RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11609
(83 letters)
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 108 bits (271), Expect = 5e-33
Identities = 38/63 (60%), Positives = 50/63 (79%)
Query: 9 SDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKI 68
SDTSLKDGL+HE+KKHGKV+ VK+ G G +RY +V F+K +DAEKA+ S K FFG +I
Sbjct: 12 SDTSLKDGLFHEFKKHGKVTSVKVHGTGSERYAIVFFRKPEDAEKALEVSKGKLFFGAEI 71
Query: 69 DVS 71
+V+
Sbjct: 72 EVT 74
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM1 domain in the Spen (split end) family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also known as one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong- to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 44.2 bits (105), Expect = 1e-07
Identities = 21/48 (43%), Positives = 31/48 (64%), Gaps = 2/48 (4%)
Query: 8 VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGD-RYGLVCFKKADDAEKA 54
+SD ++D LYHE+KK G VS V+++ G D R V F+ +DA +A
Sbjct: 13 LSDEDIEDVLYHEFKKFGDVS-VRVLHDGEDERVAYVNFRHPEDAREA 59
>gnl|CDD|240997 cd12553, RRM1_RBM15, RNA recognition motif 1 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM1 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor and component of
the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RBM15 belongs to the Spen (split
end) protein family, which contains three N-terminal
RNA recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralog and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties.
Length = 78
Score = 43.4 bits (102), Expect = 2e-07
Identities = 22/47 (46%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 8 VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKA 54
+SD +++DGL+HE+KK G VS VKI G +R V F++ +DA A
Sbjct: 13 LSDEAVEDGLFHEFKKFGDVS-VKISRLGDERVAFVNFRRPEDARAA 58
>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 = 40.8 bits (96), Expect = 2e-06
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII---GQGGDRYGLVCFKKADDAEKAILGSH 59
LF+ + + ++ L + K G++ V+I+ + V F+ +DAEKA+ +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 60 EKHFFGCKIDVS 71
K G K+ VS
Sbjct: 61 GKELDGRKLKVS 72
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 38.0 bits (89), Expect = 3e-05
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 4/72 (5%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII----GQGGDRYGLVCFKKADDAEKAILGS 58
LF+ + + ++ L + K GKV V+++ + V F+ +DAEKA+
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61
Query: 59 HEKHFFGCKIDV 70
+ K G + V
Sbjct: 62 NGKELDGRPLKV 73
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 34.4 bits (80), Expect = 4e-04
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 17 LYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSPY 73
LY + G V +K++ + + V F + AEKA+ + F G + V
Sbjct: 1 LYKLFSPFGNVEKIKLL-KKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 86
Score = 33.5 bits (77), Expect = 0.002
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 9 SDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCK 67
SD L+ + + K+G + +VK++ R Y V F DDA+ A+ G
Sbjct: 15 SDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNALAKGQGTILDGRH 74
Query: 68 IDVSP 72
I
Sbjct: 75 IRCER 79
>gnl|CDD|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation
factor (ACF). hnRNP R is a ubiquitously expressed
nuclear RNA-binding protein that specifically bind
mRNAs with a preference for poly(U) stretches and has
been implicated in mRNA processing and mRNA transport,
and also acts as a regulator to modify binding to
ribosomes and RNA translation. hnRNP Q is also a
ubiquitously expressed nuclear RNA-binding protein. It
has been identified as a component of the spliceosome
complex, as well as a component of the apobec-1
editosome, and has been implicated in the regulation of
specific mRNA transport. ACF is an RNA-binding subunit
of a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. This
family also includes two functionally unknown
RNA-binding proteins, RBM46 and RBM47. All members
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains).
