RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12245
(189 letters)
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site of
the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65 (also
termed U2AF2). U2AF35 contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 215 bits (549), Expect = 4e-73
Identities = 84/106 (79%), Positives = 93/106 (87%), Gaps = 2/106 (1%)
Query: 28 SQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN 87
SQTILL NLY NPQNS +SADG V+D E+QEH+D F+EDVFVE E+KYGEIEEMN
Sbjct: 1 SQTILLQNLYQNPQNSPQSADGLK--VKVSDVELQEHFDEFYEDVFVELEEKYGEIEEMN 58
Query: 88 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
VCDNLGDHLVGNVY+KFRREEDAEKAVNDLNNRWF G+P+YAELSP
Sbjct: 59 VCDNLGDHLVGNVYVKFRREEDAEKAVNDLNNRWFNGQPIYAELSP 104
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer composed
of large and small subunits; this family includes the
small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa
subunit B (U2AF35B or C3H60). U2AF35 directly binds to
the 3' splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF (U2AF65 or
U2AF2). Although the biological role of U2AF35B remains
unclear, it shows high sequence homolgy to U2AF35, which
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR) -rich segment
interrupted by glycines. In contrast to U2AF35, U2AF35B
has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 102
Score = 144 bits (366), Expect = 3e-45
Identities = 60/104 (57%), Positives = 80/104 (76%), Gaps = 2/104 (1%)
Query: 30 TILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC 89
TILL N+Y NP N+ S DG + +++EE+QEH+D F+EDVF+E ++GEIE++ VC
Sbjct: 1 TILLKNMYPNPDNAIASLDGQ-GVLTLSEEEIQEHFDEFYEDVFLELS-RFGEIEDLVVC 58
Query: 90 DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
DNLGDHL+GNVY+KF EEDAE A+ LN R++ GRP+Y ELSP
Sbjct: 59 DNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPELSP 102
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 127 bits (321), Expect = 2e-38
Identities = 50/105 (47%), Positives = 69/105 (65%), Gaps = 2/105 (1%)
Query: 29 QTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV 88
TILL N+Y +P A ++ E+QEH+++F+ED+F E K+GE+E +NV
Sbjct: 1 PTILLSNMYQSPIAGAPGGPRG-QGQSLDPRELQEHFEDFYEDIFEEL-SKFGEVEALNV 58
Query: 89 CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
CDNLGDH+VGNVY+KFR EE A A+ L R++ GRP+ E SP
Sbjct: 59 CDNLGDHMVGNVYVKFRDEEHAAAALKALQGRFYDGRPIIVEFSP 103
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in a
substrate-specific manner. Like U2AF35, U2AFBPL contains
two N-terminal zinc fingers, a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. .
Length = 105
Score = 80.4 bits (199), Expect = 4e-20
Identities = 35/109 (32%), Positives = 58/109 (53%), Gaps = 9/109 (8%)
Query: 30 TILLLNLYINP-----QNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIE 84
T+L+ N++ + Q D L +E++ ++ F++DV E E K+GE+
Sbjct: 1 TLLIPNMFTHFGLEQTQRDEYDTD-EGL--EYDEEDLYSDFEEFYDDVLPEFE-KFGEVV 56
Query: 85 EMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
+ VC N HL GNVY++++ EE+A A N RW+ G+ + E SP
Sbjct: 57 QFKVCCNYEPHLRGNVYVQYQSEEEALAAFKMFNGRWYAGKQLTCEFSP 105
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 68.3 bits (168), Expect = 1e-15
Identities = 30/86 (34%), Positives = 43/86 (50%), Gaps = 9/86 (10%)
Query: 52 LISNVTDEEMQEHYDNFF----EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRRE 107
++ N+ D + D + EDV EC K+G +E + V N G VY+KF+
Sbjct: 5 ILKNMFDPAEETE-DEWDDEIKEDVLEECS-KFGPVEHIKVDKN---SPEGVVYVKFKTV 59
Query: 108 EDAEKAVNDLNNRWFGGRPVYAELSP 133
E A+K + LN RWF GR + AE
Sbjct: 60 EAAQKCIQALNGRWFDGRQITAEYVD 85
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 66.3 bits (162), Expect = 5e-15
Identities = 32/70 (45%), Positives = 43/70 (61%), Gaps = 4/70 (5%)
Query: 65 YDNFFEDVFVECEDKYGEIEEMN--VCDNLG--DHLVGNVYIKFRREEDAEKAVNDLNNR 120
D FE E E+ +GE+ ++N D++G +H GNVYI F R EDA +A+ DLN R
Sbjct: 1 KDEDFERELKEEEEYFGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGR 60
Query: 121 WFGGRPVYAE 130
+F GR V AE
Sbjct: 61 YFDGRLVKAE 70
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 89
Score = 60.6 bits (148), Expect = 1e-12
Identities = 27/83 (32%), Positives = 40/83 (48%), Gaps = 8/83 (9%)
Query: 52 LISNVTDEEM---QEHYDNFFEDVFVECEDKYGEIEEMNV----CDNLGDHLVGNVYIKF 104
+ N+ E E Y+ EDV EC KYG++ + + + + VG V+++F
Sbjct: 5 CLLNMVTPEELEDDEEYEEILEDVKEECG-KYGKVLSVVIPRPEAEGVDVPGVGKVFVEF 63
Query: 105 RREEDAEKAVNDLNNRWFGGRPV 127
EDA+KA L R F GR V
Sbjct: 64 ADVEDAQKAQLALAGRKFDGRTV 86
>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 = 52.7 bits (127), Expect = 6e-10
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 12/76 (15%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+ T+E+++E F K+GEIE + + + G +++F EDAEKA+
Sbjct: 9 DTTEEDLREL----FS--------KFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKAL 56
Query: 115 NDLNNRWFGGRPVYAE 130
LN + GR +
Sbjct: 57 EALNGKELDGRKLKVS 72
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 91
Score = 49.5 bits (119), Expect = 2e-08
Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 5/69 (7%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
+D+ ECE K+G+++++ V D H G +KF+ E+A++ + LN RWF GR + A
Sbjct: 27 DDLREECE-KFGQVKKVVVFD---RHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEA 82
Query: 130 EL-SPVTDF 137
E TD+
Sbjct: 83 ERWDGKTDY 91
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 47.2 bits (113), Expect = 9e-08
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 13/80 (16%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREE 108
+L + T+EE++E F K+G++E + + D G +++F EE
Sbjct: 5 GNLPPDTTEEELRE----LFS--------KFGKVESVRLVRDKETGKSKGFAFVEFESEE 52
Query: 109 DAEKAVNDLNNRWFGGRPVY 128
DAEKA+ LN + GRP+
Sbjct: 53 DAEKALEALNGKELDGRPLK 72
>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 = 46.7 bits (112), Expect = 9e-08
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
+G +E++ + G +++F EE AEKAV LN FGGRP+ + S
Sbjct: 7 PFGNVEKIKLLKKKP----GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 46.1 bits (110), Expect = 3e-07
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 5/71 (7%)
Query: 66 DNFFEDVFVECEDKYGEIEEMNVCDN---LGDHLVGNVYIKFRREEDAEKAVNDLNNRWF 122
++ +++ ECE KYG++ + V + D V ++++F ++A KAV LN R+F
Sbjct: 17 EDLKDEIEEECE-KYGKVLNVIVHEVASSEADDAV-RIFVEFSDADEAIKAVRALNGRFF 74
Query: 123 GGRPVYAELSP 133
GGR V A
Sbjct: 75 GGRKVTARFYD 85
>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 = 48.0 bits (114), Expect = 8e-07
Identities = 35/125 (28%), Positives = 55/125 (44%), Gaps = 10/125 (8%)
Query: 23 NKPTFSQTILLLNLYIN---PQNSAKSADGSHLISNVTD--EEMQEHYDN-FFEDVFVEC 76
N P+ T L + N P + A ++SN+ D E + ++DN +DV EC
Sbjct: 334 NIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEEC 393
Query: 77 EDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTD 136
