RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2134
(104 letters)
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins. The
research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 98
Score = 92.5 bits (230), Expect = 4e-26
Identities = 41/84 (48%), Positives = 52/84 (61%), Gaps = 15/84 (17%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G V +V+IY EKQ ++E +E+IVKIFV FS EAE A ALNG
Sbjct: 30 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSLPS---------------EAEKAIQALNG 74
Query: 80 RFFAGRMVRAELYDQSLFDHNDFS 103
R+F GR V+AELYDQ+ FD +D S
Sbjct: 75 RWFGGRKVKAELYDQTKFDASDLS 98
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 85.9 bits (212), Expect = 5e-21
Identities = 40/85 (47%), Positives = 51/85 (60%), Gaps = 15/85 (17%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G V++V+I EKQ ++E +E+IVKIFV FS E + A+ AL+G
Sbjct: 543 FGVVDRVIINFEKQGEEEDAEIIVKIFVEFSDS---------------MEVDRAKAALDG 587
Query: 80 RFFAGRMVRAELYDQSLFDHNDFSG 104
RFF GR V AE YDQ LFDH D SG
Sbjct: 588 RFFGGRTVVAEAYDQILFDHADLSG 612
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 53.8 bits (130), Expect = 6e-11
Identities = 32/85 (37%), Positives = 41/85 (48%), Gaps = 21/85 (24%)
Query: 20 YGQVEKVVIYN--EKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDAL 77
YG+V KV+I+ DDEA V+IFV F +++ A A LNGRFF
Sbjct: 31 YGKVTKVLIFEIPGASPDDEA----VRIFVEFERVESAIKAVVDLNGRFF---------- 76
Query: 78 NGRFFAGRMVRAELYDQSLFDHNDF 102
GR V+A YD+ F ND
Sbjct: 77 -----GGRTVKASFYDEERFRRNDL 96
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 52.6 bits (127), Expect = 1e-10
Identities = 27/74 (36%), Positives = 35/74 (47%), Gaps = 18/74 (24%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
YG+V V+++ S+ + + V+IFV FS EA A ALNG
Sbjct: 30 YGKVLNVIVHEVASSEADDA---VRIFVEFSDA---------------DEAIKAVRALNG 71
Query: 80 RFFAGRMVRAELYD 93
RFF GR V A YD
Sbjct: 72 RFFGGRKVTARFYD 85
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 38.7 bits (91), Expect = 3e-05
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 19 AYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRF 66
YG VEK++I+ + V+ V F ++ AE A+ ALNGR
Sbjct: 24 PYGAVEKILIFEKNT--------GVQALVQFDSVESAENAKKALNGRN 63
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a highly acidic carboxyl-terminal half. The family
also includes CUS2, a yeast homolog of human Tat-SF1.
CUS2 interacts with U2 RNA in splicing extracts and
functions as a splicing factor that aids assembly of
the splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the
conserved splicing factor SF3a. Like Tat-SF1, CUS2
contains two RRMs as well. .
Length = 91
Score = 38.0 bits (89), Expect = 7e-05
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 23/85 (27%)
Query: 9 IYNEKQSDDEAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFA 68
+ ++ + + E +GQV+KVV++ D + + + K +E E
Sbjct: 25 LRDDLREECEKFGQVKKVVVF------DRHPDGVASV-----KFKEPE------------ 61
Query: 69 EAEYARDALNGRFFAGRMVRAELYD 93
EA+ +ALNGR+FAGR + AE +D
Sbjct: 62 EADRCIEALNGRWFAGRQLEAERWD 86
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Based on
the specific domain composition, RBM39 has been
classified into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually
not complexed to snRNAs. .