Length = 72
Score = 33.0 bits (76), Expect = 0.003
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 1 MALFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHE 60
L++ + ++ ++ L + ++G+V VK I Y V F++ DDA KA+ +
Sbjct: 2 KVLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD----YAFVHFEERDDAVKAMEEMNG 57
Query: 61 KHFFGCKIDVS 71
K G I+VS
Sbjct: 58 KELEGSPIEVS 68
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 33.8 bits (76), Expect = 0.005
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
LF+ + ++ L +KK G V V+++ DR + V F+ + AEKAI
Sbjct: 118 LFVGNLPYDVTEEDLRELFKKFGPVKRVRLVR---DRETGKSRGFAFVEFESEESAEKAI 174
Query: 56 LGSHEKHFFGCKIDVSP 72
+ K G + V
Sbjct: 175 EELNGKELEGRPLRVQK 191
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex
in vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the
hnRNA in the nucleus and in processing of pre-mRNA such
as splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 31.8 bits (73), Expect = 0.006
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
K+ L + K+GK+ + + +G YG V F +DA A+ G + + G K+D++
Sbjct: 15 KEDLEEIFSKYGKILGISL-HKG---YGFVQFDNEEDARAAVAGENGREIAGQKLDIN 68
>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 = 30.5 bits (69), Expect = 0.021
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 21 YKKHGKVSWVKII--GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
+ + G + V+II +G +G V F + DA++A H G KI+V
Sbjct: 21 FGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHGTVVEGRKIEV 72
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily
corresponds to the RRM2 of La and LARP7. La is a highly
abundant nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. LARP7 is an oligopyrimidine-binding
protein that binds to the highly conserved 3'-terminal
U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable
component of the 7SK small nuclear ribonucleoprotein
(7SK snRNP), intimately associates with all the nuclear
7SK and is required for 7SK stability. LARP7 also acts
as a negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. LARP7 plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. Both La and LARP7 contain an N-terminal
La motif (LAM), followed by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 30.4 bits (69), Expect = 0.028
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 6 YVVSDTSLKDGLYHE-----YKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAI 55
++ TS+ G+ E + + G+V +V G G + FK + A+KA
Sbjct: 2 VILKITSIGPGVTREDIKAVFAQFGEVKYVDFTE--GADTGYIRFKTPEAAQKAR 54
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe
CD corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 79
Score = 29.9 bits (68), Expect = 0.035
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAI 55
L++ + D+ + L E+ G ++ K++ R +G VCF ++A KA+
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAV 59
>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 = 29.9 bits (68), Expect = 0.035
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
LF+ + D + + L ++K+G V+ ++ YG V ++ +DAE AI +
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVV----KNYGFVHMEEEEDAEDAIKALNGYE 57
Query: 63 FFGCKIDV 70
F G +I+V
Sbjct: 58 FMGKRINV 65
>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 = 29.8 bits (68), Expect = 0.046
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 7/66 (10%)
Query: 8 VSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDR-YGLVCFKKADDAEKAILGSHEKHFF 64
+ D LK+ + K+GK++ K++ +G + +G V F+ + A+KA+ + K
Sbjct: 13 MDDEKLKE----LFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVN 68
Query: 65 GCKIDV 70
G K+ V
Sbjct: 69 GKKLYV 74
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM,
but unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might
share similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 29.6 bits (67), Expect = 0.046
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 17 LYHEYKKHGKVSWVKII----GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
L + K+GKV KI+ G +G V ++A K I H G I V
Sbjct: 16 LKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVISV 73
>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 = 29.5 bits (67), Expect = 0.047
Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAILGSHEKHFFGCKI 68
++ L + K G + ++I+ R + V F+ +DAEKA+ + K G ++
Sbjct: 12 EEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
>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 = 29.6 bits (67), Expect = 0.047
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 9/61 (14%)
Query: 22 KKHGKVSWVKII--------GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSPY 73
K+GK+ + GQ Y V F+ ++AEKA+ + K G K+ V
Sbjct: 21 SKYGKIKKFDFLFHKSGPLKGQPRG-YCFVTFETKEEAEKALKSLNGKTALGKKLVVRWA 79
Query: 74 H 74
H
Sbjct: 80 H 80
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 30.0 bits (68), Expect = 0.048
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 16/87 (18%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKI-IGQGGDRYGLVCFKKADDAEKAI-LGSHE 60
IYV + + + L ++ G++ + + GD YG V ++ A DA +AI G+ +
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAIEHGNDD 64
Query: 61 KHFFGCKIDV----------SPYHDVD 77
K D+ S Y D+D
Sbjct: 65 PTE--PKYDLCFGGRRQFCQSSYADLD 89
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also
stimulate translation initiation. It contains a five
stranded beta sheet which forms an atypical RNA
recognition motif.