KYG + + V G +Y+KF + A A LN R+FGG+ + A
Sbjct: 394 S-KYGGVVHIYVDTKNSA---GKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDV 449
Query: 137 FREAC 141
+ +C
Sbjct: 450 YDMSC 454
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal region,
followed by a G-patch motif and a C-terminal U2AF (U2
auxiliary factor) homology motifs (UHM) that harbors a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and an
Arg-Xaa-Phe sequence motif. SPF45 regulates alternative
splicing of the apoptosis regulatory gene FAS (also
known as CD95). It induces exon 6 skipping in FAS
pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 44.6 bits (106), Expect = 1e-06
Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 11/84 (13%)
Query: 58 DEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLG---DHLVGNVYIKFRREEDAEKAV 114
DE+++ +V EC KYG++ ++ + + G D ++++F R E A KAV
Sbjct: 17 DEDLEP-------EVKEECS-KYGKVTKVLIFEIPGASPDDEAVRIFVEFERVESAIKAV 68
Query: 115 NDLNNRWFGGRPVYAELSPVTDFR 138
DLN R+FGGR V A FR
Sbjct: 69 VDLNGRFFGGRTVKASFYDEERFR 92
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins. The
research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 98
Score = 44.7 bits (106), Expect = 1e-06
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 15/86 (17%)
Query: 58 DEEMQEHYDNFFEDVFVECEDKYGEIE------EMNVCDNLGDHLVGNVYIKFRREEDAE 111
D++++ +V EC K+G + E + + +V ++++F +AE
Sbjct: 16 DDDLEG-------EVTEECG-KFGAVNRVIIYQEKQGEEEDAEIIV-KIFVEFSLPSEAE 66
Query: 112 KAVNDLNNRWFGGRPVYAELSPVTDF 137
KA+ LN RWFGGR V AEL T F
Sbjct: 67 KAIQALNGRWFGGRKVKAELYDQTKF 92
>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 = 43.4 bits (103), Expect = 2e-06
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
K+G IE + + + G +++F EEDAEKA+ LN + GGR +
Sbjct: 21 KFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70
>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 = 40.8 bits (95), Expect = 2e-04
Identities = 26/109 (23%), Positives = 48/109 (44%), Gaps = 20/109 (18%)
Query: 24 KPTFSQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNF-FEDVFVECEDKYGE 82
+ S I+L N+ + PQ+ I + E++E F D + +K GE
Sbjct: 510 RTNRSNVIVLRNM-VTPQD----------IDEFLEGEIREECGKFGVVDRVIINFEKQGE 558
Query: 83 IEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 131
E+ + + ++++F + ++A L+ R+FGGR V AE
Sbjct: 559 EEDAEI--------IVKIFVEFSDSMEVDRAKAALDGRFFGGRTVVAEA 599
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 37.5 bits (88), Expect = 3e-04
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
YG++E + + N D G +++F EDAE A+ LN GR +
Sbjct: 21 PYGKVEGVRLVRN-KDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69
>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 = 38.3 bits (90), Expect = 3e-04
Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 79 KYGEIE--EMNVCDNLGDHLVGN--VYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
+YG+I+ +N + + Y+ + R+EDA + + ++ + GR + A
Sbjct: 31 QYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDGFYLDGRLLKA 85
>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and
similar).
Length = 27
Score = 36.0 bits (84), Expect = 4e-04
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 1 VNCSFYFKIGACRHGDRCSRIHNK 24
C F+ + G C++GDRC H +
Sbjct: 4 ELCRFFSRTGTCKYGDRCKFAHGQ 27
Score = 32.5 bits (75), Expect = 0.008
Identities = 7/25 (28%), Positives = 7/25 (28%)
Query: 136 DFREACCRQYEMGECTRSGFCNFMH 160
E C G C C F H
Sbjct: 1 YKTELCRFFSRTGTCKYGDRCKFAH 25
>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 = 39.5 bits (92), Expect = 5e-04
Identities = 27/84 (32%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 52 LISNVTDEEM--QEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL----VGNVYIKFR 105
L + VT +++ E Y+ +EDV E KYG + + + GD VG V++++
Sbjct: 414 LTNLVTGDDLMDDEEYEEIYEDVKTEFS-KYGPLINIVIPRPNGDRNSTPGVGKVFLEYA 472
Query: 106 REEDAEKAVNDLNNRWFGGRPVYA 129
AEKA+ +N R F R V A
Sbjct: 473 DVRSAEKAMEGMNGRKFNDRVVVA 496
>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 = 36.8 bits (86), Expect = 7e-04
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
++ DE+++E F KYG+I V + G ++ F E A+KAV
Sbjct: 12 DMDDEKLKE----LFG--------KYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAV 59
Query: 115 NDLNNRWFGGRPVYA 129
+LN + G+ +Y
Sbjct: 60 EELNGKEVNGKKLYV 74
>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 = 35.6 bits (82), Expect = 0.001
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
++ FR ++DAE A+N++N +W G RP+
Sbjct: 45 FVSFRSQQDAENAINEMNGKWLGSRPI 71
>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 = 35.3 bits (82), Expect = 0.002
Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 23/84 (27%)
Query: 55 NVTDEEMQEHYDNFFEDV------FVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREE 108
+ TDE+++E FF +V FV V D G Y+ F EE
Sbjct: 10 DTTDEQLEE----FFSEVGPIKRCFV-------------VKDKGSKKCRGFGYVTFALEE 52
Query: 109 DAEKAVNDLNNRWFGGRPVYAELS 132
DA++A+ + FGGR ++ E +
Sbjct: 53 DAKRALEEKKKTKFGGRKIHVEFA 76
>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 = 35.0 bits (81), Expect = 0.003
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 70 EDVFVECEDKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
E+ E + +GEI E+++ D G ++ F E A KA ++L+ F GR ++
Sbjct: 13 EEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLH 72
>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology
motif kinase 1 (UHMK1) and similar proteins. This
subgroup corresponds to the RRM of UHMK1. UHMK1, also
termed kinase interacting with stathmin (KIS) or P-CIP2,
is a serine/threonine protein kinase functionally
related to RNA metabolism and neurite outgrowth. It
contains an N-terminal kinase domain and a C-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), with
high homology to the corresponding motif of the
mammalian U2 small nuclear ribonucleoprotein auxiliary
factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1
targets two key regulators of cell proliferation and
migration, the cyclin-dependent kinase (CDK) inhibitor
p27Kip1 and the microtubule-destabilizing protein
stathmin. It plays a critical role during vascular wound
repair by preventing excessive vascular smooth muscle
cell (VSMC) migration into the vascular lesion.
Moreover, UHMK1 may control cell migration and neurite
outgrowth by interacting with and phosphorylating the
splicing factor SF1, thereby probably contributing to
the control of protein expression. Furthermore, UHMK1
may be functionally related to microtubule dynamics and
axon development. It localizes to RNA granules,
interacts with three proteins found in RNA granules
(KIF3A, NonO, and eEF1A), and further enhances the local
translation. UHMK1 is highly expressed in regions of the
brain implicated in schizophrenia and may play a role in
susceptibility to schizophrenia.