Length = 85
Score = 37.9 bits (89), Expect = 8e-05
Identities = 19/76 (25%), Positives = 27/76 (35%), Gaps = 23/76 (30%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDAL 77
+G VE + + V VK F ++ A+ ALNGR+
Sbjct: 33 SKFGPVEHIKVDKNS----PEGVVYVK----FKTVEAAQKCIQALNGRW----------- 73
Query: 78 NGRFFAGRMVRAELYD 93
F GR + AE D
Sbjct: 74 ----FDGRQITAEYVD 85
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 89
Score = 34.5 bits (80), Expect = 0.001
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFA 68
YG+V VVI +++ + K+FV F+ +++A+ A+ AL GR F
Sbjct: 33 GKYGKVLSVVI-PRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFD 82
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 33.7 bits (77), Expect = 0.009
Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 16/94 (17%)
Query: 9 IYNEKQSDDEAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFA 68
IY + +++ YG + +VI D ++ + K+F+ ++ +
Sbjct: 432 IYEDVKTEFSKYGPLINIVI-PRPNGDRNSTPGVGKVFLEYADV---------------R 475
Query: 69 EAEYARDALNGRFFAGRMVRAELYDQSLFDHNDF 102
AE A + +NGR F R+V A Y + + D+
Sbjct: 476 SAEKAMEGMNGRKFNDRVVVAAFYGEDCYKAGDY 509
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 31.8 bits (72), Expect = 0.048
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFA 68
YG V V IY + ++ KI++ FS + A A ALNGR+F
Sbjct: 394 SKYGGV--VHIYVDTKNSAG------KIYLKFSSVDAALAAFQALNGRYFG 436
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 30.7 bits (70), Expect = 0.053
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 20/72 (27%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G++E +V+ D+ ++ ++V F E A AL ALNG
Sbjct: 49 FGEIEDLVV-----CDNLGDHLLGNVYVKFE---TEEDAEAALQ------------ALNG 88
Query: 80 RFFAGRMVRAEL 91
R++AGR + EL
Sbjct: 89 RYYAGRPLYPEL 100
>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 = 30.1 bits (68), Expect = 0.054
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 46 FVSFSKMQEAEYARDALNGRFFA 68
FV F ++ A A+D+++G+
Sbjct: 37 FVEFESLESAIRAKDSVHGKVLN 59
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 30.4 bits (69), Expect = 0.071
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 65 RFFAEAEYARDALNGRFFAGRMVRAEL 91
R +AE A + LN R+F G+ + AEL
Sbjct: 76 RREEDAEKAVNDLNNRWFNGQPIYAEL 102
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM2 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 = 86
Score = 29.6 bits (67), Expect = 0.084
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 9/46 (19%)
Query: 19 AYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
+G+V ++VI+ + V+ V F + A+ A+ ALNG
Sbjct: 26 PHGKVLRIVIFRKNG---------VQAMVEFDSVDSAQRAKAALNG 62
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 28.8 bits (65), Expect = 0.19
Identities = 20/58 (34%), Positives = 26/58 (44%), Gaps = 12/58 (20%)
Query: 17 DEAY--------GQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRF 66
DEAY G+V V I KQ+ A FV F+ + AE A +LNG+
Sbjct: 12 DEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYG----FVEFATHEAAEQALQSLNGKP 65
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2
and forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3
or NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2
protein. Its message is detected exclusively in
post-mitotic regions of embryonic brain. Like RBFOX1,
both RBFOX2 and RBFOX3 bind to the hexanucleotide
UGCAUG elements and modulate brain and muscle-specific
splicing of exon EIIIB of fibronectin, exon N1 of
c-src, and calcitonin/CGRP. Members in this family also
harbor one RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 76
Score = 28.5 bits (64), Expect = 0.21
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 18 EAYGQVEKV-VIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
+G + V +I+NE+ S FV+F+ +A+ AR+ L+G
Sbjct: 22 GQFGPILDVEIIFNERGSKGFG-------FVTFANSADADRAREKLHG 62
>gnl|CDD|128350 smart00035, CLa, CLUSTERIN alpha chain.
Length = 216
Score = 29.0 bits (65), Expect = 0.30
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 11 NEKQSDDEAYGQVEKVVIYNEKQSD-DEASEVIVKIFVSF 49
N Q +D+ Y QV V + S ++V+VK+F S
Sbjct: 147 NLTQGEDQYYLQVTTVPSHTSDSSVPSGTTKVVVKLFDSD 186
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and
similar proteins. This subfamily corresponds to the
RRM of Acinus, a caspase-3-activated nuclear factor
that induces apoptotic chromatin condensation after
cleavage by caspase-3 without inducing DNA
fragmentation. It is essential for apoptotic chromatin
condensation and may also participate in nuclear
structural changes occurring in normal cells. Acinus
contains a P-loop motif and an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which indicates Acinus
might have ATPase and DNA/RNA-binding activity. .