Length = 102
Score = 29.6 bits (67), Expect = 0.069
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 4 FIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAI 55
F + TS +D + + +HG+V +V GD+ G V FK + A+KA+
Sbjct: 6 FSGLNKPTSRED-IKEAFSQHGEVKYVDF--LEGDKEGYVRFKTPEAAKKAL 54
>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 = 30.2 bits (68), Expect = 0.077
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 8 VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAILGSHEKHFF 64
V++ L++ + K G+++ ++ G R + V F+K +DA KA+ + K
Sbjct: 190 VNEDKLRE----LFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIG 245
Query: 65 GCKID 69
K
Sbjct: 246 LAKEG 250
Score = 27.1 bits (60), Expect = 1.0
Identities = 16/66 (24%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDR-YGLVCFKKADDAEKAILGSH 59
L++ + DT + L + + G+++ K++ +G R +G VCF ++A +A+ H
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMH 347
Query: 60 EKHFFG 65
+ G
Sbjct: 348 GRMLGG 353
Score = 25.9 bits (57), Expect = 2.9
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 17 LYHEYKKHGKVSWVK----IIGQGGDRYGLVCFKKADDAEKAI 55
LY +K G V V+ + + YG V F+ DAE+A+
Sbjct: 17 LYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERAL 59
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 29.2 bits (66), Expect = 0.079
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDRYGLVCFKKADDAEKAILGSHE 60
I+V +S K+ L + +HGK+ V +I + + + F++ A +A+ E
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAV--ESE 63
Query: 61 KH 62
H
Sbjct: 64 NH 65
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM1 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 76
Score = 28.5 bits (64), Expect = 0.14
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 8/54 (14%)
Query: 6 YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGG-DR---YGLVCFKKADDAEKAI 55
+ V D LK E++K G V ++I R +G V F+ +DA+KAI
Sbjct: 9 WSVDDEWLKA----EFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAI 58
>gnl|CDD|240998 cd12554, RRM1_RBM15B, RNA recognition motif 1 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subfamily corresponds to the RRM1 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 81
Score = 28.3 bits (63), Expect = 0.21
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 10/52 (19%)
Query: 8 VSDTSLKDGLYHEYKKHGKVSWVKI-----IGQGGDRYGLVCFKKADDAEKA 54
+ D L+D L+H++K+ G +S VK+ +G R V F+ +DA +A
Sbjct: 14 LPDELLEDALFHQFKRFGDIS-VKLSHTPELG----RVAYVNFRHPEDAREA 60
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger
CCHC-type and RNA-binding motif-containing protein 1
(ZCRB1) and similar proteins. This subfamily
corresponds to the RRM of ZCRB1, also termed MADP-1, or
U11/U12 small nuclear ribonucleoprotein 31 kDa protein
(U11/U12 snRNP 31 or U11/U12-31K), a novel
multi-functional nuclear factor, which may be involved
in morphine dependence, cold/heat stress, and
hepatocarcinoma. It is located in the nucleoplasm, but
outside the nucleolus. ZCRB1 is one of the components
of U11/U12 snRNPs that bind to U12-type pre-mRNAs and
form a di-snRNP complex, simultaneously recognizing the
5' splice site and branchpoint sequence. ZCRB1 is
characterized by an RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 28.1 bits (63), Expect = 0.22
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 6/74 (8%)
Query: 4 FIYVVS-DTSLKDGLYHE-YKKHGKVSWVKIIGQGGDR----YGLVCFKKADDAEKAILG 57
+YV + SL + H+ + K+GKV V I+ R + F +DA K +
Sbjct: 3 TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62
Query: 58 SHEKHFFGCKIDVS 71
+ K FG + S
Sbjct: 63 LNNKELFGRTLKCS 76
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia
(DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE.