Length = 88
Score = 35.4 bits (81), Expect = 0.003
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 55 NVTDE---EMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDA 110
NV D+ + +E Y++ ED+ EC+ KYG + + + +N G G V++++ D+
Sbjct: 10 NVLDDAHLQNEEEYEDIIEDIKEECQ-KYGPVVSLLIPKENPGK---GQVFVEYANAGDS 65
Query: 111 EKAVNDLNNRWFGGRPVYAELSP 133
+ A L R F G+ V A P
Sbjct: 66 KAAQKLLTGRIFDGKFVVATFYP 88
>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 = 35.0 bits (81), Expect = 0.003
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 13/77 (16%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDA 110
L + E ++ + F GEI + V D G ++ F ++EDA
Sbjct: 7 LSPEIDTETLRAAFAPF------------GEISDARVVKDMQTGKSKGYGFVSFVKKEDA 54
Query: 111 EKAVNDLNNRWFGGRPV 127
E A+ +N +W GGR +
Sbjct: 55 ENAIQSMNGQWLGGRAI 71
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 34.5 bits (80), Expect = 0.003
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
+G + E+ + G +++F + DAEKA+ +N + GRPV
Sbjct: 22 PFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPV 70
>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger.
Length = 27
Score = 32.6 bits (75), Expect = 0.006
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 136 DFREACCRQYEMGECTRSGFCNFMH 160
++ C+ ++ G C R C F H
Sbjct: 1 KYKTELCKFFKRGYCPRGDRCKFAH 25
Score = 28.7 bits (65), Expect = 0.19
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 5 FYFKIGACRHGDRCSRIHNK 24
+FK G C GDRC H
Sbjct: 8 KFFKRGYCPRGDRCKFAHPL 27
>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 = 33.8 bits (78), Expect = 0.007
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 9/69 (13%)
Query: 67 NFFEDVFVECEDKYGEIEEMNV----CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF 122
+ +F K+GE+E + + + G G ++ F+ AE A+ LN
Sbjct: 15 DDLRGIFS----KFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQ-LNGTEL 69
Query: 123 GGRPVYAEL 131
GGR + L
Sbjct: 70 GGRKISVSL 78
>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 = 33.7 bits (78), Expect = 0.008
Identities = 26/98 (26%), Positives = 41/98 (41%), Gaps = 25/98 (25%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLG 93
NLY+ +L ++ DE ++E + +G I V D G
Sbjct: 3 NLYVK-----------NLDDSIDDERLREEFS------------PFGTITSAKVMTDEKG 39
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 131
G ++ F E+A KAV ++N R GG+P+Y L
Sbjct: 40 -RSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVAL 76
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 33.6 bits (77), Expect = 0.010
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 13/69 (18%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREED 109
+L N+T +E++ + + GEIE + D + +G ++ + ED
Sbjct: 8 YLPQNMTQDEIRSLFSSI------------GEIESCKLIRDKVTGQSLGYGFVNYVDPED 55
Query: 110 AEKAVNDLN 118
AEKA+N LN
Sbjct: 56 AEKAINTLN 64
>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 = 32.5 bits (74), Expect = 0.023
Identities = 14/49 (28%), Positives = 26/49 (53%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
+YG++ E + G L G ++ ++ ++AE A+ + N GRPV
Sbjct: 24 RYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPV 72
>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 = 34.4 bits (79), Expect = 0.025
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 124
ED E K+GEI V + G ++ F + EDA KAV ++N + G
Sbjct: 192 EDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
Score = 34.0 bits (78), Expect = 0.036
Identities = 36/135 (26%), Positives = 58/135 (42%), Gaps = 37/135 (27%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNV-CDNLG 93
NLY+ K+ D + VTDE+++E + + GEI V D G
Sbjct: 287 NLYV------KNLDDT-----VTDEKLRELFS------------ECGEITSAKVMLDEKG 323
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEMGECTRS 153
G ++ F E+A +AV +++ R GG+P+Y L+ + R A +
Sbjct: 324 VSR-GFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQD--------- 373
Query: 154 GFCNFMHLKPISREL 168
FM L+P R+L
Sbjct: 374 ---QFMQLQPRMRQL 385
Score = 31.3 bits (71), Expect = 0.33
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 13/77 (16%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDA 110
L +VT+ ++ + + F G + + VC D++ +G Y+ F+ DA
Sbjct: 8 LDPDVTEAKLYDLFKPF------------GPVLSVRVCRDSVTRRSLGYGYVNFQNPADA 55
Query: 111 EKAVNDLNNRWFGGRPV 127
E+A+ +N + GG+P+
Sbjct: 56 ERALETMNFKRLGGKPI 72
>gnl|CDD|240958 cd12514, RRM4_RBM12_like, RNA recognition motif 4 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM4 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B show high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 31.9 bits (73), Expect = 0.030
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 90 DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
D G L G Y++F EEDA +A L+ + GR +
Sbjct: 35 DKTGKTL-GEAYVEFVSEEDAMRAE-RLHRKKLKGREIL 71
>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 = 31.9 bits (73), Expect = 0.033
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 70 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRP 126
ED E +GEI+++ V D G Y+KF + A +A+ ++N + GG
Sbjct: 16 EDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 32.2 bits (74), Expect = 0.039
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 99 NVYIKFRREEDAEKAVNDLNNRWFGGR 125
N Y+ F+ EE AEKA+ LN F G
Sbjct: 61 NAYVVFKEEESAEKALK-LNGTEFEGH 86
>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 = 31.9 bits (72), Expect = 0.041
Identities = 15/53 (28%), Positives = 29/53 (54%)
Query: 67 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 119
+ FED + +K G+I EM + + + G ++ F +++A+ A+ LNN
Sbjct: 12 DLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLNN 64
>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 = 31.4 bits (72), Expect = 0.045
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
G Y++F EDA +A+ NN+ GGR +
Sbjct: 42 GEAYVEFASPEDARRALRKHNNK-MGGRYIE 71
>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 = 31.6 bits (72), Expect = 0.050
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 81 GEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG-RPVYAEL 131
G I+ + + N G G I F+R DA KA + N R G R + E+
Sbjct: 25 GPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRIDDGNRKMKVEV 76
>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 = 31.4 bits (72), Expect = 0.053
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 13/82 (15%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHL-VGNVYIKFRREE 108
L NV + ++E + N YG ++++++ + +L G Y++F E
Sbjct: 4 GKLTRNVNKDHLKEIFSN------------YGTVKDVDLPIDREVNLPRGYAYVEFESPE 51
Query: 109 DAEKAVNDLNNRWFGGRPVYAE 130
DAEKA+ ++ G+ V E
Sbjct: 52 DAEKAIKHMDGGQIDGQEVTVE 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 = 33.4 bits (76), Expect = 0.054
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 10/71 (14%)
Query: 50 SHLISNVTDEEM-QEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRRE 107
++LI N + M QE + F + GEIE V D + +G ++ + R
Sbjct: 4 TNLIVNYLPQTMTQEEIRSLFTSI--------GEIESCKLVRDKVTGQSLGYGFVNYVRP 55
Query: 108 EDAEKAVNDLN 118
EDAEKAVN LN
Sbjct: 56 EDAEKAVNSLN 66
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 31.5 bits (72), Expect = 0.061
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 67 NFFEDVFVECEDKYGEIEEMNVC--DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 124
F +D C+ KYGE+EE+ + HL G + F + A++ V LN G
Sbjct: 17 GFLKD---MCK-KYGEVEEVKIYFHPKTNKHL-GLARVVFDSVKSAKRCVEKLNQTSVMG 71
Query: 125 RPVYAELSPVTDFREACCRQYE 146
+ + L P E R YE
Sbjct: 72 KIIKVFLDP---KGEIRKRLYE 90
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B). This
subgroup corresponds to the RRM of Setd1B, also termed
SET domain-containing protein 1B (Set1B), or lysine
N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits high
homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone H3
at Lys4. Set1B contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), an N- SET domain, and a
C-terminal catalytic SET domain followed by a post-SET
domain. .