Length = 90
Score = 28.0 bits (63), Expect = 0.35
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 46 FVSFSKMQEAEYARDALNG 64
+V++S ++EA R+AL+G
Sbjct: 43 YVTYSTVEEAVATREALHG 61
>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 = 27.7 bits (62), Expect = 0.41
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G++E V I +K + FV F ++AE A +ALNG+
Sbjct: 20 SKFGEIESVRIVRDKDGKSKGF-----AFVEFESPEDAEKALEALNGKEL 64
Score = 25.7 bits (57), Expect = 2.2
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 9/60 (15%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALN-GRFFA--------EAEYARDALNGRFFAGRMVRAE 90
E + ++F F +++ RD + FA +AE A +ALNG+ GR ++
Sbjct: 13 EDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72
>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 = 28.6 bits (64), Expect = 0.49
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 19 AYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
YG+V ++V + + + V F + A++A+ ALNG
Sbjct: 119 PYGKVLRIVTFTKNNV--------FQALVEFESVNSAQHAKAALNG 156
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing (RBP-MS).
This subfamily corresponds to the RRM of RBP-MS, also
termed heart and RRM expressed sequence (hermes), an
RNA-binding proteins found in various vertebrate
species. It contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). RBP-MS physically interacts
with Smad2, Smad3 and Smad4 and plays a role in
regulation of Smad-mediated transcriptional activity.
In addition, RBP-MS may be involved in regulation of
mRNA translation and localization during Xenopus laevis
development. .
Length = 76
Score = 27.3 bits (60), Expect = 0.56
Identities = 15/25 (60%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 46 FVSFSKMQEAEYARDALNG-RFFAE 69
FVSF EAE A++ALNG RF E
Sbjct: 43 FVSFDSRSEAEAAKNALNGIRFDPE 67
>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 = 27.2 bits (61), Expect = 0.60
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 32 KQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
+ + E FV FS Q A A DAL G
Sbjct: 33 VFKEKKGGEKQPVGFVDFSSAQCAAAAMDALQG 65
>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 = 27.1 bits (61), Expect = 0.63
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 4/47 (8%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
E YG +E+V I + D S+ FV FS +EA+ A +AL+G
Sbjct: 21 EEYGNIEEVTII--RDKDTGQSKGCA--FVKFSSREEAQKAIEALHG 63
>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 = 26.8 bits (60), Expect = 0.78
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 9/52 (17%)
Query: 18 EAYGQVEKVVIYNE--KQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G +E + I + +S A FV F ++AE A +ALNG+
Sbjct: 20 SKFGPIESIRIVRDETGRSKGFA-------FVEFEDEEDAEKALEALNGKEL 64
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic
RNA-binding protein 18 and similar proteins. This
subfamily corresponds to the RRM of RBM18, a putative
RNA-binding protein containing a well-conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The
biological role of RBM18 remains unclear. .
Length = 80
Score = 26.9 bits (60), Expect = 0.83
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV+F +EAE A +LNG+
Sbjct: 48 FVTFETKEEAEKALKSLNGK 67
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 26.4 bits (59), Expect = 1.1
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 46 FVSFSKMQEAEYARDALNGRF 66
FVS+S +++A A DALNG+
Sbjct: 43 FVSYSSIEDAAAAYDALNGKE 63
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 26.6 bits (59), Expect = 1.5
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 20/71 (28%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G+VE + + D+ ++ ++V F ++ E+A AL AL G
Sbjct: 50 FGEVEALNV-----CDNLGDHMVGNVYVKF---RDEEHAAAALK------------ALQG 89
Query: 80 RFFAGRMVRAE 90
RF+ GR + E
Sbjct: 90 RFYDGRPIIVE 100
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes.
Since the Hu proteins share high homology with the
Drosophila embryonic lethal abnormal vision (ELAV)
protein, the Hu family is sometimes referred to as the
ELAV family. Drosophila ELAV is exclusively expressed
in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress.
