RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1928
(105 letters)
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit
4 (THOC4) and similar proteins. This subgroup
corresponds to the RRM of THOC4, also termed
transcriptional coactivator Aly/REF, or ally of AML-1
and LEF-1, or bZIP-enhancing factor BEF, an mRNA
transporter protein with a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It is
involved in RNA transportation from the nucleus. THOC4
was initially identified as a transcription coactivator
of LEF-1 and AML-1 for the TCRalpha enhancer function.
In addition, THOC4 specifically binds to rhesus (RH)
promoter in erythroid. It might be a novel
transcription cofactor for erythroid-specific genes. .
Length = 75
Score = 120 bits (304), Expect = 2e-37
Identities = 47/59 (79%), Positives = 55/59 (93%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I ELF+EFG LK A +HYDRSGRSLGTAD+++ERR+DA+KAMKQYNGVPLDGRPM+IQL
Sbjct: 17 IKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQYNGVPLDGRPMKIQL 75
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a
transcription coactivator of LEF-1 and AML-1 for the
TCRalpha enhancer function. In addition, THOC4
specifically binds to rhesus (RH) promoter in
erythroid, and might be a novel transcription cofactor
for erythroid-specific genes. SKAR shows high sequence
homology with THOC4 and possesses one RRM as well. SKAR
is widely expressed and localizes to the nucleus. It
may be a critical player in the function of S6K1 in
cell and organism growth control by binding the
activated, hyperphosphorylated form of S6K1 but not
S6K2. Furthermore, SKAR functions as a protein partner
of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 98.4 bits (246), Expect = 1e-28
Identities = 34/57 (59%), Positives = 47/57 (82%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
ELF G +K K++YDRSGRS GTAD+++E+R DA +A+KQ+NGV LDG+PMQ++L
Sbjct: 19 ELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQVEL 75
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46),
belonging to the Aly/REF family of RNA binding proteins
that have been implicated in coupling transcription
with pre-mRNA splicing and nucleo-cytoplasmic mRNA
transport. SKAR is widely expressed and localizes to
the nucleus. It may be a critical player in the
function of S6K1 in cell and organism growth control by
binding the activated, hyperphosphorylated form of S6K1
but not S6K2. Furthermore, SKAR functions as a protein
partner of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. SKAR contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain).
Length = 69
Score = 66.1 bits (162), Expect = 5e-16
Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 6/59 (10%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I ELFS G LK A+L G A+++Y R+ DA+ A+ +YN LDG+PM+ +L
Sbjct: 17 IVELFSAIGALKRARL------VRPGVAEVVYVRKDDALTAIDKYNNRELDGQPMKCKL 69
>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 = 61.9 bits (151), Expect = 3e-14
Identities = 23/59 (38%), Positives = 38/59 (64%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ ELFS+FG ++S ++ D+ G+S G A + +E DA KA++ NG LDGR +++
Sbjct: 14 DLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 60.3 bits (147), Expect = 9e-14
Identities = 25/59 (42%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ ELFS+FG ++S +L D+ +G+S G A + +E DA KA++ NG LDGRP+++
Sbjct: 15 ELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 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 = 58.0 bits (141), Expect = 9e-13
Identities = 23/56 (41%), Positives = 36/56 (64%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPM 56
+ +LFS+FGP++S ++ D +GRS G A + +E DA KA++ NG L GR +
Sbjct: 14 DLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 58.8 bits (141), Expect = 1e-11
Identities = 31/100 (31%), Positives = 49/100 (49%), Gaps = 5/100 (5%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ ELF +FGP+K +L DR +G+S G A + +E A KA+++ NG L+GRP+++Q
Sbjct: 132 LRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQK 191
Query: 61 AADV----SVLENTVPRPVARGGRGGASGGYRNGTAPTYR 96
A S L N + A+ G +
Sbjct: 192 AQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 50.6 bits (122), Expect = 7e-10
Identities = 21/59 (35%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
M+YE+FS GP+ S ++ D + RSLG A + ++ +DA +A+ N + G+P++I
Sbjct: 15 MLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPIRI 73
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in
yeast. Yra1p is associated with Pse1p and Kap123p, two
members of the beta-importin family, further mediating
transport of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission
yeast as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 48.6 bits (116), Expect = 4e-09
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 2/61 (3%)
Query: 2 IYELF-SEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG-RPMQIQ 59
I E F S+ GP+K L Y+ G+S G A++ ++R DA KA ++NG DG R M+++
Sbjct: 16 IREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRIDDGNRKMKVE 75
Query: 60 L 60
+
Sbjct: 76 V 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 = 47.9 bits (115), Expect = 5e-09
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+Y+LFS FG ++ KL + G A + + A KA++ NGV GRP+++ +
Sbjct: 1 LYKLFSPFGNVEKIKL----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>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 = 48.0 bits (115), Expect = 7e-09
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ +F FG ++ +L D +GRS G + + DA KA++Q NG L GRP+++
Sbjct: 14 DLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKV 72
>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 = 48.0 bits (115), Expect = 8e-09
Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+++ F+EFG +K+ L+ DR +G G A + YE + +A A++ NG L G+ + +
Sbjct: 23 VHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVDW 82
Query: 61 A 61
A
Sbjct: 83 A 83
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2
protein homolog alpha (TRA-2 alpha) and similar
proteins. This subgroup corresponds to the RRM of
TRA2-alpha or TRA-2-alpha, also termed transformer-2
protein homolog A, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein (SRp40) that
specifically binds to gonadotropin-releasing hormone
(GnRH) exonic splicing enhancer on exon 4 (ESE4) and is
necessary for enhanced GnRH pre-mRNA splicing. It
strongly stimulates GnRH intron A excision in a
dose-dependent manner. In addition, TRA2-alpha can
interact with either 9G8 or SRp30c, which may also be
crucial for ESE-dependent GnRH pre-mRNA splicing.
TRA2-alpha contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 79
Score = 48.0 bits (114), Expect = 8e-09
Identities = 25/58 (43%), Positives = 39/58 (67%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ E+FS +GPL + YD R+GRS G A + +ER D+ +AM+ NG+ LDGR +++
Sbjct: 16 LREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRV 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 = 46.5 bits (111), Expect = 3e-08
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+LF +FG + SA++ DR +GRS G + E +A A+++ NG GR + + A
Sbjct: 18 DLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEA 76
>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 = 46.4 bits (111), Expect = 3e-08
Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 6/66 (9%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYN-----GVPLDGRP 55
+ ELFS+FG +K A++ D+ +G S GTA + ++ + A K ++ + G+ LDGR
Sbjct: 17 LKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRR 76
Query: 56 MQIQLA 61
+ + LA
Sbjct: 77 LIVTLA 82
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the
U1A/U2B"/SNF protein family. This subfamily
corresponds to the RRM1 of U1A/U2B"/SNF protein family
which contains Drosophila sex determination protein SNF
and its two mammalian counterparts, U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2
small nuclear ribonucleoprotein B" (U2 snRNP B" or
U2B"), all of which consist of two RNA recognition
motifs (RRMs), connected by a variable, flexible
linker. SNF is an RNA-binding protein found in the U1
and U2 snRNPs of Drosophila where it is essential in
sex determination and possesses a novel dual RNA
binding specificity. SNF binds with high affinity to
both Drosophila U1 snRNA stem-loop II (SLII) and U2
snRNA stem-loop IV (SLIV). It can also bind to poly(U)
RNA tracts flanking the alternatively spliced
Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal
protein (SXL). U1A is an RNA-binding protein associated
with the U1 snRNP, a small RNA-protein complex involved
in pre-mRNA splicing. U1A binds with high affinity and
specificity to stem-loop II (SLII) of U1 snRNA. It is
predominantly a nuclear protein that shuttles between
the nucleus and the cytoplasm independently of
interactions with U1 snRNA. Moreover, U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins.
U2B", initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA, is a unique protein
that comprises of the U2 snRNP. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. Moreover, U2B" does not
require an auxiliary protein for binding to RNA, and
its nuclear transport is independent of U2 snRNA
binding. .
Length = 78
Score = 46.4 bits (111), Expect = 3e-08
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 14/66 (21%)
Query: 2 IYELFSEFGP------LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
+Y LFS+FGP K+ K+ G A ++++ A A++ G P +P
Sbjct: 20 LYALFSQFGPVLDIVASKTLKMR--------GQAFVVFKDVESATNALRALQGFPFYDKP 71
Query: 56 MQIQLA 61
M+IQ A
Sbjct: 72 MRIQYA 77
>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 = 46.1 bits (110), Expect = 3e-08
Identities = 20/55 (36%), Positives = 36/55 (65%), Gaps = 1/55 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
+ E+FS +GP++ ++ YD ++GRS G + +E DA +A ++ NG+ +DGR
Sbjct: 16 LREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRR 70
>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 = 45.7 bits (109), Expect = 5e-08
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAA 62
E FSE GP+K + D+ S + G + + DA +A+++ GR + ++ A
Sbjct: 18 EFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAK 77
>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), yeast ortholog
mRNA 3'-end-processing protein RNA15 and similar
proteins. This subfamily corresponds to the RRM domain
of CSTF2, its tau variant and eukaryotic homologs.
CSTF2, also termed cleavage stimulation factor 64 kDa
subunit (CstF64), is the vertebrate conterpart of yeast
mRNA 3'-end-processing protein RNA15. It is expressed
in all somatic tissues and is one of three cleavage
stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64
at U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation
in a more limited set of tissues and cell types,
largely in meiotic and postmeiotic male germ cells, and
to a lesser extent in brain. The loss of CSTF2T will
cause male infertility, as it is necessary for
spermatogenesis and fertilization. Moreover, CSTF2T is
required for expression of genes involved in
morphological differentiation of spermatids, as well as
for genes having products that function during
interaction of motile spermatozoa with eggs. It
promotes germ cell-specific patterns of polyadenylation
by using its RRM to bind to different sequence elements
downstream of polyadenylation sites than does CstF64.
The family also includes yeast ortholog mRNA
3'-end-processing protein RNA15 and similar proteins.
RNA15 is a core subunit of cleavage factor IA (CFIA),
an essential transcriptional 3'-end processing factor
from Saccharomyces cerevisiae. RNA recognition by CFIA
is mediated by an N-terminal RRM, which is contained in
the RNA15 subunit of the complex. The RRM of RNA15 has
a strong preference for GU-rich RNAs, mediated by a
binding pocket that is entirely conserved in both yeast
and vertebrate RNA15 orthologs.