Length = 93
Score = 31.5 bits (71), Expect = 0.066
Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 66 DNFFEDVFVECEDKYGEIEEMNVCDNLGD--HLVGNVYIKFRREEDAEKAVNDLNNRWFG 123
DN E+ + KYGE+EE+ + N + HL G + F + A+ AV L+N
Sbjct: 12 DNIRENFLTDMCKKYGEVEEVEILYNPKNKKHL-GIAKVVFATVKGAKDAVQHLHNTSVM 70
Query: 124 GRPVYAELSPVTDFREACCRQYEM 147
G ++ EL + R R YE+
Sbjct: 71 GNIIHVELDTKGETRM---RFYEL 91
>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 = 31.1 bits (71), Expect = 0.070
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 79 KYGEIEEMNVCDNLGDHLVGN----VYIKFRREEDAEKAVNDLNNRWFGGR 125
KYG+I++ + + L G ++ F +E+AEKA+ LN + G+
Sbjct: 22 KYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALGK 72
>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 = 31.0 bits (71), Expect = 0.071
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 79 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
G + + VC D + +G Y+ F+ DAE+A++ LN G+P+
Sbjct: 22 PAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPIR 72
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 30.9 bits (70), Expect = 0.072
Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 11/60 (18%)
Query: 69 FEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 128
++F YG ++E+ + N +++F E A +A + ++ + P+Y
Sbjct: 16 IREIF----SPYGAVKEVKMISNFA-------FVEFESLESAIRAKDSVHGKVLNNNPLY 64
>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 = 30.6 bits (70), Expect = 0.095
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 79 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNN 119
+YG IEE+ + D G ++KF E+A+KA+ L+
Sbjct: 22 EYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63
>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 = 30.7 bits (70), Expect = 0.096
Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L +VTD +QE + + V + ++ V D + G +++F E++ +
Sbjct: 9 LAPDVTDYMLQETFRARYPSV------RGAKV----VMDPVTGRSKGYGFVRFGDEDERD 58
Query: 112 KAVNDLNNRWFGGRPVYAELSPVT 135
+A+ ++N + RP+ +SP T
Sbjct: 59 RALTEMNGVYCSSRPM--RVSPAT 80
>gnl|CDD|219788 pfam08314, Sec39, Secretory pathway protein Sec39. Mnaimneh et al
identified Sec39p as a protein involved in ER-Golgi
transport in a large scale promoter shut down analysis
of essential yeast genes. Kraynack et al. (2005) showed
that Sec39p (Dsl3p) is required for Golgi-ER retrograde
transport and is part of a very stable protein complex
that also includes Dsl1p (in mammals ZW10), Tip20p
(Rint-1) and the ER localized Q-SNARE proteins Ufe1p
(syntaxin-18), Sec20p and Use1p. This was confirmed in a
genome-wide analysis of protein complexes by Gavin et al
(2006).
Length = 675
Score = 32.8 bits (75), Expect = 0.10
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 8 KIGACRHGDRCSRIHNKPTFSQTILLLNLYINPQNSAKSADGSHLI 53
+ A + D + Q L +Y+N NS ++ S+LI
Sbjct: 267 VVNAVQQWDGEDLASLEDRLGQA-ALAIIYLNSDNSLEALSLSYLI 311
>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 = 30.6 bits (70), Expect = 0.11
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 18/80 (22%)
Query: 52 LISN----VTDEEMQEHYDNFFEDVFVECE-DKYGEIEEMNVCDNLGDHLVGNVYIKFRR 106
+SN VT+E+++E + E V+ D+ G E G + F +
Sbjct: 4 RVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSE-------------GTADVVFEK 50
Query: 107 EEDAEKAVNDLNNRWFGGRP 126
EDAE+A+ N G+P
Sbjct: 51 REDAERAIKQFNGVLLDGQP 70
>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 = 30.2 bits (68), Expect = 0.14
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 70 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 125
ED + + YG I + N+ D G ++++ + E+A+ A++ LN G
Sbjct: 14 EDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGS 70
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 29.9 bits (68), Expect = 0.17
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 17/76 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L +T+EE+Q + F G IEE+ V + G +++F E A
Sbjct: 8 LPHGLTEEELQRTFSPF------------GAIEEVRVFKD-----KGYAFVRFDTHEAAA 50
Query: 112 KAVNDLNNRWFGGRPV 127
A+ +N G+ V
Sbjct: 51 TAIVAVNGTSINGQTV 66
>gnl|CDD|225494 COG2943, MdoH, Membrane glycosyltransferase [Cell envelope
biogenesis, outer membrane].
Length = 736
Score = 32.1 bits (73), Expect = 0.17
Identities = 22/78 (28%), Positives = 33/78 (42%), Gaps = 14/78 (17%)
Query: 57 TDEEMQE--HYDNFFEDVFVECEDKYGEI---EE---MNVCDNLGDHLVGNVYIKFRREE 108
T E + H ++F D FV + + +I E+ +C LG GN++ + RR
Sbjct: 167 TYESLAATGHAEHF--DFFVLSDSRDPDIALAEQKAWAELCRELGGE--GNIFYRRRRRN 222
Query: 109 DAEKAVN--DLNNRWFGG 124
KA N D RW
Sbjct: 223 VKRKAGNIADFCRRWGSA 240
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to the
RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a TRBP-interacting
domain. RBM4 is a ubiquitously expressed splicing factor
with two isoforms, RBM4A (also known as Lark homolog)
and RBM4B (also known as RBM30), which are very similar
in structure and sequence. RBM4 may also function as a
translational regulator of stress-associated mRNAs as
well as play a role in micro-RNA-mediated gene
regulation. RBM4 contains two N-terminal RRMs, a
CCHC-type zinc finger, and three alanine-rich regions
within their C-terminal regions. This family also
includes Drosophila RNA-binding protein lark (Dlark), a
homolog of human RBM4. It plays an important role in
embryonic development and in the circadian regulation of
adult eclosion. Dlark shares high sequence similarity
with RBM4 at the N-terminal region. However, Dlark has
three proline-rich segments instead of three
alanine-rich segments within the C-terminal region. .
Length = 66
Score = 29.5 bits (67), Expect = 0.17
Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 19/80 (23%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 110
+L T EE++ FE KYG + E +V N G ++ EEDA
Sbjct: 6 NLPDATTSEELRA----LFE--------KYGTVTECDVVKNYG-------FVHMEEEEDA 46
Query: 111 EKAVNDLNNRWFGGRPVYAE 130
E A+ LN F G+ + E
Sbjct: 47 EDAIKALNGYEFMGKRINVE 66
>gnl|CDD|240732 cd12286, RRM_Man1, RNA recognition motif in inner nuclear membrane
protein Man1 (Man1) and similar proteins. This
subfamily corresponds to the RRM of Man1, also termed
LEM domain-containing protein 3 (LEMD3), an integral
protein of the inner nuclear membrane that binds to
nuclear lamins and emerin, thus playing a role in
nuclear organization. It is part of a protein complex
essential for chromatin organization and cell division.
It also functions as an important negative regulator for
the transforming growth factor (TGF) beta/activin/Nodal
signaling pathway by directly interacting with
chromatin-associated proteins and transcriptional
regulators, including the R-Smads, Smad1, Smad2, and
Smad3. Moreover, Man1 is a unique type of left-right
(LR) signaling regulator that acts on the inner nuclear
membrane. Man1 plays a crucial role in angiogenesis. The
vascular remodeling can be regulated at the inner
nuclear membrane through the interaction between Man1
and Smads. Man1 contains an N-terminal LEM domain, two
putative transmembrane domains, a MAN1-Src1p C-terminal
(MSC) domain, and a C-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The LEM domain interacts
with the DNA and chromatin-binding protein
Barrier-to-Autointegration Factor, and is also necessary
for efficient localization of MAN1 in the inner nuclear
membrane. Research has indicated that C-terminal
nucleoplasmic region of Man1 exhibits a DNA binding
winged helix domain and is responsible for both DNA- and
Smad-binding. .