Moreover, HuR has an anti-apoptotic function during
early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Hu proteins
perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 79
Score = 26.1 bits (58), Expect = 1.9
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 46 FVSFSKMQEAEYARDALNG 64
F+ F K EAE A ALNG
Sbjct: 46 FIRFDKRIEAERAIKALNG 64
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 25.6 bits (57), Expect = 2.2
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 10/59 (16%)
Query: 40 EVIVKIFVSFSKMQEAEYARDALNGRF--FA--------EAEYARDALNGRFFAGRMVR 88
E + ++F F K++ RD G+ FA +AE A +ALNG+ GR ++
Sbjct: 14 EELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72
Score = 25.6 bits (57), Expect = 2.2
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+G+VE V + +K++ FV F ++AE A +ALNG+
Sbjct: 21 SKFGKVESVRLVRDKETGKSKGFA----FVEFESEEDAEKALEALNGKEL 66
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or
CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3,
or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1
and ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
family of RNA-binding proteins that have been
implicated in regulation of pre-mRNA splicing, and
control of mRNA translation and deadenylation. CELF-1
is strongly expressed in all adult and fetal tissues
tested. The human CELF-1 is a nuclear and cytoplasmic
RNA-binding protein that regulates multiple aspects of
nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element
involved in translational control of oskar mRNA in
Drosophila, and share sequence similarity to Bruno, the
Drosophila protein that mediates this process. The
Xenopus homolog embryo deadenylation element-binding
protein (EDEN-BP) mediates sequence-specific
deadenylation of Eg5 mRNA. It binds specifically to the
EDEN motif in the 3'-untranslated regions of maternal
mRNAs and targets these mRNAs for deadenylation and
translational repression. CELF-1 contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The two N-terminal RRMs of EDEN-BP are
necessary for the interaction with EDEN as well as a
part of the linker region (between RRM2 and RRM3).
Oligomerization of EDEN-BP is required for specific
mRNA deadenylation and binding. CELF-2 is expressed in
all tissues at some level, but highest in brain, heart,
and thymus. It has been implicated in the regulation of
nuclear and cytoplasmic RNA processing events,
including alternative splicing, RNA editing, stability
and translation. CELF-2 shares high sequence identity
with CELF-1, but shows different binding specificity;
it binds preferentially to sequences with UG repeats
and UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. This
subgroup also includes Drosophila melanogaster Bruno
protein, which plays a central role in regulation of
Oskar (Osk) expression in flies. It mediates repression
by binding to regulatory Bruno response elements (BREs)
in the Osk mRNA 3' UTR. The full-length Bruno protein
contains three RRMs, two located in the N-terminal half
of the protein and the third near the C-terminus,
separated by a linker region. .
Length = 84
Score = 25.5 bits (56), Expect = 2.8
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 2 GQVEKVVIYNEKQSDDEAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDA 61
GQ+ + + + E YG V ++ + ++ + S+ FV+F + A A++A
Sbjct: 7 GQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCC--FVTFYTRKAALEAQNA 64
Query: 62 L 62
L
Sbjct: 65 L 65
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 25.4 bits (56), Expect = 2.9
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 46 FVSFSKMQEAEYARDALNG 64
FVSF K ++AE A ++NG
Sbjct: 45 FVSFVKKEDAENAIQSMNG 63
>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM2 of the sex-lethal protein (SXL)