Length = 75
Score = 44.9 bits (107), Expect = 1e-07
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E+FSE GP+ S +L DR +G+ G +E A A++ NG +GR +++
Sbjct: 15 LIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDF 74
Query: 61 A 61
A
Sbjct: 75 A 75
>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 = 44.5 bits (106), Expect = 2e-07
Identities = 18/56 (32%), Positives = 33/56 (58%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPM 56
+ ELF ++G + SAK+ D G+S G + +E A KA+++ NG ++G+ +
Sbjct: 17 KLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKL 72
>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 = 44.3 bits (105), Expect = 2e-07
Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 6 FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
F +FG + A++ DR +GRS G + +E DA KA++ +G LDGRP+ + +
Sbjct: 20 FEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 83
Score = 44.1 bits (104), Expect = 3e-07
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
++F +G ++ A + R G+ G A + ++R +A A++ NG+ +DGRP+ + A
Sbjct: 20 KIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWAVQ 79
>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 = 43.4 bits (103), Expect = 4e-07
Identities = 19/58 (32%), Positives = 34/58 (58%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ +LF E G + A + D GRS G +++E DA +A++ +NG L+GR +++
Sbjct: 14 DLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71
>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 = 46.3 bits (110), Expect = 4e-07
Identities = 21/61 (34%), Positives = 34/61 (55%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ ELFSE G + SAK+ D G S G + + +A +A+ + +G L G+P+ + L
Sbjct: 301 KLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL 360
Query: 61 A 61
A
Sbjct: 361 A 361
Score = 45.2 bits (107), Expect = 9e-07
Identities = 20/59 (33%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+Y+LF FGP+ S ++ D + RSLG + ++ +DA +A++ N L G+P++I
Sbjct: 16 KLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRI 74
Score = 40.6 bits (95), Expect = 4e-05
Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG 53
ELF++FG + SA + D SGRS G A + +E+ DA KA+++ NG +
Sbjct: 197 ELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
Score = 37.5 bits (87), Expect = 4e-04
Identities = 16/53 (30%), Positives = 33/53 (62%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+++ FS+FG + S K+ D +G+S G + +E+ A A+++ NG+ L+ +
Sbjct: 105 LFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK 157
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM2 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 43.4 bits (103), Expect = 4e-07
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAAD 63
+LFS FG + + G+ G A + + ++DA KA+K NG + GRP +A D
Sbjct: 18 KLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP----VAVD 73
Query: 64 VSV 66
+V
Sbjct: 74 WAV 76
>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 = 43.4 bits (103), Expect = 4e-07
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LFS+FG ++ L D +G S G + +E DA A++ NG L+GR ++++ A
Sbjct: 20 ALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKA 78
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in
mRNA surveillance. Furthermore, RNPS1 is a splicing
regulator whose activator function is controlled in
part by CK2 (casein kinase II) protein kinase
phosphorylation. It can also function as a
squamous-cell carcinoma antigen recognized by T cells-3
(SART3)-binding protein, and is involved in the
regulation of mRNA splicing. RNPS1 contains an
N-terminal serine-rich (S) domain, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and the
C-terminal arginine/serine/proline-rich (RS/P) domain.
.
Length = 73
Score = 43.3 bits (103), Expect = 4e-07
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ E+FS +G +K L DR G A + +E DA KA+K +G +DG+ + ++
Sbjct: 15 LKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73
>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 = 43.2 bits (102), Expect = 5e-07
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I LFS G ++S KL D+ +G+SLG + Y DA KA+ NG+ L + +++
Sbjct: 18 IRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSY 77
Query: 61 A 61
A
Sbjct: 78 A 78
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2
protein homolog beta (TRA-2 beta) and similar proteins.
This subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 43.5 bits (102), Expect = 5e-07
Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E+FS++GP+ + YD+ S RS G A + +E DA +A ++ NG+ LDGR +++ +
Sbjct: 28 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 86
>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 = 42.8 bits (101), Expect = 8e-07
Identities = 17/58 (29%), Positives = 34/58 (58%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+LF + G +KS +L +RSG+ G A + YE S A +A+ + +G + + + + ++
Sbjct: 21 KLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKEKTISVAIS 78
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is ubiquitously expressed Hu family member. It has
a variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the
cytoplasm, Hu proteins recognize and bind to AU-rich
RNA elements (AREs) in the 3' untranslated regions
(UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. This family
also includes the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own
pre-mRNA and promotes female-specific alternative
splicing. It contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 77
Score = 42.7 bits (101), Expect = 8e-07
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ LF GP++S K+ DR +G+SLG + Y +DA KA+ NG + + +++
Sbjct: 17 LRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSY 76
Query: 61 A 61
A
Sbjct: 77 A 77
>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 = 42.6 bits (101), Expect = 1e-06
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E FS FG + SAK+ D GRS G + + +A KA+ + NG + G+P+ + LA
Sbjct: 20 EEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALA 77
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 77
Score = 42.3 bits (100), Expect = 1e-06
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ E F E G + ++ D GRS G + + A KA+++ +G L GR +++ LA
Sbjct: 16 LEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK-SGEELLGREIRVDLA 74
Query: 62 A 62
Sbjct: 75 T 75
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition
motif 2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 41.9 bits (99), Expect = 1e-06
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 4 ELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
ELF FG + L D+ RS G A + + A+KA + +G GR + +
Sbjct: 18 ELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73
>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 = 41.5 bits (98), Expect = 3e-06
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 7/61 (11%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ ELFSE+G ++ K D A + +E R DA+KAM++ NG L+G P+++ L
Sbjct: 17 QLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMNGKELEGSPIEVSL 69
Query: 61 A 61
A
Sbjct: 70 A 70
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 41.5 bits (97), Expect = 3e-06
Identities = 19/57 (33%), Positives = 35/57 (61%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
E+FS G +K A + D+ G+S G + +E+ +A++A+ +NG L RPM +++
Sbjct: 19 EVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFNGQFLFDRPMHVKM 75
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. It interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20, and may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM11 is a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. It is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. Both, RBM7 and RBM11, contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 41.1 bits (97), Expect = 3e-06
Identities = 18/59 (30%), Positives = 34/59 (57%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
++YELF + GPL+ K+ D +G+ A + ++ A++ NG+ L GR ++I+
Sbjct: 17 ILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 75
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of
RBM23 remains unclear, it shows high sequence homology
to RBM39 and contains two RRMs. It may possibly
function as a pre-mRNA splicing factor. .
Length = 73
Score = 41.1 bits (97), Expect = 3e-06
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+YE FS+ G ++ ++ DR S RS G A + + A+ G L G+P+ +Q
Sbjct: 16 LYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLTGQRLLGQPIMVQ 73
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit
2 (NCBP2), or cell proliferation-inducing gene 55
protein, or NCBP-interacting protein 1 (NIP1). CBP20 is
the small subunit of the nuclear cap binding complex
(CBC), which is a conserved eukaryotic heterodimeric
protein complex binding to 5'-capped polymerase II
transcripts and plays a central role in the maturation
of pre-mRNA and uracil-rich small nuclear RNA (U
snRNA). CBP20 is most likely responsible for the
binding of capped RNA. It contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and interacts with the
second and third domains of CBP80, the large subunit of
CBC. .
Length = 78
Score = 41.0 bits (97), Expect = 4e-06
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRS-LGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
IYELFS G +K + DR ++ G + Y R DA A+K NG LD R +++
Sbjct: 15 IYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIRV 72
>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 = 43.0 bits (101), Expect = 6e-06
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ ++F FG ++ +LH D +GRS G + + +A +A++ NG L GRP+++
Sbjct: 202 ELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVG 261
Query: 60 LAADVSVLENTVPR 73
A D + L +
Sbjct: 262 YAQDSTYLLDAANT 275
Score = 35.3 bits (81), Expect = 0.003
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+YE FS+ G ++ + DR S RS G A + + IKA+ G L GRP+ +Q
Sbjct: 106 LYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQS 164
Query: 61 A 61
+
Sbjct: 165 S 165
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate
RNA-binding protein 7 (RBM7). This subfamily
corresponds to the RRM of RBM7, a ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. RBM7 interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20. It may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM7 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
.
Length = 75
Score = 40.3 bits (94), Expect = 7e-06
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+I+ELF + GP+ K+ D+ G+ A + ++ AM NG+ L GRP+ IQ
Sbjct: 17 LIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPLNIQ 75
>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 = 40.2 bits (95), Expect = 8e-06
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNG-VPLDG--RPM 56
+ LF E+G ++ + D+ G+S G A + + R +A KA++ +G V + G RP+
Sbjct: 15 DVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPGASRPL 74
Query: 57 QIQ 59
Q++
Sbjct: 75 QVK 77
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation
factor 64 kDa subunit (CstF64), is the vertebrate
conterpart of yeast mRNA 3'-end-processing protein
RNA15. It is expressed in all somatic tissues and is
one of three cleavage stimulatory factor (CstF)
subunits required for polyadenylation. CstF64 contains
an N-terminal RNA recognition motif (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a CstF77-binding domain, a repeated MEARA
helical region and a conserved C-terminal domain
reported to bind the transcription factor PC-4. During
polyadenylation, CstF interacts with the pre-mRNA
through the RRM of CstF64 at U- or GU-rich sequences
within 10 to 30 nucleotides downstream of the cleavage
site. CSTF2T, also termed tauCstF64, is a paralog of
the X-linked cleavage stimulation factor CstF64 protein
that supports polyadenylation in most somatic cells. It
is expressed during meiosis and subsequent haploid
differentiation in a more limited set of tissues and
cell types, largely in meiotic and postmeiotic male
germ cells, and to a lesser extent in brain. The loss
of CSTF2T will cause male infertility, as it is
necessary for spermatogenesis and fertilization.
Moreover, CSTF2T is required for expression of genes
involved in morphological differentiation of
spermatids, as well as for genes having products that
function during interaction of motile spermatozoa with
eggs. It promotes germ cell-specific patterns of
polyadenylation by using its RRM to bind to different
sequence elements downstream of polyadenylation sites
than does CstF64. .
Length = 75
Score = 40.2 bits (94), Expect = 8e-06
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ ++FSE GP+ S +L YDR +G+ G Y+ + A+ AM+ NG L+GR +++
Sbjct: 14 QLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLRVD 73
Query: 60 LA 61
A
Sbjct: 74 NA 75
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 39.5 bits (93), Expect = 1e-05
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
+ E FS +G ++ +L ++ R G A + + DA A+K+ NG+ LDGR
Sbjct: 14 DLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLNGLVLDGRT 67
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 39.3 bits (92), Expect = 1e-05
Identities = 17/59 (28%), Positives = 34/59 (57%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E+F G + A + D+ G+S G + +E +A++A+ +NG L RPM++++
Sbjct: 15 LKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRVKM 73
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed
U2 snRNP B") a unique protein that comprises the U2
snRNP. It was initially identified as binding to
stem-loop IV (SLIV) at the 3' end of U2 snRNA.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B"
does not require an auxiliary protein for binding to
RNA. In addition, the nuclear transport of U2B" is
independent of U2 snRNA binding. U2B" contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It also contains a nuclear localization signal (NLS) in
the central domain. However, nuclear import of U2B''
does not depend on this NLS. The N-terminal RRM is
sufficient to direct U2B" to the nucleus. .