Length = 92
Score = 30.4 bits (69), Expect = 0.18
Identities = 16/33 (48%), Positives = 18/33 (54%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAE 130
G VYIK EDA KA L+ WF GR V +
Sbjct: 48 GCVYIKCSSPEDAGKAFKALHGWWFDGRLVTVK 80
>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 = 30.0 bits (68), Expect = 0.19
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 13/82 (15%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREED 109
L +VT EE+ E F ++G+I E+N+ +H +IKF RE+
Sbjct: 9 GQLSPDVTKEELNE----RFS--------RHGKILEVNLIKR-ANHTNAFAFIKFEREQA 55
Query: 110 AEKAVNDLNNRWFGGRPVYAEL 131
A +AV N+ + ++ +
Sbjct: 56 AARAVESENHSMLKNKTMHVQY 77
>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 = 29.7 bits (67), Expect = 0.21
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGR 125
G Y +F E AEK V DLN + F R
Sbjct: 47 GIAYAEFSSPEQAEKVVKDLNGKVFKNR 74
>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 = 29.9 bits (68), Expect = 0.22
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 53 ISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAE 111
+S T E+ E +F K+G +EE+ + D G ++ F EDA+
Sbjct: 9 LSTRTTEKE-------LEALF----SKFGRVEEVLLMKDPETGESRGFGFVTFESVEDAD 57
Query: 112 KAVNDLNNRWFGGRPVYAE 130
A+ DLN + GR + E
Sbjct: 58 AAIRDLNGKELEGRVIKVE 76
>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 = 29.6 bits (67), Expect = 0.24
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 17/77 (22%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 110
HL VT+E+++ N FE +YGEI+ +++ G Y+ +DA
Sbjct: 9 HLSKKVTEEDLK----NLFE--------EYGEIQSIDMIPPRG-----CAYVCMETRQDA 51
Query: 111 EKAVNDLNNRWFGGRPV 127
+A+ L N G+ +
Sbjct: 52 HRALQKLRNVKLAGKKI 68
>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 = 29.5 bits (67), Expect = 0.26
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKA 113
NVT+E++++ F +GE+ V D G +++ E+A A
Sbjct: 10 NVTEEDLKD----LFGQ--------FGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57
Query: 114 VNDLNNRWFGGRPV 127
+ LN FGGR +
Sbjct: 58 IEKLNGTDFGGRTL 71
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and similar
proteins. This subfamily corresponds to the RRM of
Acinus, a caspase-3-activated nuclear factor that
induces apoptotic chromatin condensation after cleavage
by caspase-3 without inducing DNA fragmentation. It is
essential for apoptotic chromatin condensation and may
also participate in nuclear structural changes occurring
in normal cells. Acinus contains a P-loop motif and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), which
indicates Acinus might have ATPase and DNA/RNA-binding
activity. .
Length = 90
Score = 29.9 bits (68), Expect = 0.26
Identities = 8/43 (18%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 101 YIKFRREEDAEKAVNDLNN-RW--FGGRPVYAELSPVTDFREA 140
Y+ + E+A L+ +W + + + P + EA
Sbjct: 43 YVTYSTVEEAVATREALHGLQWPSSNPKRLKVDFVPQEELEEA 85
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing
protein 1 (RDM1) and similar proteins. This subfamily
corresponds to the RRM of RDM1, also termed RAD52
homolog B, a novel factor involved in the cellular
response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 29.7 bits (67), Expect = 0.26
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVY--IKFRREEDAEKAVNDLNNRW-FGGRPV 127
++G + + V N Y +KF A +A N +W F G P+
Sbjct: 27 QFGLLYSVKVFPNAA-VATPGFYAFVKFYSARAASRAQKACNGKWLFQGSPL 77
>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 = 29.2 bits (66), Expect = 0.29
Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 17/77 (22%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L VT++E++ + F E V+V+ G C +++F AE
Sbjct: 9 LDPAVTEDELRSLFGPFGEIVYVKIPPGKG-------CG----------FVQFVHRAAAE 51
Query: 112 KAVNDLNNRWFGGRPVY 128
A+ L GG +
Sbjct: 52 AAIQQLQGTIIGGSRIR 68
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 29.2 bits (66), Expect = 0.29
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 102 IKFRREEDAEKAVNDLNNRWFGGRPV 127
+ FR+ EDAEKA+ + F G +
Sbjct: 46 VFFRKPEDAEKALEVSKGKLFFGAEI 71
>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 = 29.3 bits (66), Expect = 0.30
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 69 FEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 125
E +F K+GE+ E++V D G Y+ F EDA KA +L+ + F GR
Sbjct: 19 LEKLF----SKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGR 72
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 28.8 bits (65), Expect = 0.35
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 24/87 (27%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGD 94
N+YI L N TDE++++ C+ +G+I +
Sbjct: 2 NVYIRG-----------LPPNTTDEDLEKL-----------CQ-PFGKIISTKAILDKKT 38
Query: 95 HLV-GNVYIKFRREEDAEKAVNDLNNR 120
+ G ++ F E A KA+ LN R
Sbjct: 39 NKCKGYGFVDFDSPEAALKAIEGLNGR 65
>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 = 28.8 bits (65), Expect = 0.37
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 104 FRREEDAEKAVNDLNNRWFGGRPVYAEL 131
+ R++DA A++ NNR G+P+ +L
Sbjct: 42 YVRKDDALTAIDKYNNRELDGQPMKCKL 69
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of 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). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It 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 with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 28.7 bits (65), Expect = 0.38
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 102 IKFRREEDAEKAVNDLNNRWFGGRPV 127
++F +ED E+A+ L+ F GR V
Sbjct: 42 VEFTSQEDMERALRKLDGTEFRGRRV 67
>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 = 28.9 bits (65), Expect = 0.38
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 12/83 (14%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREED 109
S L +VT EE+ E +F K+G ++ + + N G Y+++ E
Sbjct: 8 SGLPFSVTKEEL--------EKLF----KKHGVVKSVRLVTNRSGKPKGLAYVEYENESS 55
Query: 110 AEKAVNDLNNRWFGGRPVYAELS 132
A +AV ++ + + +S
Sbjct: 56 ASQAVLKMDGTEIKEKTISVAIS 78
>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 = 30.8 bits (69), Expect = 0.39
Identities = 15/42 (35%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 79 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNN 119
KYG+I + N+ D L G +++F + E+A++A++ LNN
Sbjct: 216 KYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN 257
>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 = 28.9 bits (64), Expect = 0.44
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
G ++ F + DAE A+ + +W GGR +
Sbjct: 44 GYGFVSFFNKWDAENAIQQMGGQWLGGRQI 73
>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 = 28.8 bits (64), Expect = 0.46
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
G ++F+ EE +KAV LN GRP+
Sbjct: 42 GCAVVEFKMEESMKKAVEVLNKHVLNGRPL 71
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 28.6 bits (64), Expect = 0.47
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
++ R E A++A+ +LN R GR + E S
Sbjct: 38 FVHLRGEAAADRAIEELNGRELHGRKLVVEHS 69
>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 = 28.7 bits (65), Expect = 0.48
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 79 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 124
++GE++ + D L H G ++KF+ +E A+K + +N G
Sbjct: 23 QFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSG 69
>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 = 28.7 bits (64), Expect = 0.48
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 131
D + ++ REE+A A+ LN + GR + EL
Sbjct: 31 DKVKDYAFVHMEREEEALAAIEALNGKEVKGRRINVEL 68
>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 = 28.9 bits (64), Expect = 0.50
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 75 ECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLN 118
E + +G I E+ C + D + G ++ + +DAEKA+N LN
Sbjct: 20 ELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 67
>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 = 28.9 bits (64), Expect = 0.54
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 10/71 (14%)
Query: 50 SHLISNVTDEEM-QEHYDNFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRRE 107
++LI N + M QE + + F + GEIE V D + +G ++ +
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSI--------GEIESCKLVRDKITGQSLGYGFVNYIDP 54
Query: 108 EDAEKAVNDLN 118
+DAEKA+N LN
Sbjct: 55 KDAEKAINTLN 65
