQ + +E
Sbjct: 1 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKNQAFIEME 45
>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 = 31.7 bits (73), Expect = 0.019
Identities = 7/34 (20%), Positives = 17/34 (50%)
Query: 35 IRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
+ +P TE ++ L +G + V +++ K+
Sbjct: 4 VGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDT 37
Score = 24.4 bits (54), Expect = 9.5
Identities = 5/25 (20%), Positives = 13/25 (52%)
Query: 74 EAEIIHLGIPFGRVTNVLVLKGKNQ 98
E ++ L +G + V +++ K+
Sbjct: 13 EEDVRALFEEYGNIEEVTIIRDKDT 37
>gnl|CDD|241225 cd12781, RRM1_hnRPLL, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). This subgroup corresponds to the RRM1 of
hnRNP-LL, which plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 31.2 bits (70), Expect = 0.036
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
S V+H+R + V EA+++ FG + V+++ K Q L+ E
Sbjct: 3 SPVVHVRGLCESVVEADLVEALEKFGPICYVMMMPFKRQALVEFE 47
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and four hnRNP K homology (KH) domains. .
Length = 76
Score = 30.8 bits (70), Expect = 0.036
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
R I I NIP V ++ L +G V N
Sbjct: 1 RKIQISNIPPHVRWEDLDSLLSTYGTVKNC 30
>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 = 30.7 bits (70), Expect = 0.039
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ + N+P + TE ++ L FG + +V +++ K+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD 35
>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 = 30.7 bits (70), Expect = 0.044
Identities = 7/28 (25%), Positives = 15/28 (53%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+++ + EV E + IPFG + ++
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDI 28
>gnl|CDD|241160 cd12716, RRM1_2_NP220, RNA recognition motif 1 and 2 in
vertebrate nuclear protein 220 (NP220). This subgroup
corresponds to RRM1 and RRM2 of NP220, also termed zinc
finger protein 638 (ZN638), or cutaneous T-cell
lymphoma-associated antigen se33-1, or zinc finger
matrin-like protein, a large nucleoplasmic DNA-binding
protein that binds to cytidine-rich sequences, such as
CCCCC (G/C), in double-stranded DNA (dsDNA). NP220
contains multiple domains, including MH1, MH2, and MH3,
domains homologous to the acidic nuclear protein matrin
3; RS, an arginine/serine-rich domain commonly found in
pre-mRNA splicing factors; PstI-HindIII, a domain
essential for DNA binding; acidic repeat, a domain with
nine repeats of the sequence LVTVDEVIEEEDL; and a
Cys2-His2 zinc finger-like motif that is also present
in matrin 3. It may be involved in packaging,
transferring, or processing transcripts. This subgroup
corresponds to the domain of MH2 that contains two
tandem RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains).
Length = 76
Score = 30.5 bits (69), Expect = 0.056
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 32 VIHIRNIPNE-VTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
V+ I N+P + +E EI +L PFG++ ++L+L + L +
Sbjct: 2 VVLISNLPEKGYSEEEIYNLAKPFGKLKDILILSSHKKAYLEMN 45
>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 = 29.5 bits (67), Expect = 0.096
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+ +RN+P E T+ E+ L PFG+V +V
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSV 30
>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 = 29.7 bits (67), Expect = 0.097
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLH 72
SR ++I N+P +E E+ FG + + ++K KN +H
Sbjct: 3 SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVH 45
>gnl|CDD|241158 cd12714, RRM1_MATR3, RNA recognition motif 1 in vertebrate
matrin-3. This subgroup corresponds to the RRM1 of
Matrin 3 (MATR3 or P130), a highly conserved inner
nuclear matrix protein with a bipartite nuclear
localization signal (NLS), two zinc finger domains
predicted to bind DNA, and two RNA recognition motifs
(RRM), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that are known to interact
with RNA. MATR3 has been implicated in various
biological processes. It is involved in RNA processing
by interacting with other nuclear proteins to anchor
hyperedited RNAs to the nuclear matrix. It plays a role
in mRNA stabilization through maintaining the stability
of certain mRNA species. Besides, it modulates the
activity of proximal promoters by binding to highly
repetitive sequences of matrix/scaffold attachment
region (MAR/SAR). The phosphorylation of MATR3 is
assumed to cause neuronal death. It is phosphorylated
by the protein kinase ATM, which activates the cellular
response to double strand breaks in the DNA. Its
phosphorylation by protein kinase A (PKA) is
responsible for the activation of the
N-methyl-d-aspartic acid (NMDA) receptor. Furthermore,
MATR3 has been identified as both a Ca2+-dependent
CaM-binding protein and a downstream substrate of
caspases. Additional research indicates that matrin 3
also binds Rev/Rev responsive element (RRE)-containing
viral RNA and functions as a cofactor that mediates the
post-transcriptional regulation of HIV-1. .