Length = 91
Score = 39.2 bits (91), Expect = 3e-05
Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 14/66 (21%)
Query: 2 IYELFSEFG------PLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
+Y LFS+FG LK+ K+ G A +I++ S A A++Q G P G+P
Sbjct: 22 LYALFSQFGHVVDIVALKTMKMR--------GQAFVIFKELSSATNALRQLQGFPFYGKP 73
Query: 56 MQIQLA 61
M+IQ A
Sbjct: 74 MRIQYA 79
>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 = 38.3 bits (89), Expect = 4e-05
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
++ FS F A++ +D +SGRS G + + + DA A+ + NG L RP++
Sbjct: 16 LFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIRC 73
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein
3 (RBM3) and similar proteins. This subfamily
corresponds to the RRM domain of two structurally
related heterogenous nuclear ribonucleoproteins, CIRBP
(also termed CIRP or A18 hnRNP) and RBM3 (also termed
RNPL), both of which belong to a highly conserved cold
shock proteins family. The cold shock proteins can be
induced after exposure to a moderate cold-shock and
other cellular stresses such as UV radiation and
hypoxia. CIRBP and RBM3 may function in
posttranscriptional regulation of gene expression by
binding to different transcripts, thus allowing the
cell to response rapidly to environmental signals.
However, the kinetics and degree of cold induction are
different between CIRBP and RBM3. Tissue distribution
of their expression is different. CIRBP and RBM3 may be
differentially regulated under physiological and stress
conditions and may play distinct roles in cold
responses of cells. CIRBP, also termed glycine-rich
RNA-binding protein CIRP, is localized in the nucleus
and mediates the cold-induced suppression of cell cycle
progression. CIRBP also binds DNA and possibly serves
as a chaperone that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore,
RBM3 may be essential for cell proliferation and
mitosis. Both, CIRBP and RBM3, contain an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), that
is involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 38.3 bits (89), Expect = 4e-05
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ ++FS++G + + DR + RS G + +E DA AM NG +DGR +++
Sbjct: 17 LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQ 76
Query: 61 AAD 63
A
Sbjct: 77 AGK 79
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers. hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 38.1 bits (88), Expect = 5e-05
Identities = 18/57 (31%), Positives = 34/57 (59%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
E+FS G + A + D+ G+S G + +E+ +A++A+ +NG L RPM +++
Sbjct: 19 EVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHVKM 75
>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 = 37.9 bits (89), Expect = 6e-05
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 3 YELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNG 48
ELF FGP+ L D+ +G+S G A + + R DA +A+++ NG
Sbjct: 17 RELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA
branch site protein p14 (SF3B14) and similar proteins.
This subfamily corresponds to the RRM of SF3B14 (also
termed p14), a 14 kDa protein subunit of SF3B which is
a multiprotein complex that is an integral part of the
U2 small nuclear ribonucleoprotein (snRNP) and the
U11/U12 di-snRNP. SF3B is essential for the accurate
excision of introns from pre-messenger RNA and has been
involved in the recognition of the pre-mRNA's branch
site within the major and minor spliceosomes. SF3B14
associates directly with another SF3B subunit called
SF3B155. It is also present in both U2- and
U12-dependent spliceosomes and may contribute to branch
site positioning in both the major and minor
spliceosome. Moreover, SF3B14 interacts directly with
the pre-mRNA branch adenosine early in spliceosome
assembly and within the fully assembled spliceosome.
SF3B14 contains one well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 77
Score = 37.6 bits (88), Expect = 7e-05
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+Y+LF ++G ++ ++ + R GTA ++YE DA A +G + R
Sbjct: 19 LYDLFGKYGAIRQIRIGNTKETR--GTAFVVYEDIYDAKNACDHLSGFNVANR 69
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 37.6 bits (88), Expect = 1e-04
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 4 ELFSEFGPLKSAKL--HYDRSGR----SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
+ F + G ++S + D G S+G + ++ + A KA+K+ G LDG ++
Sbjct: 19 KHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLDGHALE 78
Query: 58 IQL 60
++L
Sbjct: 79 LKL 81
>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 = 37.2 bits (87), Expect = 1e-04
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 4 ELFSEFGPLKSAKLHYDRS----GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ F FGPL S K+ + R+ R+ + + R+DA +A+ + +G + G +++
Sbjct: 20 QEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERALDELDGKDVMGYELKL 78
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM5 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 37.1 bits (86), Expect = 1e-04
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 2 IYELFSEFGPLKSAKL--HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ LFS +G LKS ++ +D+S R + + +A+ AM L GR + +Q
Sbjct: 17 VRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAK--EALNAMNALKDTHLLGRRLVLQ 74
Query: 60 LA 61
A
Sbjct: 75 YA 76
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 36.8 bits (86), Expect = 2e-04
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 5 LFSEFGPLKSAKLHY--DRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD 52
+FS+FG K ++ D +G++ G A + + +A +A+K NG LD
Sbjct: 27 IFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the
RRM of SLIRP, a widely expressed small steroid receptor
RNA activator (SRA) binding protein, which binds to
STR7, a functional substructure of SRA. SLIRP is
localized predominantly to the mitochondria and plays a
key role in modulating several nuclear receptor (NR)
pathways. It functions as a co-repressor to repress
SRA-mediated nuclear receptor coactivation. It
modulates SHARP- and SKIP-mediated co-regulation of NR
activity. SLIRP contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is required for
SLIRP's corepression activities. .
Length = 73
Score = 36.5 bits (85), Expect = 2e-04
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
E FS+FG +KS + +D+ +G S G + + R D ++ Q L+G +Q+Q
Sbjct: 18 EYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR-DGLENALQKQKHILEGNKLQVQ 73
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 38.8 bits (90), Expect = 2e-04
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I LF+ G ++S KL D+ G+SLG + Y R DA KA+ NG+ L + +++
Sbjct: 20 IRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSY 79
Query: 61 A 61
A
Sbjct: 80 A 80
Score = 26.8 bits (59), Expect = 2.2
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
++++LF FG +++ K+ D + + G + +A A+ NG L R +Q+
Sbjct: 285 VLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family
of histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes
Set1A and Set1B that are ubiquitously expressed
vertebrates histone methyltransferases exhibiting high
homology to yeast Set1. Set1A and Set1B proteins
exhibit a largely non-overlapping subnuclear
distribution in euchromatic nuclear speckles, strongly
suggesting that they bind to a unique set of target
genes and thus make non-redundant contributions to the
epigenetic control of chromatin structure and gene
expression. With the exception of the catalytic
component, the subunit composition of the Set1A and
Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The
genomic targeting of these complexes is determined by
the identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast
to Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 36.9 bits (86), Expect = 2e-04
Identities = 9/58 (15%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 4 ELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ ++G ++ K+++ ++ + LG A ++++ A + +++ N + G+ +++ L
Sbjct: 21 DMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTSVMGKIIKVFL 78
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 76
Score = 36.6 bits (85), Expect = 2e-04
Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I + FS FGP+KS + +D + + G A + YE A A++Q NGV L GR +++
Sbjct: 16 TIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in
eukaryotic RNA-binding protein RBM24, RBM38 and similar
proteins. This subfamily corresponds to the RRM of
RBM24 and RBM38 from vertebrate, SUPpressor family
member SUP-12 from Caenorhabditis elegans and similar
proteins. Both, RBM24 and RBM38, are preferentially
expressed in cardiac and skeletal muscle tissues. They
regulate myogenic differentiation by controlling the
cell cycle in a p21-dependent or -independent manner.
RBM24, also termed RNA-binding region-containing
protein 6, interacts with the 3'-untranslated region
(UTR) of myogenin mRNA and regulates its stability in
C2C12 cells. RBM38, also termed CLL-associated antigen
KW-5, or HSRNASEB, or RNA-binding region-containing
protein 1(RNPC1), or ssDNA-binding protein SEB4, is a
direct target of the p53 family. It is required for
maintaining the stability of the basal and
stress-induced p21 mRNA by binding to their 3'-UTRs. It
also binds the AU-/U-rich elements in p63 3'-UTR and
regulates p63 mRNA stability and activity. SUP-12 is a
novel tissue-specific splicing factor that controls
muscle-specific splicing of the ADF/cofilin pre-mRNA in
C. elegans. All family members contain a conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 36.4 bits (85), Expect = 2e-04
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ + FS+FG ++ A + DR +G+S G + ++ + A +A K N + +DGR + L
Sbjct: 17 LRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPNPI-IDGRKANVNL 75
Query: 61 A 61
A
Sbjct: 76 A 76
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast
nucleolar protein 3 (Npl3p) and similar proteins. This
subfamily corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or
nuclear polyadenylated RNA-binding protein 1. Npl3p is
a major yeast RNA-binding protein that competes with
3'-end processing factors, such as Rna15, for binding
to the nascent RNA, protecting the transcript from
premature termination and coordinating transcription
termination and the packaging of the fully processed
transcript for export. It specifically recognizes a
class of G/U-rich RNAs. Npl3p is a multi-domain protein
containing two central RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a short
linker and a C-terminal domain rich in glycine,
arginine and serine residues. .
Length = 67
Score = 36.3 bits (84), Expect = 2e-04
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I E+FS +G +K K+ A + +E AI+A +G L+ P+ +
Sbjct: 16 IREIFSPYGAVKEVKMIS-------NFAFVEFESLESAIRAKDSVHGKVLNNNPLYV 65
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 38.1 bits (88), Expect = 2e-04
Identities = 31/97 (31%), Positives = 45/97 (46%), Gaps = 6/97 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+I + FSEF P K +R + A + +E R DA+KAM + NG L+G +++ L
Sbjct: 249 IIEKSFSEFKPGK-----VERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL 303
Query: 61 AADVSVLENTVPRPVARGGRGGASGGYRNGTAPTYRP 97
A V ++ V GGRG R Y P
Sbjct: 304 AKPVDK-KSYVRYTRGTGGRGKERQAARQSLGQVYDP 339
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise
role of PPIase remains unclear. PPIase contains a
conserved N-terminal peptidyl-prolyl cistrans isomerase
(PPIase) motif, a central RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 36.1 bits (84), Expect = 4e-04
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 6 FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
FS FG +KS ++ D+ +G SL A + +E + D +A + + V +D R
Sbjct: 24 FSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDR 73
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM3 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 83
Score = 35.8 bits (82), Expect = 4e-04
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 33 YERRSDAIKAMKQYNGVPLDGRPMQIQLAADV 64
+ R DA+ AM NG +DG P+++ LA V
Sbjct: 51 FSNREDAVDAMNALNGKVIDGSPIEVTLAKPV 82
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP
complex, which is one of the key factors facilitating
the splicing of pre-mRNA via interaction at the 5'
splice site, and is involved in regulation of
polyadenylation of some viral and cellular genes,
enhancing or inhibiting efficient poly(A) site usage.