>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 = 28.4 bits (64), Expect = 0.58
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRP 126
+ +F E A A+ +LN F GR
Sbjct: 44 FCEFEDIETAASAIRNLNGYEFNGRA 69
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the RRM
of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved in
termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs. Its
localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 28.4 bits (64), Expect = 0.61
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
ED F +KYG + + V N G +++F DAE AV L+ R G V
Sbjct: 17 EDEF----EKYGPLRSVWVARNPP----GFAFVEFEDPRDAEDAVRALDGRRICGNRVRV 68
Query: 130 ELS 132
ELS
Sbjct: 69 ELS 71
>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 = 28.4 bits (63), Expect = 0.64
Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 24/86 (27%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLG 93
NLY+ S L +T +E+ E +F +YG I + D L
Sbjct: 2 NLYV-----------SGLPKTMTQKEL--------EQLF----SQYGRIITSRILRDQLT 38
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNN 119
G +I+F + +AE+A+ LN
Sbjct: 39 GVSRGVGFIRFDKRIEAEEAIKGLNG 64
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 28.4 bits (63), Expect = 0.70
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
G YI+F DAE A+ +LN +W GR +
Sbjct: 43 GFAYIQFEDVRDAEDALYNLNRKWVCGRQI 72
>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 = 28.1 bits (63), Expect = 0.73
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
ED+F KYG I+ +++ + +++F DAE AV + F G +
Sbjct: 17 EDLF----YKYGPIKAIDLKNRRRG--PPFAFVEFEDPRDAEDAVRGRDGYDFDGYRLRV 70
Query: 130 EL 131
E
Sbjct: 71 EF 72
>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 = 28.3 bits (63), Expect = 0.85
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 66 DNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGG 124
+ E VF KYG+I E+ V D G ++ F +DA+ A+ +N + G
Sbjct: 14 EQSLEQVF----SKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDG 69
Query: 125 R 125
R
Sbjct: 70 R 70
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 29.5 bits (65), Expect = 0.87
Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 11/73 (15%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
+VT+E+++E + F V + E +++F EE AEKA+
Sbjct: 126 DVTEEDLRELFKKFGPVKRV----RLVRDRETGKSRGFA-------FVEFESEESAEKAI 174
Query: 115 NDLNNRWFGGRPV 127
+LN + GRP+
Sbjct: 175 EELNGKELEGRPL 187
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 of MRD1. RBM19, also termed RNA-binding
domain-1 (RBD-1), is a nucleolar protein conserved in
eukaryotes involved in ribosome biogenesis by processing
rRNA and is essential for preimplantation development.
It has a unique domain organization containing 6
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). MRD1 is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well conserved in
yeast and its homologues exist in all eukaryotes. MRD1
is present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 28.0 bits (63), Expect = 0.88
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 102 IKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
++F DA KA L + F P+Y E +P
Sbjct: 41 VEFLEPSDARKAFKSLAYKRFKHVPLYLEWAP 72
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich
splicing factor 10 (SRSF10) and similar proteins. This
subgroup corresponds to the RRM of SRSF10, also termed
40 kDa SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). SRSF10 is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 28.0 bits (62), Expect = 0.92
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
G Y++F DAE A+++L+ +W GR +
Sbjct: 43 GFAYVQFEDVRDAEDALHNLDRKWICGRQI 72
>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 = 30.0 bits (67), Expect = 0.92
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 67 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 119
+ +ED V +K G I E+ + + G ++ F +E+A++AV LNN
Sbjct: 69 DLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNN 121
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 28.0 bits (63), Expect = 0.98
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 100 VYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
++ FR EE+ +KA+ L+ + GR + A L+
Sbjct: 45 AFVTFRSEEERQKALEILDGFKWKGRVLSARLA 77
>gnl|CDD|240851 cd12405, RRM3_NCL, RNA recognition motif 3 in vertebrate nucleolin.
This subfamily corresponds to the RRM3 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 72
Score = 27.6 bits (61), Expect = 1.1
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 131
G +++F EDA++A+N NN GR + E
Sbjct: 39 GYAFVEFESAEDAKEALNSCNNTEIEGRSIRLEF 72
>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 = 28.1 bits (62), Expect = 1.1
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTD 136
++ F EDA A+N LN + G P+ L+ D
Sbjct: 48 FVHFSNREDAVDAMNALNGKVIDGSPIEVTLAKPVD 83
>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM2
of nucleolysin TIAR, also termed TIA-1-related protein,
a cytotoxic granule-associated RNA-binding protein that
shows high sequence similarity with 40-kDa isoform of
T-cell-restricted intracellular antigen-1 (p40-TIA-1).
TIAR is mainly localized in the nucleus of hematopoietic
and nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. TIAR possesses nucleolytic
activity against cytolytic lymphocyte (CTL) target
cells. It can trigger DNA fragmentation in permeabilized
thymocytes, and thus may function as an effector
responsible for inducing apoptosis. TIAR is composed of
three N-terminal, highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. It interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 27.7 bits (61), Expect = 1.1
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
G ++ F + DAE A+ + +W GGR +
Sbjct: 44 GYGFVSFYNKLDAENAIVHMGGQWLGGRQI 73
>gnl|CDD|217006 pfam02382, RTX, RTX N-terminal domain. The RTX family of bacterial
toxins are a group of cytolysins and cytotoxins. This
Pfam family represents the N-terminal domain which is
found in association with a glycine-rich repeat domain
and hemolysinCabind pfam00353.
Length = 653
Score = 29.4 bits (66), Expect = 1.2
Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 10/78 (12%)
Query: 52 LISNVTD---EEMQEHYDNFFEDVFVECEDKYGEIEEMNVCD-----NLGDHLVGNVYIK 103
LIS + + + M EH N D VE E K+G+ N D L D+ +
Sbjct: 402 LISGILEASKQAMFEHVANKIADKIVEWEKKHGKNYFENGYDARHLAFLEDNF--KLLSN 459
Query: 104 FRREEDAEKAVNDLNNRW 121
+E E+ V RW
Sbjct: 460 LNKEYQVERVVAITQQRW 477
>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 = 27.7 bits (61), Expect = 1.3
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 10/71 (14%)
Query: 50 SHLISNVTDEEM-QEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRRE 107
++LI N + M Q+ + F + GE+E + D + H +G ++ +
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSI--------GEVESAKLIRDKVAGHSLGYGFVNYVNA 53
Query: 108 EDAEKAVNDLN 118
+DAE+A+N LN
Sbjct: 54 KDAERAINTLN 64
>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 26.9 bits (60), Expect = 1.6
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 79 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
YG I E+N+ + G +++F DA+ AV +LN + G V E +
Sbjct: 22 GYGRIREINLKNGFG-------FVEFEDPRDADDAVYELNGKELCGERVIVEHA 68
>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 = 27.3 bits (61), Expect = 1.7
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 79 KYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
KYG I ++ + D G Y++F DAE A+ L+ F GR +
Sbjct: 23 KYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREI 72
>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 = 27.0 bits (60), Expect = 1.7
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
Y++F +E A+ A++ L GRPV
Sbjct: 44 YVEFSSQEAAQAALDALGGTDLLGRPV 70
>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 = 27.1 bits (61), Expect = 1.7
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
Y++F E A AV LN + G + ++S
Sbjct: 45 YVQFTSPESAAAAVALLNGKLGEGYKLVVKIS 76
>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 = 27.2 bits (61), Expect = 1.7
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFG 123
++ F+ EEDA++AV N +
Sbjct: 45 FVGFKSEEDAQQAVKYFNKTFID 67
>gnl|CDD|220003 pfam08752, Gamma-COP, Coatomer gamma subunit appendage domain.