This subfamily corresponds to the RRM domain of two
Deleted in AZoospermia (DAZ) autosomal homologs, DAZL
(DAZ-like) and BOULE. BOULE is the founder member of
the family and DAZL arose from BOULE in an ancestor of
vertebrates. The DAZ gene subsequently originated from
a duplication transposition of the DAZL gene.
Invertebrates contain a single DAZ homolog, BOULE,
while vertebrates, other than catarrhine primates,
possess both BOULE and DAZL genes. The catarrhine
primates possess BOULE, DAZL, and DAZ genes. The family
members encode closely related RNA-binding proteins
that are required for fertility in numerous organisms.
These proteins contain an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a varying number of
copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 28.0 bits (63), Expect = 0.23
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 10/58 (17%)
Query: 21 YKKHGKVSWVKIIGQGGDR------YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
+ + G V VKII DR YG V F+ +DAEK IL +F G K+++ P
Sbjct: 23 FSRFGSVKDVKIIT---DRAGVSKGYGFVTFETQEDAEK-ILAMGNLNFRGKKLNIGP 76
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 27.5 bits (62), Expect = 0.29
Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDRYGLVCFKKADDAEKAILGSHE 60
L++ + + ++ L + +GKV V+++ + V F +DAE A+ +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 61 KHFFGCKI 68
G +
Sbjct: 61 LVLDGRTL 68
>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 = 27.6 bits (62), Expect = 0.34
Identities = 16/61 (26%), Positives = 32/61 (52%)
Query: 13 LKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
L+D L E +K G+V V + + D V FK+ ++A++ I + + F G +++
Sbjct: 25 LRDDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEAER 84
Query: 73 Y 73
+
Sbjct: 85 W 85
>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 = 27.6 bits (62), Expect = 0.35
Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 4/57 (7%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKI-IGQGGDR---YGLVCFKKADDAEKAI 55
+FI + + ++ L + + G+V + +I + V FK + A+K +
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed
in the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 27.4 bits (61), Expect = 0.40
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII-GQGGDRYGL--VCFKKADDAEKAILGSH 59
LF+ + + K+ L +KKHG V V+++ + G GL V ++ A +A+L
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64
Query: 60 EKHFFGCKIDVS 71
I V+
Sbjct: 65 GTEIKEKTISVA 76
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in
muscle differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 27.4 bits (61), Expect = 0.42
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 40 YGLVCFKKADDAEKAI 55
YG V + +DAEKAI
Sbjct: 45 YGFVNYVDPEDAEKAI 60
>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 = 26.6 bits (59), Expect = 0.71
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 8 VSDTSLKDGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKAI 55
+ +L+ + G++S +++ G + YG V F K +DAE AI
Sbjct: 11 IDTETLRA----AFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAI 58
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or
ASF-1), serine/arginine-rich splicing factor 9 (SRSF9
or SRp30C), and plant pre-mRNA-splicing factor SF2
(SR1). SRSF1 is a shuttling SR protein involved in
constitutive and alternative splicing,
nonsense-mediated mRNA decay (NMD), mRNA export and
translation. It also functions as a splicing-factor
oncoprotein that regulates apoptosis and proliferation
to promote mammary epithelial cell transformation.
SRSF9 has been implicated in the activity of many
elements that control splice site selection, the
alternative splicing of the glucocorticoid receptor
beta in neutrophils and in the gonadotropin-releasing
hormone pre-mRNA. It can also interact with other
proteins implicated in alternative splicing, including
YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both,
SRSF1 and SRSF9, contain two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
RS domains rich in serine-arginine dipeptides. In
contrast, SF2 contains two N-terminal RRMs and a
C-terminal PSK domain rich in proline, serine and
lysine residues. .