U1-70K plays an essential role in targeting the U1
snRNP to the 5' splice site through protein-protein
interactions with regulatory RNA-binding splicing
factors, such as the RS protein ASF/SF2. Moreover,
U1-70K protein can specifically bind to stem-loop I of
the U1 small nuclear RNA (U1 snRNA) contained in the U1
snRNP complex. It also mediates the binding of U1C,
another U1-specific protein, to the U1 snRNP complex.
U1-70K contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region at the N-terminal half, and two
serine/arginine-rich (SR) domains at the C-terminal
half. The RRM is responsible for the binding of
stem-loop I of U1 snRNA molecule. Additionally, the
most prominent immunodominant region that can be
recognized by auto-antibodies from autoimmune patients
may be located within the RRM. The SR domains are
involved in protein-protein interaction with SR
proteins that mediate 5' splice site recognition. For
instance, the first SR domain is necessary and
sufficient for ASF/SF2 Binding. The family also
includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but
its SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 35.7 bits (83), Expect = 6e-04
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 6 FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
F E+GP+K +L D+ +G+ G A + +E D A K +G +DGR
Sbjct: 22 FEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKIDGR 71
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate
RNA-binding protein 11 (RBM11). This subfamily
corresponds to the RRM or RBM11, a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. RBM11 is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. RBM11 contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a region
lacking known homology at the C-terminus. The RRM of
RBM11 is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 35.3 bits (81), Expect = 6e-04
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
++YELF + GPL + D+ G+ + ++ A+ NG+ L GRP+++
Sbjct: 17 ILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLNGIRLYGRPIKVH 75
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM2 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 80
Score = 35.3 bits (82), Expect = 7e-04
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 1 MIYELFSEFGP-LKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
M+ E F P ++ AK+ D +GRS G + + + +A+ + NGV RPM++
Sbjct: 17 MLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPMRV 76
Query: 59 QLAA 62
A
Sbjct: 77 SPAT 80
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), an RNA-binding protein associated with the U1
snRNP, a small RNA-protein complex involved in pre-mRNA
splicing. U1A binds with high affinity and specificity
to stem-loop II (SLII) of U1 snRNA. It is predominantly
a nuclear protein and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large
number of non-snRNP proteins, including polypyrimidine
tract binding protein (PTB), polypyrimidine-tract
binding protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an
important role in virus replication. U1A contains two
RNA recognition motifs (RRMs); the N-terminal RRM
(RRM1) binds tightly and specifically to the U1 snRNA
SLII and its own 3'-UTR, while in contrast, the
C-terminal RRM (RRM2) does not appear to associate with
any RNA and may be free to bind other proteins. U1A
also contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 89
Score = 35.0 bits (80), Expect = 0.001
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
++ +FS FG + + RS + G A +I++ S A A++ G P +PM+IQ
Sbjct: 24 LHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 79
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This
subgroup corresponds to the RRM3 of the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like)
proteins, a family of structurally related RNA-binding
proteins involved in the regulation of pre-mRNA
splicing in the nucleus and in the control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2
(also termed BRUNOL-3, or ETR-3, or CUG-BP2, or
NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or
ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed
BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also
termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region
and the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and
function, the CELF family can be divided into two
subfamilies, the first containing CELFs 1 and 2, and
the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts. .
Length = 73
Score = 34.5 bits (80), Expect = 0.001
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 3 YELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
Y+LF+ FG + SAK+ D+ +G+S + Y+ A A+K NG + G+ +++Q
Sbjct: 16 YQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73
>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1) and similar
proteins. This subfamily corresponds to the RRM3 of
hnRNP H proteins and GRSF-1. The hnRNP H protein family
includes hnRNP H (also termed mcs94-1), hnRNP H2 (also
termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also
termed hnRNP 2H9), which represent a group of nuclear
RNA binding proteins that are involved in pre-mRNA
processing. These proteins have similar RNA binding
affinities and specifically recognize the sequence
GGGA. They can either stimulate or repress splicing
upon binding to a GGG motif. hnRNP H binds to the RNA
substrate in the presence or absence of these proteins,
whereas hnRNP F binds to the nuclear mRNA only in the
presence of cap-binding proteins. hnRNP H and hnRNP H2
are almost identical; both have been found to bind
nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements
downstream of the 5' splice site in the transcripts of
c-src, human immunodeficiency virus type 1 (HIV-1),
Bcl-X, GRIN1, and myelin. It silences exons when bound
to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
hnRNP H3 may be involved in the splicing arrest induced
by heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and they play an important role in
efficiently silencing the exon. For instance, members
in this family can regulate the alternative splicing of
the fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced
silencing activity within hnRNP H3. In addition, the
family members have an extensive glycine-rich region
near the C-terminus, which may allow them to homo- or
heterodimerize. The family also includes a cytoplasmic
poly(A)+ mRNA binding protein, GRSF-1, which interacts
with RNA in a G-rich element-dependent manner. It may
function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. GRSF-1 also contains three potential RRMs
responsible for the RNA binding, and two auxiliary
domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 34.6 bits (80), Expect = 0.001
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 4 ELFSEFGPLKSAKLH--YDRSGRSLGTADLIYERRSDAIKAMKQ 45
++F F PL + Y+ GR+ G AD+ + DA+ AM +
Sbjct: 16 DIFEFFSPLNPVNVRIEYNADGRATGEADVEFATHEDAVAAMSK 59
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated
apoptosis.TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 34.2 bits (79), Expect = 0.001
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ ELFS+ GP+KS KL + + Y A A++ NG + G+ +++ A
Sbjct: 15 LAELFSQIGPIKSCKLIREHGNDPYAFVE--YYDHRSAAAALQTMNGRLILGQEIKVNWA 72
>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 = 34.2 bits (79), Expect = 0.002
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ E FS G + L + + A + +ER A +A++ N L + M +Q
Sbjct: 20 LNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESENHSMLKNKTMHVQY 77
>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2
and similar proteins. This subfamily corresponds to
the RRM2 of yeast protein gar2, a novel nucleolar
protein required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture
with nucleolin from vertebrates and NSR1 from
Saccharomyces cerevisiae. The highly phosphorylated
N-terminal domain of gar2 is made up of highly acidic
regions separated from each other by basic sequences,
and contains multiple phosphorylation sites. The
central domain of gar2 contains two closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RGG (or GAR) domain of gar2 is
rich in glycine, arginine and phenylalanine residues. .
Length = 73
Score = 33.9 bits (78), Expect = 0.002
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
IYE F E+G + S +L D SGR G + + + A A+ G L GRP+++
Sbjct: 15 IYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPVRL 72
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM2 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 79
Score = 34.3 bits (79), Expect = 0.002
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 5 LFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
LFS+FG L + D +SG+S G A +++ DA+KA K+ +G GR + I
Sbjct: 22 LFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGRLIHI 76
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. hnRNP R is predominantly located
in axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, as well as in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP R binds RNA through its RRM domains. .
Length = 72
Score = 33.8 bits (77), Expect = 0.002
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 6 FSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
FSEFG L+ K D A + +E R A++AM + NG ++G ++I LA
Sbjct: 22 FSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMNGKEIEGEEIEIVLA 70
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 34.2 bits (78), Expect = 0.002
Identities = 19/65 (29%), Positives = 41/65 (63%), Gaps = 3/65 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNG--VPLDGRPMQI 58
+ ++FS FG + ++++ D+ +G S G A + +++RS+A +A+ +NG P P+ +
Sbjct: 17 VEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITV 76
Query: 59 QLAAD 63
+ AA+
Sbjct: 77 KFAAN 81
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1),
a ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response; it binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
Meanwhile, HuR also has pro-apoptotic function by
promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Like other Hu proteins, HuR contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 81
Score = 33.9 bits (77), Expect = 0.002
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LFS G ++SAKL D+ +G SLG + Y DA +A+ NG+ L + +++ A
Sbjct: 21 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTIKVSYA 78
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM1 of SXL which governs sexual
differentiation and X chromosome dosage compensation in
Drosophila melanogaster. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 33.5 bits (77), Expect = 0.003
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 3 YELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF GP+K+ K+ D R+G S G + Y+ DA +A++ NG+ L + +++ A
Sbjct: 18 RSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYA 77
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 33.4 bits (77), Expect = 0.003
Identities = 14/58 (24%), Positives = 29/58 (50%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+LF FG + +L Y + G+ + Y+ +A KA+K +N +D + +++
Sbjct: 19 KLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKITVEIC 76
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 33.5 bits (77), Expect = 0.003
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPL--DGRPMQIQL 60
E F+ FG ++ + D+ + S G A + + + S A +AM++ NG L D +P+++ +
Sbjct: 21 EAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPLKVLI 80
Query: 61 A 61
A
Sbjct: 81 A 81
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 84
Score = 33.6 bits (76), Expect = 0.003
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF G ++S KL D+ +G+SLG + Y +DA KA+ NG+ L + +++ A
Sbjct: 23 LFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYA 80
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 34.6 bits (79), Expect = 0.003
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 6 FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLAADV 64
F+ FG + AK+ DR +GRS G + + A A+ + +G L+GR +++ A D
Sbjct: 55 FAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDR 114
Query: 65 SVLENTVPRPVARGGRGGASGG 86
G GG GG
Sbjct: 115 PSAPRAYGGGGGYSGGGGGYGG 136
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved
poly(A) binding protein containing poly(A) tails that
can be attached to the 3'-ends of mRNAs. The yeast PABP
and its homologs may play important roles in the
initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 77
Score = 33.3 bits (77), Expect = 0.003
Identities = 17/53 (32%), Positives = 32/53 (60%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+Y+ FS FG + S K+ D +G S G + +E A++A+++ NG+ L+ +
Sbjct: 19 LYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDK 71
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins.
This subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can
accumulate in the perinucleolar compartment, a dynamic
nuclear substructure that harbors PTB. Raver-1 also
modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes,
particularly in differentiated muscle tissue. Raver-2
is a novel member of the heterogeneous nuclear
ribonucleoprotein (hnRNP) family. It shows high
sequence homology to raver-1. Raver-2 exerts a
spatio-temporal expression pattern during embryogenesis
and is mainly limited to differentiated neurons and
glia cells. Although it displays nucleo-cytoplasmic
shuttling in heterokaryons, raver2 localizes to the
nucleus in glia cells and neurons. Raver-2 can interact
with PTB and may participate in PTB-mediated
RNA-processing. However, there is no evidence
indicating that raver-2 can bind to cytoplasmic
proteins. Both, raver-1 and raver-2, contain three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. They binds to RNA through the
RRMs. In addition, the two [SG][IL]LGxxP motifs serve
as the PTB-binding motifs in raver1. However, raver-2
interacts with PTB through the SLLGEPP motif only. .