COPI-coated vesicles function in retrograde transport
from the Golgi to the ER, and in intra-Golgi transport.
This domain corresponds to the coatomer gamma subunit
appendage domain. It contains a protein-protein
interaction site and a second proposed binding site that
interacts with the alpha, beta,epsilon COPI subcomplex.
Length = 269
Score = 28.8 bits (65), Expect = 1.7
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 69 FEDVFVECEDKYGEIEEMNV--CDNLGDHLVGNVYIKFRREEDAE 111
E+V VE E E EE+ + D L + G+VY+ + E +
Sbjct: 65 LENVSVELEPSEEEYEELFIIPIDKLPYNQPGSVYVLLEKPEGED 109
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 77
Score = 27.2 bits (61), Expect = 1.8
Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 11/76 (14%)
Query: 52 LISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAE 111
L +++T+ E++EH+ GEI ++ + +I ++ EE+A+
Sbjct: 8 LPASLTEAELKEHFSK-----------HGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQ 56
Query: 112 KAVNDLNNRWFGGRPV 127
KA + NN + +
Sbjct: 57 KAKDYFNNTYINTSKI 72
>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 = 26.9 bits (60), Expect = 1.9
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 79 KYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 120
G IE V D + +G ++ + E DA+KA+N LN
Sbjct: 23 AIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGF 65
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 26.8 bits (60), Expect = 2.0
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 11/58 (18%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
E++F KYG+I +++ G +++F EEDA AV N R G+ +
Sbjct: 19 EEIF----SKYGKILGISLHKGYG-------FVQFDNEEDARAAVAGENGREIAGQKL 65
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 26.9 bits (59), Expect = 2.1
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 67 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 119
+ +ED V + G I EM + + G ++ + ++ +A++AV +LNN
Sbjct: 12 DVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELNN 64
>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 = 26.8 bits (60), Expect = 2.3
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 11/73 (15%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
N+T+++++ ++ F E FV+ + E G +I+F EDA+KA+
Sbjct: 9 NITEDDLRGIFEPFGEIEFVQLQRD----PETGRSKGYG-------FIQFADAEDAKKAL 57
Query: 115 NDLNNRWFGGRPV 127
LN GRP+
Sbjct: 58 EQLNGFELAGRPI 70
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and
similar proteins. This subfamily corresponds to the
RRM2 of polypyrimidine tract-binding protein 1 (PTB or
hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2
or nPTB), regulator of differentiation 1 (Rod1),
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), polypyrimidine tract-binding protein homolog
3 (PTBPH3), polypyrimidine tract-binding protein homolog
1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and
RRM3 of PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. Rod1 is a mammalian polypyrimidine tract
binding protein (PTB) homolog of a regulator of
differentiation in the fission yeast Schizosaccharomyces
pombe, where the nrd1 gene encodes an RNA binding
protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity to
other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Although
their biological roles remain unclear, both PTBPH1 and
PTBPH2 show significant sequence similarity to PTB.
However, in contrast to PTB, they have three RRMs. .
Length = 85
Score = 26.7 bits (60), Expect = 2.4
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 78 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 120
YG +E++ + + ++F E AE A LN R
Sbjct: 23 SPYGAVEKI-LIFEKNTGV--QALVQFDSVESAENAKKALNGR 62
>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 = 26.4 bits (59), Expect = 2.6
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 78 DKYGEIEEMNV-CDNLGDHLVGNVYIKFRREEDAEKAVNDLN 118
++GEIEE V D G ++ F+ +E AE+A D N
Sbjct: 22 SQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPN 63
>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 = 26.5 bits (58), Expect = 2.9
Identities = 13/50 (26%), Positives = 25/50 (50%)
Query: 78 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
+K GE+ + + + G ++F+ EE +KA+ +N GRP+
Sbjct: 22 EKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVMNKYDLNGRPL 71
>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 = 26.4 bits (59), Expect = 3.0
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVY 128
++ F EE A +A+ +N + V+
Sbjct: 47 FVHFETEEAAVRAIEKVNGMLLNDKKVF 74
>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 = 26.3 bits (59), Expect = 3.3
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 80 YGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV---YA 129
+G + ++ L + G ++ F+ E A A+ L F +P+ YA
Sbjct: 27 FGPVLDIVASKTLK--MRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQYA 77
>gnl|CDD|240888 cd12442, RRM_RBM48, RNA recognition motif in RNA-binding protein 48
(RBM48) and similar proteins. This subfamily
corresponds to the RRM of RBM48, a putative RNA-binding
protein of unknown function. It contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 100
Score = 26.9 bits (60), Expect = 3.3
Identities = 25/65 (38%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 80 YGEIEEMNVCDNLGDHLVGNVY-IKFRREEDAEKAVNDLNNR-WFGGR--PVYA-ELSPV 134
YG IEE + D VY IKF + A A L+ R +FGG YA E V
Sbjct: 34 YGTIEEYRLLDEYPCEEFTEVYLIKFETIQSARFAKRKLDERSFFGGLLHVCYAPEYETV 93
Query: 135 TDFRE 139
D RE
Sbjct: 94 QDTRE 98
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 26.3 bits (58), Expect = 3.5
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 9/55 (16%)
Query: 78 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFG--GRPVYAE 130
KYG ++ + D G ++ E DAE A+ L+N FG R + E
Sbjct: 22 GKYGRVDRV-------DMKSGFAFVYMEDERDAEDAIRGLDNFEFGRQRRRLRVE 69
>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 = 26.1 bits (58), Expect = 3.5
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGR 125
G +I F EDA K V LNN+ GR
Sbjct: 44 GVAFILFLDREDAHKCVKALNNKELFGR 71
>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 = 26.1 bits (58), Expect = 3.7
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 75 ECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGR 125
+KYGE+ ++ + D G +++F + DAE A++ ++ + GR
Sbjct: 17 RVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGR 68
>gnl|CDD|240876 cd12430, RRM_LARP4_5_like, RNA recognition motif in La-related
protein 4 (LARP4), La-related protein 5 (LARP5 or
LARP4B) and similar proteins. This subfamily
corresponds to the RRM of LARP4 and LARP5. LARP4 is a
cytoplasmic factor that can bind poly(A) RNA and
interact with poly(A) binding protein (PABP). It may
play a role in promoting translation by stabilizing
mRNA. LARP5 is a cytosolic protein that co-sediments
with polysomes and accumulates upon stress induction in
cellular stress granules. It can interact with the
cytosolic poly(A) binding protein 1 (PABPC1) and the
receptor for activated C Kinase (RACK1), a component of
the 40S ribosomal subunit. LARP5 may function as a
stimulatory factor of translation through bridging mRNA
factors of the 3' end with initiating ribosomes. Both,
LARP4 and LARP5, are structurally related to the La
autoantigen. Like other La-related proteins (LARPs)
family members, LARP4 and LARP5 contain a La motif (LAM)
and an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 76
Score = 26.1 bits (58), Expect = 3.7
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 101 YIKFRREEDAEKAVNDLNNRW--FGGRPVYA 129
++ F EEDA++A L F G+P+ A
Sbjct: 41 FVTFETEEDAQEAYRYLREEVKTFQGKPIMA 71
>gnl|CDD|241193 cd12749, RRM4_RBM12, RNA recognition motif 4 in RNA-binding protein
12 (RBM12) and similar proteins. This subgroup
corresponds to the RRM4 of RBM12, also termed SH3/WW
domain anchor protein in the nucleus (SWAN), which 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. The biological role of RBM12 remains unclear. .