Length = 72
Score = 26.2 bits (58), Expect = 0.90
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 21 YKKHGKVSWVKI-IGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
+ K+G + + + + G + V F+ DAE A+ G F G ++ V
Sbjct: 20 FYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGYDFDGYRLRV 70
>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 = 25.9 bits (57), Expect = 1.0
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 4/48 (8%)
Query: 24 HGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
+G V VK+I + V F+ + A +A H K + V+
Sbjct: 23 YGAVKEVKMI----SNFAFVEFESLESAIRAKDSVHGKVLNNNPLYVT 66
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of
specific mRNAs during gametogenesis. .
Length = 81
Score = 26.3 bits (58), Expect = 1.1
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 9/62 (14%)
Query: 17 LYHEYKKHGKVSWVKIIGQGGDR------YGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
L + ++G V VKI+ DR YG V F+ +DA+K + ++ F K+++
Sbjct: 19 LRKFFSQYGTVKEVKIVN---DRAGVSKGYGFVTFETQEDAQKILQEANRLCFRDKKLNI 75
Query: 71 SP 72
Sbjct: 76 GQ 77
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein
3 (RBM3) and similar proteins. This subfamily
corresponds to the RRM domain of two structurally
related heterogenous nuclear ribonucleoproteins, CIRBP
(also termed CIRP or A18 hnRNP) and RBM3 (also termed
RNPL), both of which belong to a highly conserved cold
shock proteins family. The cold shock proteins can be
induced after exposure to a moderate cold-shock and
other cellular stresses such as UV radiation and
hypoxia. CIRBP and RBM3 may function in
posttranscriptional regulation of gene expression by
binding to different transcripts, thus allowing the
cell to response rapidly to environmental signals.
However, the kinetics and degree of cold induction are
different between CIRBP and RBM3. Tissue distribution
of their expression is different. CIRBP and RBM3 may be
differentially regulated under physiological and stress
conditions and may play distinct roles in cold
responses of cells. CIRBP, also termed glycine-rich
RNA-binding protein CIRP, is localized in the nucleus
and mediates the cold-induced suppression of cell cycle
progression. CIRBP also binds DNA and possibly serves
as a chaperone that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore,
RBM3 may be essential for cell proliferation and
mitosis. Both, CIRBP and RBM3, contain an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), that
is involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 26.0 bits (57), Expect = 1.1
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 10/75 (13%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
LFI +S + + L + K+G++S V ++ DR +G V F+ DDA+ A+
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVK---DRETQRSRGFGFVTFENPDDAKDAM 59
Query: 56 LGSHEKHFFGCKIDV 70
+ + K G +I V
Sbjct: 60 MAMNGKSVDGRQIRV 74
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor 12 (SRSF12) and
similar proteins. This subgroup corresponds to the RRM
of SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19). SRSF12 is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates
distal alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. SRSF12 contains a single N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
followed by a C-terminal RS domain rich in
serine-arginine dipeptides. .