Length = 92
Score = 33.4 bits (77), Expect = 0.004
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+LFS+ G +L +G+ G A + Y DA +A + NG L G P+++
Sbjct: 22 KLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76
>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 = 34.7 bits (79), Expect = 0.004
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
I F FGP+KS + +D +G+ G A + YE A A++Q NG L GR +++
Sbjct: 123 TIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG 182
Query: 60 LAADV 64
+++
Sbjct: 183 RPSNM 187
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. The family also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 33.0 bits (76), Expect = 0.004
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQ 45
++ + FS+FG ++ A + D GRS G + + R+ A A+K+
Sbjct: 15 LLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKR 59
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila sex
determination and possesses a novel dual RNA binding
specificity. SNF binds with high affinity to both
Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA
stem-loop IV (SLIV). It can also bind to poly(U) RNA
tracts flanking the alternatively spliced Sex-lethal
(Sxl) exon, as does Drosophila Sex-lethal protein
(SXL). SNF contains two RNA recognition motifs (RRMs);
it can self-associate through RRM1, and each RRM can
recognize poly(U) RNA binding independently. .
Length = 78
Score = 33.4 bits (76), Expect = 0.004
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 14/66 (21%)
Query: 2 IYELFSEFGP------LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
+Y +FS+FG LK+ K+ G A ++++ S A A++ G P +P
Sbjct: 20 LYAIFSQFGQILDIVALKTLKMR--------GQAFVVFKDISSATNALRSMQGFPFYDKP 71
Query: 56 MQIQLA 61
M+I +
Sbjct: 72 MRIAYS 77
>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM1 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 79
Score = 33.3 bits (76), Expect = 0.004
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ FS+ P+K A + D +G S G + + DA +A+ + L GR +++ +A
Sbjct: 18 DFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRLDIA 76
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 33.0 bits (76), Expect = 0.005
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 4 ELFSEFGPLKSAKL---HYDRSGRS-LGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+FS+FG ++S ++ ++ GR G A + ++ S A A+ Q NG L GR + +
Sbjct: 19 GIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL-QLNGTELGGRKISVS 77
Query: 60 L 60
L
Sbjct: 78 L 78
>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 = 32.7 bits (75), Expect = 0.005
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 6 FSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
F+ FG + A++ D ++G+S G + + ++ DA A++ NG L GR ++
Sbjct: 20 FAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAIRT 73
>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 = 32.6 bits (75), Expect = 0.006
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ FS FG +K K+ DR+G S G + +E + DA K + N + G+ + I
Sbjct: 21 DFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGN-LNFRGKKLNI 74
>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 = 32.7 bits (75), Expect = 0.006
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGR-SLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
++++FS++G + + D+ R S G A +++ R DA K +K N L GR ++
Sbjct: 17 DLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKCS 76
Query: 60 LA 61
+A
Sbjct: 77 IA 78
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to
the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15)
family of RNA-binding proteins. This ubiquitously
expressed family of similarly structured proteins
predominantly localizing to the nuclear, includes FUS
(also known as TLS or Pigpen or hnRNP P2), EWS (also
known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N
or RPB56), and Drosophila Cabeza (also known as SARFH).
The corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a
degenerate hexapeptide repeat motif at the N-terminus.
The C-terminal region consists of a conserved nuclear
import and retention signal (C-NLS), a putative
zinc-finger domain, and a conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 32.7 bits (75), Expect = 0.007
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 2 IYELFSEFGPLKS--------AKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG 53
+ ELF G +K K++ D+ G A + Y+ S A A++ +NG G
Sbjct: 15 LAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAAQAAIEWFNGYEFRG 74
Query: 54 RPMQIQL 60
+++ L
Sbjct: 75 NKIKVSL 81
>gnl|CDD|241177 cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM3 of G-rich sequence factor 1
(GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. GRSF-1 contains three potential RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which are responsible for the RNA binding. In addition,
GRSF-1 has two auxiliary domains, an acidic
alpha-helical domain and an N-terminal alanine-rich
region, that may play a role in protein-protein
interactions and provide binding specificity. .
Length = 75
Score = 32.5 bits (74), Expect = 0.008
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 9 FGPLKSAK--LHYDRSGRSLGTADLIYERRSDAIKAM 43
F PLK + + Y GR+ G AD+ +E DA+ AM
Sbjct: 21 FAPLKPTRILIEYSSDGRATGEADVHFESHDDAVAAM 57
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate
putative RNA exonuclease NEF-sp. This subfamily
corresponds to the RRM1 of NEF-sp., including
uncharacterized putative RNA exonuclease NEF-sp found
in vertebrates. Although its cellular functions remains
unclear, NEF-sp contains an exonuclease domain and two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
suggesting it may possess both exonuclease and
RNA-binding activities. .
Length = 71
Score = 32.0 bits (73), Expect = 0.009
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ LF GP++ + S A + +E A A++ NG +DG +++Q
Sbjct: 16 VKRLFETCGPVRKVTM---LSRTVQPHAFITFENLEAAQLAIETLNGASVDGNCIKVQ 70
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM1 of nucleolysin TIAR, also termed TIA-1-related
protein, and a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 81
Score = 32.4 bits (73), Expect = 0.010
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+I +LFS+ GP KS K+ + + YE R DA A+ NG + G+ +++
Sbjct: 15 LILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR-DAAAALAAMNGRKILGKEVKVNW 73
Query: 61 AADVS 65
A S
Sbjct: 74 ATTPS 78
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear
molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial
growth factor (VEGF), the glucose transporter GLUT1,
eotaxin and c-fos, and stabilize those ARE-containing
mRNAs. They also bind and regulate the translation of
some target mRNAs, such as neurofilament M, GLUT1, and
p27. In the nucleus, Hu proteins function as regulators
of polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an ARE. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 78
Score = 31.9 bits (73), Expect = 0.011
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRS---GRSLGTADLI-YERRSDAIKAMKQYNGVPLDGRPMQ 57
+++LFS FG + + K+ D + + G + YE +A A+ NG L GR +Q
Sbjct: 18 LWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYE---EAYSAIASLNGYRLGGRVLQ 74
Query: 58 I 58
+
Sbjct: 75 V 75
>gnl|CDD|241179 cd12735, RRM3_hnRNPH3, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM3 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), and hnRNP F. This
family is involved in mRNA processing and exhibit
extensive sequence homology. Currently, little is known
about the functions of hnRNP H3 except for its role in
the splicing arrest induced by heat shock. In addition,
the typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
except for hnRNP H3, in which the RRM1 is absent. RRM1
and RRM2 are responsible for the binding to the RNA at
DGGGD motifs, and they play an important role in
efficiently silencing the exon. Members in this family
can regulate the alternative splicing of the fibroblast
growth factor receptor 2 (FGFR2) transcripts, and
function as silencers of FGFR2 exon IIIc through an
interaction with the exonic GGG motifs. The lack of
RRM1 could account for the reduced silencing activity
within hnRNP H3. In addition, like other hnRNP H
protein family members, hnRNP H3 has an extensive
glycine-rich region near the C-terminus, which may
allow it to homo- or heterodimerize. .
Length = 75
Score = 31.9 bits (72), Expect = 0.012
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 9 FGPLKSAKLHYD--RSGRSLGTADLIYERRSDAIKAMKQ 45
F PL ++H D GR+ G AD+ + DA+ AM +
Sbjct: 21 FSPLTPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSK 59
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads and is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 83
Score = 32.0 bits (72), Expect = 0.014
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF G ++S KL D+ +G+SLG + Y DA KA+ NG+ L + +++ A
Sbjct: 24 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 81
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 31.7 bits (72), Expect = 0.015
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRS---DAIKAMKQYNGVPLDGRPMQI 58
+ +F+ FG ++ + D++G+S G A + + R +AIKAM + P+ +
Sbjct: 18 VRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMHHSQTMEGCSSPLVV 77
Query: 59 QLA 61
+ A
Sbjct: 78 KFA 80
>gnl|CDD|240959 cd12515, RRM5_RBM12_like, RNA recognition motif 5 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM5 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several
putative transmembrane domains. RBM12B show high
sequence semilarity with RBM12. It contains five
distinct RRMs as well. The biological roles of both
RBM12 and RBM12B remain unclear. .
Length = 75
Score = 31.6 bits (72), Expect = 0.016
Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLK-SAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I + F + + S L Y+ +G G A + ++ +A+ A+++ NG P+ R +++
Sbjct: 17 ILDFFYGYRVIPGSVSLLYNDNGAPTGEATVAFDTHREAMAAVRELNGRPIGTRKVKL 74
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 77
Score = 31.4 bits (72), Expect = 0.016
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ EL FG LK+ L D +G S G A Y S +A+ NG+ L + + +Q
Sbjct: 16 QVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLTVQ 75
Query: 60 LA 61
A
Sbjct: 76 RA 77
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells, as well as the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 31.6 bits (71), Expect = 0.020
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF G ++S KL D+ +G+SLG + Y DA KA+ NG+ L + +++ A
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 31.5 bits (72), Expect = 0.021
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 6 FSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
FS++G + L D+ +G+S G A L YE + I A+ NG+ L GR +++
Sbjct: 30 FSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 31.2 bits (71), Expect = 0.022
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF E+G ++S + R G A + E R DA +A+++ V L G+ +++ A
Sbjct: 21 NLFEEYGEIQSIDMIPPR-----GCAYVCMETRQDAHRALQKLRNVKLAGKKIKVAWA 73
>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 = 31.2 bits (71), Expect = 0.023
Identities = 14/58 (24%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
++F +FGP+ ++ ++ G S G + + +DA +A ++ +G ++GR +++ A
Sbjct: 19 QMFGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREKLHGTVVEGRKIEVNNA 75
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP
2H9), which represent a group of nuclear RNA binding
proteins that are involved in pre-mRNA processing.
GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2
(also termed RBM35B) are epithelial-specific RNA
binding proteins that promote splicing of the
epithelial variant of fibroblast growth factor receptor
2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1
(also termed p120-Catenin) transcripts. Fusilli shows
high sequence homology to ESRPs. It can regulate
endogenous FGFR2 splicing and functions as a splicing
factor. The biological roles of both, RBM12 and RBM12B,
remain unclear. RBM19 is a nucleolar protein conserved
in eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 31.0 bits (71), Expect = 0.024
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 2 IYELFSEFGPLKSA-KLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I + FS + YD GR G A + + DA +A++++N + GR +++
Sbjct: 16 IRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNK-MGGRYIEV 72
>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 = 30.7 bits (70), Expect = 0.030
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGPLKSAKLHY-DRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
EL S FG ++ L Y + +G S G + Y ++ A+KA Q +G + GR +Q+ A
Sbjct: 18 ELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKLQVDWA 76
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 30.8 bits (70), Expect = 0.031
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ +LFS++GPL L D+ + + G A + Y A+KA + +G GR + +
Sbjct: 19 LEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAELDGTVFQGRLLHL 76
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM1 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and it is highly conserved between
plants and fungi. Up to date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 77
Score = 30.7 bits (70), Expect = 0.032
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ LF +FG +++ L+ + + G + Y A +A + G L GR + I
Sbjct: 18 LRALFEQFGDIRT--LYT--ACKHRGFIMVSYYDIRAARRAKRALQGTELGGRKLDIH 71
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 30.4 bits (68), Expect = 0.037
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 6 FSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
F +FG L+ K D A + ++ R A+KAM++ NG L+G ++I A
Sbjct: 22 FGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMNGKELEGENIEIVFA 70
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 30.4 bits (68), Expect = 0.037
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+I +LFS+ GP KS K+ D +G +E R A ++ NG + G+ +++
Sbjct: 15 LILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRH-AAASLAAMNGRKIMGKEVKVNW 73
Query: 61 A 61
A
Sbjct: 74 A 74
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 30.6 bits (70), Expect = 0.037
Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+++ELF + GP+ + + DR + G + + DA A+K N + L G+P+++
Sbjct: 14 LLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRV 72
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12
small nuclear ribonucleoprotein 35 kDa protein
(U11/U12-35K) and similar proteins. This subfamily
corresponds to the RRM of U11/U12-35K, also termed
protein HM-1, or U1 snRNP-binding protein homolog, and
is one of the components of the U11/U12 snRNP, which is
a subunit of the minor (U12-dependent) spliceosome
required for splicing U12-type nuclear pre-mRNA
introns. U11/U12-35K is highly conserved among
bilateria and plants, but lacks in some organisms, such
as Saccharomyces cerevisiae and Caenorhabditis elegans.
Moreover, U11/U12-35K shows significant sequence
homology to U1 snRNP-specific 70 kDa protein (U1-70K or
snRNP70). It contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5'
splice site recognition in the minor spliceosome and
play a role in exon bridging, interacting with
components of the major spliceosome bound to the
pyrimidine tract of an upstream U2-type intron. The
family corresponds to the RRM of U11/U12-35K that may
directly contact the U11 or U12 snRNA through the RRM
domain.
Length = 93
Score = 30.7 bits (70), Expect = 0.037
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+ E+FS +G ++ +L D +G S G A + YE DA++A + + + +DG
Sbjct: 20 LREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGS 73
>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
similar proteins. This subfamily corresponds to the
RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation
factor (ACF), and dead end protein homolog 1 (DND1).
hnRNP R is a ubiquitously expressed nuclear RNA-binding
protein that specifically binds mRNAs with a preference
for poly(U) stretches. It has been implicated in mRNA
processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP Q is also a ubiquitously expressed
nuclear RNA-binding protein. It has been identified as
a component of the spliceosome complex, as well as a
component of the apobec-1 editosome, and has been
implicated in the regulation of specific mRNA
transport. ACF is an RNA-binding subunit of a core
complex that interacts with apoB mRNA to facilitate C
to U RNA editing. It may also act as an apoB mRNA
recognition factor and chaperone, and play a key role
in cell growth and differentiation. DND1 is essential
for maintaining viable germ cells in vertebrates. It
interacts with the 3'-untranslated region (3'-UTR) of
multiple messenger RNAs (mRNAs) and prevents micro-RNA
(miRNA) mediated repression of mRNA. This family also
includes two functionally unknown RNA-binding proteins,
RBM46 and RBM47. All members in this family, except for
DND1, contain three conserved RNA recognition motifs
(RRMs); DND1 harbors only two RRMs. .
Length = 78
Score = 30.6 bits (70), Expect = 0.039
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPL 51
+ LF + GP+ +L D SG + G A + Y + A +A+KQ + +
Sbjct: 18 LVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLHNYEI 67
>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 = 30.6 bits (69), Expect = 0.041
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 5 LFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGVPLDGR--PMQIQLA 61
+F +G + L D+S G G A + Y++R +A A+ NG G P+ ++ A
Sbjct: 20 IFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGSTMPLSVRYA 79
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline-
and glutamine-rich splicing factor, or 100 kDa
DNA-pairing protein (POMp100), or 100 kDa subunit of
DNA-binding p52/p100 complex, a multifunctional protein
that mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response
element (IGFRE). Moreover, PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. PSF is an essential pre-mRNA
splicing factor and is dissociated from PTB and binds
to U1-70K and serine-arginine (SR) proteins during
apoptosis. PSF forms a heterodimer with the nuclear
protein p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO). The PSF/p54nrb complex
displays a variety of functions, such as DNA
recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), which are
responsible for interactions with RNA and for the
localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. .
Length = 80
Score = 30.5 bits (68), Expect = 0.045
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 15/75 (20%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ E FS+FGP++ A + D GRS G + + + A KA ++
Sbjct: 15 LLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFER--------------- 59
Query: 61 AADVSVLENTVPRPV 75
+ L T PRPV
Sbjct: 60 CTEGVFLLTTTPRPV 74
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is the ubiquitously expressed Hu family member. It
has a variety of biological functions mostly related to
the regulation of cellular response to DNA damage and
other types of stress. Hu proteins perform their
cytoplasmic and nuclear molecular functions by
coordinately regulating functionally related mRNAs. In
the cytoplasm, Hu proteins recognize and bind to
AU-rich RNA elements (AREs) in the 3' untranslated
regions (UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. Also included
in this subfamily is the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 30.3 bits (68), Expect = 0.045
Identities = 17/61 (27%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQIQL 60
+LFS++G + ++++ D+ +G S G + +++R +A +A+K NG +G P+ ++
Sbjct: 19 QLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEGASEPITVKF 78
Query: 61 A 61
A
Sbjct: 79 A 79
>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 = 29.9 bits (68), Expect = 0.061
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
+++ F FG +K ++ D + + G A + +E DA A+ N L GR
Sbjct: 14 VLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGR 68
>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 = 30.0 bits (68), Expect = 0.067
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 4 ELFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQYNGVPLDG 53
LFS +G + ++++ D G S G + +++R +A +A+K NG G
Sbjct: 19 ALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIPPG 69
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the
RRM of SRSF2 and SRSF8. SRSF2, also termed protein
PR264, or splicing component, 35 kDa (splicing factor
SC35 or SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of
pre-mRNA. It is also involved in transcription
elongation by directly or indirectly mediating the
recruitment of elongation factors to the C-terminal
domain of polymerase II. SRSF2 is exclusively localized
in the nucleus and is restricted to nuclear processes.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory
elements on the pre-mRNA. The RS domain modulates SRSF2
activity through phosphorylation, directly contacts
RNA, and promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 29.6 bits (67), Expect = 0.079
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ +F ++G + + DR + S G A + + + DA AM +G LDGR +++Q
Sbjct: 14 DLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRVQ 73
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 29.6 bits (66), Expect = 0.083
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 15/75 (20%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ + FS+FGP++ A + D GR G + + + A KA+++
Sbjct: 15 LLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALER--------------- 59
Query: 61 AADVSVLENTVPRPV 75
AD + L T PRPV
Sbjct: 60 CADGAFLLTTTPRPV 74
>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 = 0.088
Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 2 IYELFSEFGPLKSAKLHYDRSG----RSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQ 57
+ +LFS++G +K + +SG + G + +E + +A KA+K NG G+ +
Sbjct: 16 LLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLV 75
Query: 58 IQLA 61
++ A
Sbjct: 76 VRWA 79
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM2 of RBM40 and the RRM
of RBM41. RBM40, also known as RNA-binding
region-containing protein 3 (RNPC3) or U11/U12 small
nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K
protein). It serves as a bridging factor between the
U11 and U12 snRNPs. It contains two RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), connected by a
linker that includes a proline-rich region. It binds to
the U11-associated 59K protein via its RRM1 and employs
the RRM2 to bind hairpin III of the U12 small nuclear
RNA (snRNA). The proline-rich region might be involved
in protein-protein interactions. RBM41 contains only
one RRM. Its biological function remains unclear. .
Length = 82
Score = 29.5 bits (67), Expect = 0.090
Identities = 17/63 (26%), Positives = 24/63 (38%), Gaps = 2/63 (3%)
Query: 1 MIYELFSEFGPLKSAKLHYD--RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
I+ F + + GR G A + + A KA+ NG L G+PM I
Sbjct: 20 YIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKALNLVNGYVLKGKPMVI 79
Query: 59 QLA 61
Q
Sbjct: 80 QFG 82
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 29.3 bits (66), Expect = 0.093
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIY---ERRSDAIKAMKQYNGVPLDGRPMQ 57
E F E G K K++ D G +Y ER DA +A+ NG DGR ++
Sbjct: 14 EYFGEVG--KINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVK 68
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an
N-terminal C4C4 type RING finger motif, followed by a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RING fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 29.8 bits (68), Expect = 0.10
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 3 YELFSEFGPLK----SAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPM 56
E F ++G +K + Y+ S +A + Y R+ DA++ ++ +G LDGR +
Sbjct: 26 PEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDGFYLDGRLL 83
>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 = 29.4 bits (66), Expect = 0.10
Identities = 15/46 (32%), Positives = 28/46 (60%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN 47
+ + FS++G +K K+ DR+G S G + +E + DA K +++ N
Sbjct: 19 LRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEAN 64
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 107
Score = 29.9 bits (67), Expect = 0.10
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 5 LFSEFGPLKSAKLHYDRS-GRSLGTADLIYERRSDAIKAMKQ 45
FS+FG ++ A D+S GR+ GT + ++ + +K
Sbjct: 21 HFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKN 62
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM2 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contains three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains): two consecutive RRMs
(RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The two
N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including
alternative splicing, RNA editing, stability and
translation. CELF-2 shares high sequence identity with
CELF-1, but shows different binding specificity; it
preferentially binds to sequences with UG repeats and
UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 29.3 bits (65), Expect = 0.11
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRS---DAIKAMKQYNGVPLDGRPMQI 58
I +FS FG ++ ++ G S G A + + R+ AIKAM Q + P+ +
Sbjct: 18 IRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPIVV 77
Query: 59 QLA 61
+ A
Sbjct: 78 KFA 80
>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 = 29.3 bits (66), Expect = 0.12
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 5 LFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
LF ++GP+ + D + R G A + +E DA A+ + GR ++IQ A
Sbjct: 20 LFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFA 77
>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 = 30.6 bits (69), Expect = 0.12
Identities = 20/61 (32%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I EL FG LK+ L D +G S G A Y+ S A+ NG + +Q
Sbjct: 312 IKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQR 371
Query: 61 A 61
A
Sbjct: 372 A 372
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 29.1 bits (66), Expect = 0.14
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ ELFS FG +KS +L G G A + + + +A AM+ L GR + ++ A
Sbjct: 17 LRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 76
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 28.8 bits (64), Expect = 0.15
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 33 YERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
+ R DA+ AM NG L+G +++ LA
Sbjct: 44 FTSREDAVHAMNNLNGTELEGSCIEVTLA 72
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 30.0 bits (67), Expect = 0.17
Identities = 16/61 (26%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+Y LF GP+ + ++ D ++G S G A + + +D+ +A+K NG+ + + +++
Sbjct: 124 LYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY 183
Query: 61 A 61
A
Sbjct: 184 A 184
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 72
Score = 28.4 bits (64), Expect = 0.23
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPM 56
+ +LFS+ G + +L + G+S G A + +E +A+K + + GRPM
Sbjct: 16 LRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL-DRELIKGRPM 69
>gnl|CDD|241178 cd12734, RRM3_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM3 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F, which represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth
factor receptor 2 (FGFR2) transcripts. The presence of
Fox 2 can allows hnRNP H and hnRNP F to better compete
with the SR protein ASF/SF2 for binding to FGFR2 exon
IIIc. Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; bothe have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP
H2 has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently
silencing the exon. In addition, the family members
have an extensive glycine-rich region near the
C-terminus, which may allow them to homo- or
heterodimerize. .