which governs sexual differentiation and X chromosome
dosage compensation in Drosophila melanogaster. It
induces female-specific alternative splicing of the
transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 25.2 bits (55), Expect = 3.2
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 46 FVSFSKMQEAEYARDALNGRFF 67
FV + K +EA+ A +LNG
Sbjct: 46 FVRYDKREEAQAAISSLNGTIP 67
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 25.2 bits (56), Expect = 3.3
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 45 IFVSFSKMQEAEYARDALNGRFF 67
FV F+ +EA+ A ALNG
Sbjct: 53 AFVEFATPEEAKEAVKALNGYKL 75
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 25.3 bits (56), Expect = 3.3
Identities = 12/32 (37%), Positives = 12/32 (37%), Gaps = 7/32 (21%)
Query: 41 VIVKI-------FVSFSKMQEAEYARDALNGR 65
V VKI FV F AE A L G
Sbjct: 29 VYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGT 60
>gnl|CDD|189014 cd09607, M3B_PepF_2, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 581
Score = 26.0 bits (58), Expect = 3.8
Identities = 15/38 (39%), Positives = 25/38 (65%), Gaps = 3/38 (7%)
Query: 26 VVIYNEKQSDDEASEVIVKIFVSFS-KMQEAEYARDAL 62
V ++K S +EA+E IV+ F +FS K+ A++A+ A
Sbjct: 296 VGESDKKFSYEEAAEFIVEHFRTFSPKL--ADFAQMAF 331
>gnl|CDD|241136 cd12692, RRM2_PTBPH3, RNA recognition motif 2 in plant
polypyrimidine tract-binding protein homolog 3
(PTBPH3). This subfamily corresponds to the RRM2 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 = 88
Score = 25.3 bits (55), Expect = 4.3
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGR 65
+G VEK+V + + ++ + ++ Q A AR L GR
Sbjct: 28 HGFVEKIVTFQKSAG--------LQALIQYTSQQSAVQARTNLQGR 65
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 77
Score = 24.9 bits (55), Expect = 4.6
Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 10/63 (15%)
Query: 18 EAYGQVEKV-VIYNEK--QSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYAR 74
+G VE+ ++Y+E +S FV ++ A A++ L+G+ +
Sbjct: 21 SPFGAVERCFLVYSESTGESKGYG-------FVEYASKASALKAKNQLDGKQIGGRKLQV 73
Query: 75 DAL 77
D
Sbjct: 74 DWA 76
>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 = 24.4 bits (54), Expect = 5.7
Identities = 19/73 (26%), Positives = 26/73 (35%), Gaps = 24/73 (32%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G VEK+ + +K FV FS + AE A LNG
Sbjct: 8 FGNVEKIKLLKKKPG---------FAFVEFSTEEAAEKAVQYLNGV-------------- 44
Query: 80 RFFAGRMVRAELY 92
F GR +R +
Sbjct: 45 -LFGGRPLRVDYS 56
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the
RRM of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). This
family also includes yeast eIF3-p33, a homolog of
vertebrate eIF-3G, plays an important role in the
initiation phase of protein synthesis in yeast. It
binds both, mRNA and rRNA, fragments due to an RRM near
its C-terminus. .
Length = 77
Score = 24.4 bits (54), Expect = 5.8
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FV+F ++AE A + LNG
Sbjct: 45 FVTFHTREDAERAIEKLNGF 64
>gnl|CDD|241135 cd12691, RRM2_PTBPH1_PTBPH2, RNA recognition motif 2 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM2 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 = 95
Score = 24.8 bits (54), Expect = 6.1
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 19 AYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGR 65
A+G V K+ + EK + +A V FS + A AR AL+GR
Sbjct: 27 AFGFVHKIATF-EKTAGFQA-------LVQFSDAETASAARSALDGR 65
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
An octapeptide sequence called the RS-ERK motif is
repeated six times in the RS region of RBM39. Although
the cellular function of RBM23 remains unclear, it
shows high sequence homology to RBM39 and contains two
RRMs. It may possibly function as a pre-mRNA splicing
factor. .