Length = 84
Score = 26.1 bits (57), Expect = 1.2
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 2 ALFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR----YGLVCFKKADDAEKAILG 57
+LF+ V+D + + L E+ ++G + V + R + + F+ DAE A+
Sbjct: 2 SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61
Query: 58 SHEKHFFGCKIDV 70
+ K G +I++
Sbjct: 62 LNRKWVCGRQIEI 74
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 25.7 bits (57), Expect = 1.2
Identities = 13/40 (32%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 22 KKHGKVSWVKIIGQGGDR----YGLVCFKKADDAEKAILG 57
+ GK+ K I YG V F + A KAI G
Sbjct: 22 QPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM1 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 26.0 bits (58), Expect = 1.3
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 8/61 (13%)
Query: 14 KDGLYHEYKKHGKVSWVKII--GQGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
+D L ++ G+V+ VK++ G R +G V FK +DA++A+ K+F ID
Sbjct: 14 EDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAV-----KYFNKTFIDT 68
Query: 71 S 71
S
Sbjct: 69 S 69
>gnl|CDD|180344 PRK05994, PRK05994, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 427
Score = 26.6 bits (59), Expect = 1.6
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 22 KKHGKVSWVKIIGQGGDRY 40
K H KVSWV G D Y
Sbjct: 310 KGHPKVSWVNYAGLPDDPY 328
>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 = 25.5 bits (56), Expect = 1.7
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 40 YGLVCFKKADDAEKAI 55
YG V F+ DAE AI
Sbjct: 43 YGFVSFRSQQDAENAI 58
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein
orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which
is a putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 25.3 bits (56), Expect = 2.2
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 7/46 (15%)
Query: 17 LYHEYKKHGKVSWVKIIGQGGD--RY-----GLVCFKKADDAEKAI 55
L E+ + G ++ VKI+ + R G V F DAE+A+
Sbjct: 18 LCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
>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 = 25.3 bits (56), Expect = 2.3
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
+ V F++ +DA AI +E FG I V+
Sbjct: 42 FAFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73
>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM1 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 79
Score = 25.3 bits (56), Expect = 2.4
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
+G V F +DA++A+ + F G KI V
Sbjct: 43 FGYVTFALEEDAKRALEEKKKTKFGGRKIHV 73
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 24.9 bits (55), Expect = 3.1
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 14/57 (24%)
Query: 6 YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
Y V++ LKD L+ + G+V+ ++I DR +G V + A++A AI
Sbjct: 9 YNVTEEDLKD-LFGQ---FGEVTSARVIT---DRETGRSRGFGFVEMETAEEANAAI 58
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the
RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. SRSF12, also
termed 35 kDa SR repressor protein (SRrp35), or
splicing factor, arginine/serine-rich 13B (SFRS13B), or
splicing factor, arginine/serine-rich 19 (SFRS19), is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice
site of the adenovirus E1A pre-mRNA in vivo. Both,
SRSF10 and SRSF12, contain a single N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a C-terminal RS domain rich in serine-arginine
dipeptides. .
Length = 84
Score = 25.0 bits (55), Expect = 3.1
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 2 ALFIYVVSDTSLKDGLYHEYKKHGKVSWVKI----IGQGGDRYGLVCFKKADDAEKAILG 57
+L++ V+D + D L + K+G + V I + + V F+ DAE A+
Sbjct: 2 SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61
Query: 58 SHEKHFFGCKIDV 70
F G +I++
Sbjct: 62 LDRTRFLGREIEI 74
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM1 of SXL which governs sexual
differentiation and X chromosome dosage compensation in
Drosophila melanogaster. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 25.1 bits (55), Expect = 3.3
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 40 YGLVCFKKADDAEKAI 55
+G V ++ A+DA++AI
Sbjct: 44 FGFVDYQSAEDAQRAI 59
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 24.9 bits (55), Expect = 3.6
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
Y L+ ++ +A+ AI G + K G I V
Sbjct: 50 YALIEYETKKEAQAAIEGLNGKELLGQTISVD 81
>gnl|CDD|217578 pfam03468, XS, XS domain. The XS (rice gene X and SGS3) domain is
found in a family of plant proteins including gene X and
SGS3. SGS3 is thought to be involved in
post-transcriptional gene silencing (PTGS). This domain
contains a conserved aspartate residue that may be
functionally important. The XS domain has recently been
predicted to possess an RRM-like RNA-binding domain by
fold recognition.