Length = 76
Score = 28.5 bits (63), Expect = 0.26
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 4 ELFSEFGPLKSAKLHYD--RSGRSLGTADLIYERRSDAIKAMKQ 45
++++ F PL ++H + GR G AD+ + DA+ AM +
Sbjct: 16 DIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSK 59
>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 = 28.4 bits (64), Expect = 0.32
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN 47
+ + F FG ++ LH+ G + G + Y DA +A++ N
Sbjct: 19 LRQRFQPFGEIEEITLHFRDDGDNYGF--VTYRYACDAFRAIEHGN 62
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 83
Score = 28.0 bits (63), Expect = 0.41
Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 8/66 (12%)
Query: 1 MIYELFSEFGP-LKSAKLHYD-RSGRSLGTADLIYE--RRSD-AIKAMKQYNGVPLDGRP 55
++Y+ FS FG L++ K+ D +G S G A + Y+ SD AI+AM NG L RP
Sbjct: 17 LLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAM---NGQYLCNRP 73
Query: 56 MQIQLA 61
+ + A
Sbjct: 74 ITVSYA 79
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the
RRM of TRMT2A, also known as HpaII tiny fragments locus
9c protein (HTF9C), a novel cell cycle regulated
protein. It is an independent biologic factor expressed
in tumors associated with clinical outcome in HER2
expressing breast cancer. The function of TRMT2A
remains unclear although by sequence homology it has a
RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
related to RNA methyltransferases. .
Length = 79
Score = 27.6 bits (62), Expect = 0.41
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 38 DAIKAMKQYNGVPLDGRPMQIQLAA 62
+ KA++ +G GR + +LA
Sbjct: 54 ERQKALEILDGFKWKGRVLSARLAK 78
>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM2 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects
in a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 68
Score = 27.5 bits (61), Expect = 0.41
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
+ LF EFG + D A + ER +A+ A++ NG + GR + ++L
Sbjct: 17 LRGLFEEFGRVVECDKVKD-------YAFVHMEREEEALAAIEALNGKEVKGRRINVEL 68
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar
proteins. This subfamily corresponds to the RRM1 of
RBM19 and MRD1. RBM19, also termed RNA-binding domain-1
(RBD-1), is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 77
Score = 27.6 bits (62), Expect = 0.44
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 4 ELFSEFGP-LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E FS+ G + KL G+S A + Y+ +A KA +N ++ + ++ A
Sbjct: 19 EHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNNTYINTSKISVEFA 77
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. This subfamily also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 27.2 bits (61), Expect = 0.59
Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
ELFS++G + L+ ++ G + + R++A KA + +G+ GR +++
Sbjct: 20 ELFSKYGEVSEVFLNKEK-----GFGFIRLDTRTNAEKAKAELDGIMRKGRQLRV 69
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate
nucleolin. This subfamily corresponds to the RRM2 of
ubiquitously expressed protein nucleolin, also termed
protein C23, a multifunctional major nucleolar
phosphoprotein that has been implicated in various
metabolic processes, such as ribosome biogenesis,
cytokinesis, nucleogenesis, cell proliferation and
growth, cytoplasmic-nucleolar transport of ribosomal
components, transcriptional repression, replication,
signal transduction, inducing chromatin decondensation,
etc. Nucleolin exhibits intrinsic self-cleaving, DNA
helicase, RNA helicase and DNA-dependent ATPase
activities. It can be phosphorylated by many protein
kinases, such as the major mitotic kinase Cdc2, casein
kinase 2 (CK2), and protein kinase C-zeta. Nucleolin
shares similar domain architecture with gar2 from
Schizosaccharomyces pombe and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of nucleolin is made up of highly acidic regions
separated from each other by basic sequences, and
contains multiple phosphorylation sites. The central
domain of nucleolin contains four closely adjacent
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which suggests that nucleolin is potentially
able to interact with multiple RNA targets. The
C-terminal RGG (or GAR) domain of nucleolin is rich in
glycine, arginine and phenylalanine residues, and
contains high levels of NG,NG-dimethylarginines.RRM2,
together with RRM1, binds specifically to RNA
stem-loops containing the sequence (U/G)CCCG(A/G) in
the loop. .
Length = 77
Score = 27.5 bits (61), Expect = 0.59
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 21 RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQI 58
+ G S G A + ++ ++A KA+++ G +DGR + +
Sbjct: 36 KDGSSKGIAYIEFKTEAEAEKALEEKQGAEVDGRSIVV 73
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 27.3 bits (60), Expect = 0.61
Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
E FS+ G + A++ + +G+S G + ++ A KA + NG+ ++GR + ++L
Sbjct: 18 EKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLMNGIKINGREIDVRL 73
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54
kDa nuclear RNA- and DNA-binding protein (p54nrb).
This subgroup corresponds to the RRM2 of p54nrb, also
termed non-POU domain-containing octamer-binding
protein (NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is
a multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses
inherent carbonic anhydrase activity. p54nrb forms a
heterodimer with paraspeckle component 1 (PSPC1 or
PSP1), localizing to paraspeckles in an RNA-dependent
manner. It also forms a heterodimer with polypyrimidine
tract-binding protein-associated-splicing factor (PSF).
p54nrb contains two conserved RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 27.3 bits (60), Expect = 0.63
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 15/75 (20%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
++ E FS FG ++ A + D GR G + + + A KA+ +
Sbjct: 15 LLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDR--------------- 59
Query: 61 AADVSVLENTVPRPV 75
+D + L PRPV
Sbjct: 60 CSDGAFLLTAFPRPV 74
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 27.3 bits (60), Expect = 0.64
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 35 RRSDAIKAMKQYNGVPLDGRPMQIQLA 61
R DA+ AM NG +DG +++ LA
Sbjct: 46 NREDAVAAMSVMNGKCIDGASIEVTLA 72
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 27.2 bits (61), Expect = 0.65
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 2 IYELFSEFGP-LKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGR 54
I F + GP ++ +L D G A + +E SDA KA NG G+
Sbjct: 17 IKAFFEKIGPDVRKIELFPDHEG-----ALVEFESPSDAGKASLSLNGSQFGGK 65
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM2 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 71
Score = 27.2 bits (61), Expect = 0.67
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
+ LFS+FG +K + S + Y+ R A A+ NG P G ++++
Sbjct: 17 ELRSLFSQFGEVKD--IRETPLRPSQKFVEF-YDIR-AAEAALDALNGRPFLGGRLKVK 71
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 27.7 bits (62), Expect = 0.69
Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 15/87 (17%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLG-----------TADLIYERRSDAIKAMKQYNGV 49
I FS FG + + D + LG D + A+KA+++
Sbjct: 19 IKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAKA---ALKAVRKAQDC 75
Query: 50 PLDGRPMQIQLAADVSVLENTVPRPVA 76
+ G +++L + LE + +
Sbjct: 76 RIGGAEFKVELNPNERKLEKIKDKLIK 102
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1). PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. Research indicates that PUF60
binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 77
Score = 27.2 bits (61), Expect = 0.74
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 2 IYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERR---SDAIKAMKQY 46
I +F FG +KS L D +G+ G + YE DAI +M +
Sbjct: 17 IKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLF 65
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering
time control protein FCA and similar proteins. This
subgroup corresponds to the RRM2 of FCA, a gene
controlling flowering time in Arabidopsis, which
encodes a flowering time control protein that functions
in the posttranscriptional regulation of transcripts
involved in the flowering process. The flowering time
control protein FCA contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 27.1 bits (60), Expect = 0.83
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGV 49
+ E+FS +G ++ + D +S G A + Y + A A+K NGV
Sbjct: 16 VEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALNGV 63
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein
44 (RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 26.8 bits (59), Expect = 0.93
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 29 ADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
A L ++R SDA+ A+K+ NG L G +++++
Sbjct: 39 ASLHFDRASDALLAVKKMNGGVLSGLSIKVRM 70
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 86
Score = 27.0 bits (60), Expect = 0.97
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
E FS++G L K+ D R + DA A+ + G LDGR ++ + A
Sbjct: 25 EHFSKYGTLVFVKVLRDWRQRPYAFVQ--FTNDDDAKNALAKGQGTILDGRHIRCERA 80
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein
42 (RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 83
Score = 26.8 bits (60), Expect = 0.98
Identities = 18/60 (30%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
++ FS++ + AK+ D R+G+S G + + +D +KAMK+ NG + RP++++
Sbjct: 22 VLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNGKYVGNRPIKLR 81
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM1 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 26.7 bits (59), Expect = 1.1
Identities = 11/48 (22%), Positives = 27/48 (56%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG 48
++ ++F GP+++ K+ D++ + + + Y + DA A++ NG
Sbjct: 14 ILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLNG 61
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0, a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. It has also been identified
as an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 26.2 bits (58), Expect = 1.4
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 2 IYELFSEFGPLKSAKLHYDRS 22
I E F +FG + +L D+
Sbjct: 16 IREYFGKFGNIVEIELPMDKK 36
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in
yeast. Yra2p belongs to the evolutionarily conserved
REF (RNA and export factor binding proteins) family of
hnRNP-like proteins. It is a major component of
endogenous Yra1p complexes. It interacts with Yra1p and
functions as a negative regulator of Yra1p. Yra2p
consists of two highly conserved N- and C-terminal
boxes and a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 26.2 bits (58), Expect = 1.5
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I +L EFG +K + + R TA +E S K +++YNG L+G +++++
Sbjct: 17 IEDLIKEFGEPVYSKFYDHKDSR---TAVFEFEDPSILEKVVEKYNGKELNGAKIEVEI 72
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 26.2 bits (58), Expect = 1.7
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG--RPMQI 58
+ + +G + S ++ D G+S G E R + ++NG L G P+ +
Sbjct: 16 DLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFNGKYLKGEGEPLLV 75
Query: 59 QLA 61
+ A
Sbjct: 76 KFA 78
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living
cells. RRM2/3 are implicated in ACF interaction with
APOBEC-1. .