Length = 73
Score = 24.5 bits (54), Expect = 6.3
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 18 EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
E +G++E V + Q D E F+ F+ ++A+ A + LNG
Sbjct: 20 EPFGEIEFVQL----QRDPETGRSKGYGFIQFADAEDAKKALEQLNG 62
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein
orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which
is a putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 24.5 bits (54), Expect = 6.4
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 46 FVSFSKMQEAEYARDALNG 64
FV+F +AE A D L+G
Sbjct: 50 FVAFMNRADAERALDELDG 68
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 25.4 bits (55), Expect = 6.6
Identities = 8/45 (17%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 1 YGQVEKVVIYNEKQSDDEAYGQVEKVVIYNEKQSDDEASEVIVKI 45
YG+++K+V+ + S + + Y + ++A+ I ++
Sbjct: 144 YGKIKKIVVNKKTSSLNSTASHAGVYITY---STKEDAARCIAEV 185
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM2 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA). However, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 75
Score = 24.4 bits (53), Expect = 7.0
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 46 FVSFSKMQEAEYARDALNGR 65
FVSF Q+AE A + +NG+
Sbjct: 45 FVSFRSQQDAENAINEMNGK 64
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element
(TAR) RNA which is synthesized by cellular RNA
polymerase II at the viral long terminal repeat. NELF
is a heterotetrameric protein consisting of NELF A, B,
C or the splice variant D, and E. NELF-E contains an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). It
plays a role in the control of HIV transcription by
binding to TAR RNA. In addition, NELF-E is associated
with the NELF-B subunit, probably via a leucine zipper
motif. .
Length = 75
Score = 24.2 bits (53), Expect = 7.7
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 46 FVSFSKMQEAEYARDALNG 64
FV+F KM+ A+ A LNG
Sbjct: 42 FVTFEKMESADRAIAELNG 60
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2),
TRA2-alpha, TRA2-beta (also termed SFRS10), and similar
proteins found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent
GnRH pre-mRNA splicing. TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. Both, TRA2-alpha and TRA2-beta, contains a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), flanked by the N- and C-terminal
arginine/serine (RS)-rich regions. .
Length = 78
Score = 24.1 bits (53), Expect = 8.0
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 4/45 (8%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
YG +EKV + ++++ FV F +++A+ A++ LNG
Sbjct: 23 YGPIEKVQVVYDQKTGRSRGFG----FVYFESVEDAKEAKERLNG 63
>gnl|CDD|181597 PRK08963, fadI, 3-ketoacyl-CoA thiolase; Reviewed.
Length = 428
Score = 24.9 bits (55), Expect = 8.4
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 52 MQEAEYARDALNGRFFAEAEYARDALN 78
M EA A+ N + FA +AR+ L
Sbjct: 334 MHEAFAAQTLANLQMFASERFAREKLG 360
>gnl|CDD|234709 PRK00275, glnD, PII uridylyl-transferase; Provisional.
Length = 895
Score = 25.0 bits (55), Expect = 9.2
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 54 EAEYARDALNGRFFAEA-EYARDALNGRFFAGRMVRAELYDQSLF 97
+AE A A F +A AR+ L+ RF +GR +R + D++ F
Sbjct: 15 QAELALKASPIAAFKKAIRQAREVLDERFRSGRDIRRLIEDRAWF 59
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein. The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
being highly expressed throughout the brain and in
glandular tissues, moderately expressed in heart,
skeletal muscle, and liver, is also known as bruno-like
protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor
4. Like CELF-3, CELF-4 also contain three highly
conserved RRMs. The splicing activation or repression
activity of CELF-4 on some specific substrates is
mediated by its RRM1/RRM2. On the other hand, both RRM1
and RRM2 of CELF-4 can activate cardiac troponin T
(cTNT) exon 5 inclusion. CELF-5, expressed in brain, is
also known as bruno-like protein 5 (BRUNOL-5), or
CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, being strongly
expressed in kidney, brain, and testis, is also known
as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in a muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In addition to three highly conserved RRMs,
CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 23.9 bits (52), Expect = 9.8
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 11/60 (18%)
Query: 11 NEKQSDD------EAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNG 64
+++Q++D E +G +E+ I + D S+ FV FS EA+ A +AL+G
Sbjct: 10 SKQQTEDDVRRLFEPFGTIEECTIL---RGPDGNSKGCA--FVKFSSHAEAQAAINALHG 64
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 24.1 bits (53), Expect = 10.0
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 46 FVSFSKMQEAEYARDALNGRF 66
+V F+ + A A LNG+
Sbjct: 45 YVQFTSPESAAAAVALLNGKL 65
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
0.317 0.133 0.364
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,412,118
Number of extensions: 466317
Number of successful extensions: 565
Number of sequences better than 10.0: 1
Number of HSP's gapped: 545
Number of HSP's successfully gapped: 90
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.3 bits)