Length = 116
Score = 25.0 bits (55), Expect = 3.8
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 18 YHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADD 50
+ E + HGK W+ GQ YG V +ADD
Sbjct: 79 HFEKQGHGKKDWLARRGQDSKLYGWV--ARADD 109
>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome
proliferator-activated receptor gamma
coactivator-related protein 1 (PRC) and similar
proteins. This subgroup corresponds to the RRM of PRC,
also termed PGC-1-related coactivator, one of the
members of PGC-1 transcriptional coactivators family,
including peroxisome proliferator-activated receptor
gamma coactivators PGC-1alpha and PGC-1beta. Unlike
PGC-1alpha and PGC-1beta, PRC is ubiquitous and more
abundantly expressed in proliferating cells than in
growth-arrested cells. PRC has been implicated in the
regulation of several metabolic pathways, mitochondrial
biogenesis, and cell growth. It functions as a
growth-regulated transcriptional cofactor activating
many nuclear genes specifying mitochondrial respiratory
function. PRC directly interacts with nuclear
transcriptional factors implicated in respiratory chain
expression including nuclear respiratory factors 1 and
2 (NRF-1 and NRF-2), CREB (cAMP-response
element-binding protein), and estrogen-related receptor
alpha (ERRalpha). It interacts indirectly with the
NRF-2beta subunit through host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. Furthermore, like
PGC-1alpha and PGC-1beta, PRC can transactivate a
number of NRF-dependent nuclear genes required for
mitochondrial respiratory function, including those
encoding cytochrome c, 5-aminolevulinate synthase,
Tfam, and TFB1M, and TFB2M. Further research indicates
that PRC may also act as a sensor of metabolic stress
that orchestrates a redox-sensitive program of
inflammatory gene expression. PRC is a multi-domain
protein containing an N-terminal activation domain, an
LXXLL coactivator signature, a central proline-rich
region, a tetrapeptide motif (DHDY) responsible for HCF
binding, a C-terminal arginine/serine-rich (SR) domain,
and an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 91
Score = 24.8 bits (54), Expect = 3.9
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 37 GDRYGLVCFKKADDAEKAILGSHE 60
GD YG V ++ ++A AI H+
Sbjct: 40 GDNYGFVTYRYTEEAFAAIENGHK 63
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 24.5 bits (54), Expect = 4.4
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 7/62 (11%)
Query: 12 SLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAILGSHEKHFFGCKI 68
LKD +++ G V + R +G V F+ +DA++AI + G ++
Sbjct: 14 DLKD----LFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGREL 69
Query: 69 DV 70
+V
Sbjct: 70 EV 71
>gnl|CDD|234102 TIGR03075, PQQ_enz_alc_DH, PQQ-dependent dehydrogenase,
methanol/ethanol family. This protein family has a
phylogenetic distribution very similar to that coenzyme
PQQ biosynthesis enzymes, as shown by partial
phylogenetic profiling. Genes in this family often are
found adjacent to the PQQ biosynthesis genes themselves.
An unusual, strained disulfide bond between adjacent Cys
residues contributes to PQQ-binding, as does a Trp
residue that is part of a PQQ enzyme repeat (see
pfam01011). Characterized members include the
dehydrogenase subunit of a membrane-anchored, three
subunit alcohol (ethanol) dehydrogenase of Gluconobacter
suboxydans, a homodimeric ethanol dehydrogenase in
Pseudomonas aeruginosa, and the large subunit of an
alpha2/beta2 heterotetrameric methanol dehydrogenase in
Methylobacterium extorquens.
Length = 526
Score = 24.9 bits (55), Expect = 5.4
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 25 GKVSWVKIIGQGGDRYGLVCFKKADDAE 52
GKV I G G +G+ + A DA+
Sbjct: 166 GKV----ITGISGGEFGVRGYVTAYDAK 189
>gnl|CDD|147194 pfam04901, RAMP, Receptor activity modifying family. The
calcitonin-receptor-like receptor can function as
either a calcitonin-gene-related peptide or an
adrenomedullin receptor. The receptors function is
modified by receptor-activity-modifying protein or
RAMP. RAMPs are single-transmembrane-domain proteins.