Length = 78
Score = 26.1 bits (57), Expect = 1.8
Identities = 11/43 (25%), Positives = 22/43 (51%)
Query: 5 LFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYN 47
L + G + ++ D +G + G A + + + +A A+KQ N
Sbjct: 21 LCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of
the lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the
modulation of rDNA transcription. RRT5 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 84
Score = 26.2 bits (58), Expect = 1.8
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 2 IYELFSEFGPL----KSAKLHYDRSG--RSLGTADLIYERRSDAIKAMKQYNGVPLDGRP 55
+ E +F P+ S + RS R LG A + A K +K NG R
Sbjct: 16 LEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKVVKDLNGKVFKNRK 75
Query: 56 MQIQL 60
+ ++L
Sbjct: 76 LFVKL 80
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and four hnRNP K homology (KH) domains. .
Length = 76
Score = 25.8 bits (57), Expect = 2.0
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDG 53
+ L S +G +K+ + +S + T ++ YE A +A+ + NG +G
Sbjct: 17 LDSLLSTYGTVKNCEQVPTKSETA--TVNVTYESPEQAQQAVNKLNGHEYEG 66
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has
been identified as a regulator of the hematopoietic
stem cell (HSC) compartment and of leukemic stem cells
after transplantation of cells with loss and gain of
function of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
along with other domains of unknown function. .
Length = 74
Score = 25.9 bits (57), Expect = 2.1
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 2 IYELFSEFGPLKSAKLHYDR 21
+ + FS+FG ++ A L +D+
Sbjct: 16 VKKYFSQFGKVEDAMLMFDK 35
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers.
Moreover, hnRNP M is able to interact with early
spliceosomes, further influencing splicing patterns of
specific pre-mRNAs. hnRNP M functions as the receptor
of carcinoembryonic antigen (CEA) that contains the
penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 25.7 bits (56), Expect = 2.2
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
M+ + F+E G + A + + +G+S G + +E A +A + NG L+GR + +++
Sbjct: 15 MLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMMNGYKLNGREIDVRI 73
>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 = 25.8 bits (57), Expect = 2.2
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 2 IYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I +LF ++GP+K+ L R G A + +E DA A++ +G DG ++++
Sbjct: 16 IEDLFYKYGPIKAIDLKNRRRGPPF--AFVEFEDPRDAEDAVRGRDGYDFDGYRLRVEF 72
>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 = 25.7 bits (57), Expect = 2.5
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 5 LFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
LF FG + K+ G+ G + R+ A A++Q G + G +++
Sbjct: 21 LFGPFGEIVYVKI---PPGKGCGFVQ--FVHRAAAEAAIQQLQGTIIGGSRIRLS 70
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 26.6 bits (58), Expect = 2.7
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTAD------LIYERRSDAIKAMKQYNGVPLDGR 54
E F ++G +K K+ ++ SL + + Y + DA + + + +G LDGR
Sbjct: 139 EYFGQYGKIK--KIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR 193
>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 = 25.6 bits (57), Expect = 3.0
Identities = 11/60 (18%), Positives = 26/60 (43%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQL 60
I +LF ++G + S + R ++ + + A A+ NG +G + +++
Sbjct: 16 DIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLNGKLGEGYKLVVKI 75
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly
development. Cabeza contains one RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 25.1 bits (55), Expect = 3.8
Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 9/70 (12%)
Query: 1 MIYELFSEFGPLKSAK--------LHYDR-SGRSLGTADLIYERRSDAIKAMKQYNGVPL 51
+ E F G +K K L+ D+ +G G A + Y+ A A++ +N
Sbjct: 14 DLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHAASAAIEWFNNKDF 73
Query: 52 DGRPMQIQLA 61
G +++ LA
Sbjct: 74 MGNTIKVSLA 83
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 26.2 bits (57), Expect = 3.8
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 7/40 (17%)
Query: 48 GVPLDGRPMQIQLA-------ADVSVLENTVPRPVARGGR 80
G L + M++ + ADV VL + P P A GR
Sbjct: 275 GTGLPRKDMEVHIPGVGDFRMADVEVLIDPCPPPDADHGR 314
>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM1 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers.
Moreover, hnRNP M is able to interact with early
spliceosomes, further influencing splicing patterns of
specific pre-mRNAs. hnRNP M functions as the receptor
of carcinoembryonic antigen (CEA) that contains the
penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 25.4 bits (55), Expect = 3.9
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 10 GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
G + +L D G+S G A + ++ KA++ N L+GRP++++
Sbjct: 25 GEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEVLNKHVLNGRPLKVK 74
>gnl|CDD|215834 pfam00275, EPSP_synthase, EPSP synthase (3-phosphoshikimate
1-carboxyvinyltransferase).
Length = 415
Score = 25.7 bits (57), Expect = 4.8
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 13/51 (25%)
Query: 45 QYNGVPLDG------RPMQI------QLAADVSVLENTVPRPVA-RGGRGG 82
Q V L G RP+ QL A++ E P+ RG + G
Sbjct: 105 QSGEVVLTGDDSIGERPIDRLLDGLRQLGAEIEYREGYGYAPLKVRGLKLG 155
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subfamily corresponds to the
RRM2 of SREK1, also termed
serine/arginine-rich-splicing regulatory protein 86-kDa
(SRrp86), or splicing factor arginine/serine-rich 12
(SFRS12), or splicing regulatory protein 508 amino acid
(SRrp508). SREK1 belongs to a family of proteins
containing regions rich in serine-arginine dipeptides
(SR proteins family), which is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. It is a unique SR family member and it may play
a crucial role in determining tissue specific patterns
of alternative splicing. SREK1 can alter splice site
selection by both positively and negatively modulating
the activity of other SR proteins. For instance, SREK1
can activate SRp20 and repress SC35 in a dose-dependent
manner both in vitro and in vivo. In addition, SREK1
contains two (some contain only one) RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains)
separated by an unusual glutamic acid-lysine (EK) rich
region. The RRM and SR domains are highly conserved
among other members of the SR superfamily. However, the
EK domain is unique to SREK1. It plays a modulatory
role controlling SR domain function by involvement in
the inhibition of both constitutive and alternative
splicing and in the selection of splice-site. .
Length = 85
Score = 24.9 bits (55), Expect = 4.9
Identities = 8/20 (40%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 40 IKAMKQYNGVPLDGRPMQIQ 59
I A+K NG GRP+++
Sbjct: 58 INALK-LNGAMFGGRPLKVN 76
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 80
Score = 25.0 bits (54), Expect = 5.1
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 6 FSEFGPLKSAKLHYD-RSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQLA 61
F+ FG + A++ D +G+S G + + + DA A++Q G L GR ++ A
Sbjct: 22 FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 78
>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 = 24.9 bits (55), Expect = 5.3
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 4 ELFSEFGPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNG 48
E F G + K+ R G+S + ++ DA +A+K +N
Sbjct: 19 EHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNK 63
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM2 of hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 73
Score = 24.5 bits (54), Expect = 5.5
Identities = 9/27 (33%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 4 ELFSEFGPLKSAKLHYDR-SGRSLGTA 29
E FS++G ++S ++ D+ +G+ G A
Sbjct: 18 EYFSQYGNVESVEIVTDKETGKKRGFA 44
>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 24.6 bits (53), Expect = 5.8
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 10 GPLKSAKLHYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLDGRPMQIQ 59
G + +L D G+S G + ++ KA++ N L+GRP+ I+
Sbjct: 25 GEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVMNKYDLNGRPLNIK 74
>gnl|CDD|180592 PRK06498, PRK06498, isocitrate lyase; Provisional.
Length = 531
Score = 25.4 bits (56), Expect = 6.4
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 1 MIYELFSEFGPLKSAKLHYDRSGRSLGTADLIYE-----RRSDA 39
M+ L SEFGPL +H S LI E R++DA
Sbjct: 104 MVAALRSEFGPLPDQSMHEKTS-----VPALIEELYTFLRQADA 142
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are
putative RNA-binding proteins carrying three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and TEL characteristic motifs that allow sequence and
putative functional discrimination between the terminal
EAR1-like proteins and Mei2-like proteins. .
Length = 71
Score = 24.4 bits (53), Expect = 6.4
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 38 DAIKAMKQYNGVPLDGRPMQIQ 59
DA KA++ NG + G+P+ I+
Sbjct: 50 DAAKALRAMNGKEISGKPVVIE 71
>gnl|CDD|197380 cd09971, SdiA-regulated, SdiA-regulated. This model represents a
bacterial family of proteins that may be regulated by
SdiA, a member of the LuxR family of transcriptional
regulators. The C-terminal domain included in the
alignment forms a five-bladed beta-propeller structure.
The X-ray structure of Escherichia coli yjiK (C-terminal
domain) exhibits binding of calcium ions (Ca++) in what
appears to be an evolutionarily conserved site. Sequence
analysis suggests a distant relationship to proteins
that are characterized as containing NHL-repeats. The
latter also form beta-propeller structures, with several
examples known to form six-bladed beta-propellers.
Several of the six-bladed beta-propellers containing NHL
repeats have been characterized functionally, including
members with enzymatic functions that are dependent on
metal ions. No functional characterization is available
for this family of five-bladed propellers, though.
Length = 242
Score = 25.3 bits (56), Expect = 8.0
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 13 KSAKL-HYDRSGRSLGTADLIYERRSDAIKAMKQYNGVPLD 52
+S L DR GR + + L + K + Q GV +D
Sbjct: 185 ESRLLVELDRQGRVVSSLSLTRG-FNGLSKTIPQAEGVAMD 224
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 0.137 0.400
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: 5,455,747
Number of extensions: 461540
Number of successful extensions: 687
Number of sequences better than 10.0: 1
Number of HSP's gapped: 640
Number of HSP's successfully gapped: 205
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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)