Length = 76
Score = 29.7 bits (67), Expect = 0.10
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 31 RVIHIRNIP-NEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAE 76
RV+ + +++ L PFG + N L+L N+ L +
Sbjct: 1 RVVVVAKFQRGPNLREQLLQLAKPFGTIVNHLILNKINEAFLEMSTH 47
Score = 25.1 bits (55), Expect = 5.1
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 76 EIIHLGIPFGRVTNVLVLKGKNQ 98
+++ L PFG + N L+L N+
Sbjct: 17 QLLQLAKPFGTIVNHLILNKINE 39
>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 = 29.6 bits (67), Expect = 0.11
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
I + N+P + E+ + L PFG VTNV V++
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIR 35
>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 = 29.5 bits (67), Expect = 0.11
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+V+++RN+P TE ++ L +G V V +K
Sbjct: 2 KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIK 35
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 3 in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM4 of RBM19 and the RRM3 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 homologues 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. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 72
Score = 28.3 bits (64), Expect = 0.25
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVL 61
VI ++N+P TE E+ L FG + +L
Sbjct: 1 TVILVKNLPFGTTEEELRELFEKFGSLGRLL 31
>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 = 28.7 bits (64), Expect = 0.25
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRV--TNVLVLKGKNQ 68
+ I ++P E +AE++ + +PFG V V V + NQ
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQ 44
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM1 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding protein family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 71
Score = 28.3 bits (63), Expect = 0.34
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
SR + + N+P +VTE+ + L +G V V
Sbjct: 1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGV 31
>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 = 27.2 bits (61), Expect = 0.79
Identities = 14/40 (35%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 30 SRVIHIRNIPNEVTEAEII-HLGIPFGRVTNVLVLKGKNQ 68
SR+I ++N+P +TEAE+ H G +T+V +L+ ++
Sbjct: 1 SRLI-VKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDG 39
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 28.4 bits (62), Expect = 0.80
Identities = 10/51 (19%), Positives = 24/51 (47%)
Query: 17 QAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++ + + + + N+P +VTE ++ L FG V V +++ +
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRE 152
>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 = 26.9 bits (60), Expect = 0.96
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 37 NIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
N+PN++TE E L +G V+ V + K K
Sbjct: 8 NLPNDITEEEFKELFSKYGEVSEVFLNKEKG 38
>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 = 26.7 bits (60), Expect = 0.99
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 77 IIHLGIPFGRVTNVLVLKGKNQVSLISGYRNRQSAALMM 115
+ L PFG V + +LK K + + + ++A +
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVE-FSTEEAAEKAV 38
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2,
Smad3 and Smad4, and stimulates Smad-mediated
transactivation. Cpo may play an important role in
regulating normal function of the nervous system,
whereas mutations in Mec-8 affect mechanosensory and
chemosensory neuronal function. All members contain a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). Some uncharacterized family members contain
two RRMs; this subfamily includes their RRM1. Their
RRM2 shows high sequence homology to the RRM of yeast
proteins scw1, Whi3, and Whi4.
Length = 79
Score = 26.8 bits (60), Expect = 1.0
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPF-GRVTNVLVLKGKN 67
R + + +P++V E E+ HL PF G + LV K K
Sbjct: 1 RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKK 38
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein
zinc fingers (zf-RanBP), and an asparagine-rich region.
It may possess RNA-binding and zinc ion binding
activities. Additional research had indicated that ARP
may function as a factor involved in the stress
response. .