Length = 115
Score = 24.6 bits (54), Expect = 5.4
Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 2/38 (5%)
Query: 38 DRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSPYHD 75
D+ G CF E+ L H +F C + D
Sbjct: 45 DKLG--CFWPNPLVERFFLEIHRHYFSNCSLSGRALED 80
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 24.1 bits (53), Expect = 5.8
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 12/76 (15%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQ---GGDR-YGLVCFKKADDAEKA 54
LF+ ++ L+ + K G+V V ++ G R +G V F+ +DA+ A
Sbjct: 4 LFVSGLSTRTTEKELEA----LFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59
Query: 55 ILGSHEKHFFGCKIDV 70
I + K G I V
Sbjct: 60 IRDLNGKELEGRVIKV 75
>gnl|CDD|187610 cd05352, MDH-like_SDR_c, mannitol dehydrogenase (MDH)-like,
classical (c) SDRs. NADP-mannitol dehydrogenase
catalyzes the conversion of fructose to mannitol, an
acyclic 6-carbon sugar. MDH is a tetrameric member of
the SDR family. This subgroup also includes various
other tetrameric SDRs, including Pichia stipitis
D-arabinitol dehydrogenase (aka polyol dehydrogenase),
Candida albicans Sou1p, a sorbose reductase, and
Candida parapsilosis (S)-specific carbonyl reductase
(SCR, aka S-specific alcohol dehydrogenase) which
catalyzes the enantioselective reduction of
2-hydroxyacetophenone into (S)-1-phenyl-1,2-ethanediol.
SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRS are
approximately 350 residues. Sequence identity between
different SDR enzymes are typically in the 15-30%
range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser).
Length = 252
Score = 25.0 bits (55), Expect = 6.0
Identities = 6/32 (18%), Positives = 13/32 (40%)
Query: 46 KKADDAEKAILGSHEKHFFGCKIDVSPYHDVD 77
+A++ + + + K DVS V+
Sbjct: 43 PRAEEKAEELAKKYGVKTKAYKCDVSSQESVE 74
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a
role in the pre-mRNA splicing process, but is not
essential for growth. Srp1p is closely related to the
SR protein family found in Metazoa. It contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a glycine hinge and a RS domain in the middle, and a
C-terminal domain. The family also includes a novel
group of arginine/serine (RS) or serine/arginine (SR)
splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RRMs at their N-terminus and an RS
domain at their C-terminus.
Length = 70
Score = 23.9 bits (52), Expect = 6.1
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
+ V F+ ++DA KA+ H G + V
Sbjct: 36 FAFVEFEDSEDATKALEALHGSRIDGSVLTV 66
>gnl|CDD|216247 pfam01019, G_glu_transpept, Gamma-glutamyltranspeptidase.
Length = 495
Score = 24.9 bits (55), Expect = 6.4
Identities = 5/15 (33%), Positives = 10/15 (66%)
Query: 15 DGLYHEYKKHGKVSW 29
GL +K++G++ W
Sbjct: 88 AGLEEAHKRYGRLPW 102
>gnl|CDD|223482 COG0405, Ggt, Gamma-glutamyltransferase [Amino acid transport and
metabolism].
Length = 539
Score = 24.9 bits (55), Expect = 6.9
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 15 DGLYHEYKKHGKVSWVKII 33
GL +K++G + W ++
Sbjct: 121 AGLEEAHKRYGTLPWADLL 139
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 23.6 bits (51), Expect = 8.7
Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 21 YKKHGKVSWVKIIGQGGD-RYGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
+ K+G++ +++ + G + V F+ DAE A+ G + F C++ V
Sbjct: 20 FYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGYDFGQCRLRV 70
>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 = 23.7 bits (52), Expect = 8.7
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 4/56 (7%)
Query: 20 EYKKHGKVSWVKII--GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSPY 73
E K G V +K+ G Y V FK + A+K I + + F G +I
Sbjct: 31 ECSKFGPVEHIKVDKNSPEGVVY--VKFKTVEAAQKCIQALNGRWFDGRQITAEYV 84
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
0.324 0.143 0.451
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: 4,331,451
Number of extensions: 345580
Number of successful extensions: 373
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 79
Length of query: 83
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 31
Effective length of database: 8,631,194
Effective search space: 267567014
Effective search space used: 267567014
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)