Length = 88
Score = 27.1 bits (60), Expect = 1.0
Identities = 6/17 (35%), Positives = 13/17 (76%)
Query: 31 RVIHIRNIPNEVTEAEI 47
+V++I N+P + T+ E+
Sbjct: 1 KVLYISNLPPDTTQLEL 17
>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 = 26.8 bits (60), Expect = 1.1
Identities = 6/32 (18%), Positives = 21/32 (65%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
++++N+ ++ + ++ L +G++T+ V+K
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMK 35
>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 = 27.1 bits (59), Expect = 1.1
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++IR +P T+ ++I L P+G++ + + KN
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKN 41
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 73
Score = 26.5 bits (59), Expect = 1.2
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 32 VIHIRNIPNEVTEAEIIH 49
I I+NIP +VT+ E++
Sbjct: 1 CIKIKNIPFDVTKGEVLA 18
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM3 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 = 72
Score = 26.6 bits (59), Expect = 1.2
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 32 VIHIRNIPNEVTEAEIIHLGIPFGRVTNVLV 62
I ++N P T E+ L P G++T VL+
Sbjct: 2 TILVKNFPYGTTAEELRDLFEPHGKLTRVLM 32
>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 = 27.0 bits (59), Expect = 1.3
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
I + N+ E E+ + L PFG VTNV V++
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIR 35
>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 = 26.4 bits (59), Expect = 1.4
Identities = 7/35 (20%), Positives = 20/35 (57%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ + N+P + TE ++ L FG + ++ +++ +
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDET 35
>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 = 26.8 bits (60), Expect = 1.4
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGK 66
R + IRN+P + TE E+ L FG V ++K K
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDK 36
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-beta (PGC-1-beta) and similar proteins. This
subfamily corresponds to the RRM of PGC-1beta, also
termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta,
or PGC-1-related estrogen receptor alpha coactivator,
which is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial
oxidative energy metabolism and affects both, insulin
sensitivity and mitochondrial biogenesis, and functions
in a number of oxidative tissues. It is involved in
maintaining baseline mitochondrial function and cardiac
contractile function following pressure overload
hypertrophy by preserving glucose metabolism and
preventing oxidative stress. PGC-1beta induces
hypertriglyceridemia in response to dietary fats
through activating hepatic lipogenesis and lipoprotein
secretion. It can stimulate apolipoprotein C3 (APOC3)
expression, further mediating hypolipidemic effect of
nicotinic acid. PGC-1beta also drives nuclear
respiratory factor 1 (NRF-1) target gene expression and
NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can
be increased through binding to host cell factor (HCF),
a cellular protein involved in herpes simplex virus
(HSV) infection and cell cycle regulation. PGC-1beta is
a multi-domain protein containing an N-terminal
activation domain, an LXXLL coactivator signature, a
tetrapeptide motif (DHDY) responsible for HCF binding,
two glutamic/aspartic acid-rich acidic domains, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). In
contrast to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible
for the regulation of RNA processing. .
Length = 79
Score = 26.4 bits (58), Expect = 1.6
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVL 63
RVI+IRN+ + ++ E+ FG + VL
Sbjct: 3 RVIYIRNLSSSMSSTELKKRFEVFGEIEECKVL 35
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 26.4 bits (59), Expect = 1.6
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 25 SDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+K S I+I +P E+TE +I+ + +G + ++
Sbjct: 4 DQYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDI 39
>gnl|CDD|182223 PRK10073, PRK10073, putative glycosyl transferase; Provisional.
Length = 328
Score = 27.7 bits (62), Expect = 1.6
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 31 RVIH-IRNIPNEVTEAEIIH----LGIPFGRVTNVLVLKGKNQLLL 71
RV H +R P+ +T +I G+ N +K QLLL
Sbjct: 273 RVCHAVRKEPDILTRQRMIAEIFTSGMYKRIWKNARSVKLGYQLLL 318
>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 = 27.5 bits (61), Expect = 1.7
Identities = 12/51 (23%), Positives = 26/51 (50%)
Query: 17 QAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
K +R+ + K ++++N+ V E ++ L FG +T+ V+K +
Sbjct: 165 IKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS 215
>gnl|CDD|216810 pfam01959, DHQS, 3-dehydroquinate synthase (EC 4.6.1.3).
3-Dehydroquinate synthase is an enzyme in the common
pathway of aromatic amino acid biosynthesis that
catalyzes the conversion of
3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP)
into 3-dehydroquinic acid. This synthesis of aromatic
amino acids is an essential metabolic function for most
prokaryotic as well as lower eukaryotic cells, including
plants. The pathway is absent in humans; therefore, DHQS
represents a potential target for the development of
novel and selective antimicrobial agents. Owing to the
threat posed by the spread of pathogenic bacteria
resistant to many currently used antimicrobial drugs,
there is clearly a need to develop new anti-infective
drugs acting at novel targets. A further potential use
for DHQS inhibitors is as herbicides.
Length = 347
Score = 27.6 bits (62), Expect = 1.7
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 45 AEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAEIIHLGIP 83
AE I L P G +V LK +++L++LE H G+
Sbjct: 301 AETIRLVRPDGTPVSVTELKPGDKVLVYLEEGARHFGMA 339
>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 = 26.3 bits (58), Expect = 1.8
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVL 63
+ + N+P V E I +GRV +V +L
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKIL 32
>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 = 26.0 bits (57), Expect = 1.8
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 35 IRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEA 75
+ N+P ++TE E L +G V + KGK + LE+
Sbjct: 6 VGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLES 46
>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 = 26.5 bits (59), Expect = 1.8
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRV 57
RVI++ IP + T +E+ PFG +
Sbjct: 3 RVIYVGKIPIDTTRSELRQRFQPFGEI 29
>gnl|CDD|240873 cd12427, RRM4_hnRNPL_like, RNA recognition motif 4 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM4 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 84
Score = 26.0 bits (58), Expect = 2.1
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHL 50
PS+V+H N P TE ++ L
Sbjct: 1 PSKVLHFFNAPPTFTEEDLREL 22
>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 = 26.2 bits (58), Expect = 2.2
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQL 69
R IH+ I ++E ++ G VT V L G Q
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRV-RLCGDRQH 38
>gnl|CDD|241148 cd12704, RRM4_hnRNPL, RNA recognition motif 4 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM4 of hnRNP-L, 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-L shows significant sequence homology
with polypyrimidine tract-binding protein (PTB or hnRNP
I). Both hnRNP-L and PTB are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 26.1 bits (57), Expect = 2.3
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFG--RVTNVLVLKGKNQ 68
PS V+H N P +VTE + G R +V V GK++
Sbjct: 1 PSNVLHFFNAPPDVTEENFSEICDELGVKRPASVKVFSGKSE 42
>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3). This subgroup corresponds to the RRM2 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 contain 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 = 88
Score = 26.2 bits (57), Expect = 2.3
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++I N+P + E E+ ++ PFG V + +L+ N
Sbjct: 4 LYISNLPVSMDEQELENMLKPFGHVISTRILRDAN 38
>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 = 25.6 bits (57), Expect = 3.2
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 32 VIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
V++I ++P+ E E+ FG VT + + + K
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKK 36
>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 = 25.4 bits (56), Expect = 3.3
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLH 72
I +RNIP E T E+ L FG + V + K H
Sbjct: 3 ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSH 42
>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 = 25.5 bits (56), Expect = 3.4
Identities = 8/33 (24%), Positives = 18/33 (54%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
+++R P + +E+ I + P+G V V ++
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN 34
>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 = 25.6 bits (57), Expect = 3.7
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGK 66
+ + + TE E+ L FGRV VL++K
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDP 37
>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM2 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein
2 (RBMS2), or suppressor of CDC2 with RNA-binding motif
3 (SCR3). MSSP-2 is 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 = 86
Score = 25.8 bits (56), Expect = 3.8
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++I N+P + E E+ + PFG+V + +L+ +
Sbjct: 3 LYISNLPLSMDEQELESMLKPFGQVISTRILRDAS 37
>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 = 25.4 bits (56), Expect = 4.8
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 38 IPNEVTEAEIIHLGIPFGRVTNVLVLKGK 66
IP + E ++ L FG++ + VLK K
Sbjct: 13 IPRNLEEKDLRPLFEQFGKIYELTVLKDK 41
>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM2 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein
1 (RBMS1), or suppressor of CDC2 with RNA-binding motif
2 (SCR2). MSSP-1 is 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 = 85
Score = 25.1 bits (54), Expect = 5.2
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
++I N+P + E E+ ++ PFG+V + +L+
Sbjct: 3 LYISNLPLSMDEQELENMLKPFGQVISTRILR 34
>gnl|CDD|180954 PRK07380, PRK07380, adenylosuccinate lyase; Provisional.
Length = 431
Score = 26.2 bits (58), Expect = 5.7
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 10/39 (25%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+ K++F P R++ I EAE+ H I F +TNV
Sbjct: 49 KAKANFDPQRILEI--------EAEVRHDVIAF--LTNV 77
>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 = 24.5 bits (54), Expect = 6.0
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAE 76
+ + N+P+ T E+ L +G VT V+ KN +H+E E
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVV--KNYGFVHMEEE 43
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 of PTBP2, also known
as neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein
(PTB) and perhaps specific to the vertebrates. Unlike
PTB, PTBP2 is enriched in the brain and in some neural
cell lines. It binds more stably to the downstream
control sequence (DCS) RNA than PTB does but is a
weaker repressor of splicing in vitro. PTBP2 also
greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 25.0 bits (54), Expect = 6.0
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 29 PSRVIHIRNIPNEVTEAEI 47
PS +H+ NIP VTE ++
Sbjct: 2 PSATLHLSNIPQSVTEEDL 20
>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 = 24.7 bits (54), Expect = 6.2
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTN 59
R +++ +I +VTE ++ L G+V +
Sbjct: 3 RTVYVSDIDQQVTEEQLAALFSNCGQVVD 31
>gnl|CDD|235142 PRK03624, PRK03624, putative acetyltransferase; Provisional.
Length = 140
Score = 25.3 bits (56), Expect = 6.4
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 67 NQLLLHLEAEIIHLGIPFGRVTNVLVLKGKNQV 99
L+ LE ++I G P N+ V + + V
Sbjct: 87 RALVARLEKKLIARGCP---KINLQVREDNDAV 116
>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 = 25.0 bits (54), Expect = 6.5
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
I I N+ + E + + PFG VTNV V++ N
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFN 38
>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 = 24.4 bits (53), Expect = 6.7
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
+ + N+P E TE EI L +G+V ++ KN +H++
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDII--KNYGFVHMD 42
>gnl|CDD|151156 pfam10640, Pox_ATPase-GT, mRNA capping enzyme N-terminal, ATPase
and guanylyltransferase. This domain is the N-terminus
of the large subunit viral mRNA capping enzyme, and
carries both the ATPase and the guanylyltransferase
activities of the enzyme. The guanylyltransferase
enzymatic region runs from residues 242
(leucine)-273(arginine), the core of the acitve site
being the lysine residue at 260. The ATPase activity is
at the very N-terminal part of the domain.
Length = 314
Score = 25.7 bits (57), Expect = 7.1
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 1 MKDIGGNVKYTLVMVVQAKLDRQKSDFK 28
K +++ LV +VQAK+ DFK
Sbjct: 111 YKKYLSSIRLELVNLVQAKIKNIVVDFK 138
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM4 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 24.5 bits (54), Expect = 7.3
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 32 VIHIRNIPNEVTEAEIIHL 50
+H+ NIP VTE ++ L
Sbjct: 1 TLHLSNIPPSVTEEDLKEL 19
>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 = 24.4 bits (54), Expect = 8.7
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 32 VIHIRNIPNEVTEAEIIH----LGIPFGRVTNVLVLKGK 66
V+ +R +P TE +I L IP + V G+
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGR 39
>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 = 24.4 bits (53), Expect = 9.1
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
I + N+ + ++ E+ L +G V + V++
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVMR 34
>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 = 24.0 bits (53), Expect = 9.3
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 30 SRVIHIRNIPNEVTEAEII--HLGIPFGRVTNVLVLKGKNQLLL----HLEAE 76
+ + +RNIP E+ + H FG + N+ V L+ EA+
Sbjct: 1 NTTLEVRNIPPELNNITKLNEHFS-KFGTIVNIQVNYNPESALVQFSTSEEAK 52
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
0.323 0.141 0.390
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,919,680
Number of extensions: 523741
Number of successful extensions: 507
Number of sequences better than 10.0: 1
Number of HSP's gapped: 506
Number of HSP's successfully gapped: 105
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)