Length = 88
Score = 26.3 bits (58), Expect = 3.7
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 90 DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 139
DN G L G ++F+ E+DA K+ L+ + GR V+ L + R+
Sbjct: 35 DNNGQGL-GQALVQFKSEDDARKS-ERLHRKKLNGRDVFLHLVTAEEMRD 82
>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 = 26.0 bits (58), Expect = 3.9
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
++ F +DA KA+ ++N + G P+
Sbjct: 39 FVHFEERDDAVKAMEEMNGKELEGSPI 65
>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 = 26.4 bits (59), Expect = 4.0
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 14/90 (15%)
Query: 44 AKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNV--Y 101
+S +G + EE QE D F E +GEI+ +++ NL D G V Y
Sbjct: 1 QRSVEGWIIFVTGVHEEAQEED---VHDKFAE----FGEIKNLHL--NL-DRRTGFVKGY 50
Query: 102 --IKFRREEDAEKAVNDLNNRWFGGRPVYA 129
I++ +++A+ A+ LN + G+ +
Sbjct: 51 ALIEYETKKEAQAAIEGLNGKELLGQTISV 80
>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 = 26.0 bits (58), Expect = 4.0
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+++F EEDA+ A+ +N G+P+
Sbjct: 44 FVEFLSEEDADYAIKIMNMIKLYGKPI 70
>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 = 25.9 bits (57), Expect = 4.6
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 98 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
G + F +A AV +LN R G R V
Sbjct: 43 GEATVAFDTHREAMAAVRELNGRPIGTRKV 72
>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM1 of FCA, a gene controlling
flowering time in Arabidopsis, encoding a flowering time
control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNP (ribonucleoprotein domains), and
a WW protein interaction domain. .
Length = 80
Score = 26.1 bits (57), Expect = 4.6
Identities = 10/44 (22%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 78 DKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 120
+++G + E+ + D H G ++K+ ++A++A+ L+N+
Sbjct: 21 EEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRALHNQ 64
>gnl|CDD|221931 pfam13136, DUF3984, Protein of unknown function (DUF3984). This
family of proteins is functionally uncharacterized. This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 393 and 442 amino
acids in length.
Length = 301
Score = 27.4 bits (61), Expect = 4.7
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 166 RELRRYLYSRRKRSSRRSRSRS 187
RE R +R+SRR RS
Sbjct: 167 REAAREREHSSRRASRRGRSGY 188
>gnl|CDD|193577 cd09888, NGN_Euk, Eukaryotic N-Utilization Substance G (NusG)
N-terminal (NGN) domain, including plant KTF1 (KOW
domain-containing Transcription Factor 1). The
N-Utilization Substance G (NusG) protein and its
eukaryotic homolog, Spt5, are involved in transcription
elongation and termination. NusG contains an NGN domain
at its N-terminus and Kyrpides Ouzounis and Woese (KOW)
repeats at its C-terminus. Spt5 forms an Spt4-Spt5
complex that is an essential RNA polymerase II
elongation factor. NusG was originally discovered as an
N-dependent antitermination enhancing activity in
Escherichia coli, and has a variety of functions such as
its involvement in RNA polymerase elongation and
Rho-termination in bacteria. Orthologs of the NusG gene
exist in all bacteria, but their functions and
requirements are different. Spt5-like is homologous to
the Spt5 proteins present in all eukaryotes, which is
unique as it encodes a protein with an additional long
carboxy-terminal extension that contains WG/GW motifs.
Spt5-like, or KTF1 (KOW domain-containing Transcription
Factor 1), is a RNA-directed DNA methylation (RdDM)
pathway effector in plants.
Length = 86
Score = 26.0 bits (58), Expect = 4.9
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 94 DHLVGNVYIKFRREEDAEKAVNDLNN 119
D L G +YI+ R+E + A+ L
Sbjct: 42 DGLKGYIYIEARKEAHVKDAIEGLRG 67
>gnl|CDD|177566 PHA03242, PHA03242, envelope glycoprotein M; Provisional.
Length = 428
Score = 27.5 bits (61), Expect = 4.9
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 166 RELRRYLYSRRKRSS-----RRSRSRSR 188
R +R YLY RR RS R +R R+R
Sbjct: 343 RLVRAYLYHRRHRSRFYGHVRDARHRAR 370
>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509). This
family consists of several uncharacterized viral
proteins from the Marek's disease-like viruses. Members
of this family are typically around 400 residues in
length. The function of this family is unknown.
Length = 377
Score = 27.3 bits (60), Expect = 5.2
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 174 SRRKRSSRRSRSRSR 188
RR RS RSRSRSR
Sbjct: 328 RRRNRSESRSRSRSR 342
>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 = 25.8 bits (56), Expect = 5.3
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 67 NFFEDVFVECEDKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLN 118
N ++ F GEIE V D + +G ++ + DA+KA+N LN
Sbjct: 14 NMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLN 66
>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 = 26.0 bits (57), Expect = 5.5
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGR 125
++ F EDA++A+ L N+ GR
Sbjct: 45 FVTFAMLEDAQEALAKLKNKKLHGR 69
>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 = 25.8 bits (57), Expect = 5.8
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
Y+ F EDA+KA+ ++ + GRP+ + S
Sbjct: 45 YVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76
>gnl|CDD|240992 cd12548, RRM_Set1A, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1A (Set1A). This
subgroup corresponds to the RRM of Setd1A, also termed
SET domain-containing protein 1A (Set1A), or lysine
N-methyltransferase 2F, or Set1/Ash2 histone
methyltransferase complex subunit Set1, a ubiquitously
expressed vertebrates histone methyltransferase that
exhibits high homology to yeast Set1. Set1A is localized
to euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1A contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), an N- SET
domain, and a C-terminal catalytic SET domain followed
by a post-SET domain. In contrast to Set1B, Set1A
additionally contains an HCF-1 binding motif that
interacts with HCF-1 in vivo. .
Length = 95
Score = 26.1 bits (57), Expect = 6.3
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 66 DNFFEDVFVECEDKYGEIEEMNVC--DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFG 123
DN E + K+GE+EE+ + HL G + F A+ V L+N
Sbjct: 12 DNVREPFLADMCRKFGEVEEVEILLHPKTRKHL-GLARVLFTSTRGAKDTVKHLHNTSVM 70
Query: 124 GRPVYAEL 131
G ++A+L
Sbjct: 71 GNIIHAQL 78
>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 = 25.6 bits (57), Expect = 6.4
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 67 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWF-GGR 125
+ FED V +K G I E+ + + G ++ + +E A++AV L+N G+
Sbjct: 12 DLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGK 71
Query: 126 PVYAELS 132
+ +S
Sbjct: 72 RLGVCIS 78
>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 = 25.3 bits (56), Expect = 6.5
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 78 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
++GE++++ +++F AE A++ LN R F G +
Sbjct: 23 SQFGEVKDIRETPLRPSQ----KFVEFYDIRAAEAALDALNGRPFLGGRL 68
>gnl|CDD|234925 PRK01233, glyS, glycyl-tRNA synthetase subunit beta; Validated.
Length = 682
Score = 27.0 bits (61), Expect = 7.0
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 66 DNFFEDVFVECEDK 79
D FF++V V ED+
Sbjct: 641 DAFFDNVMVMAEDE 654
>gnl|CDD|107384 cd06389, PBP1_iGluR_AMPA_GluR2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR2 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR2 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 370
Score = 26.9 bits (59), Expect = 7.5
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 11/59 (18%)
Query: 53 ISNVTDEEMQEHYDNFFED--------VFVECE-DKYGEIEEMNVCDNLGDHLVGNVYI 102
+ N+ ++ E Y + F+D V ++CE DK +I + + +G H+ G YI
Sbjct: 153 VGNINNDRKDEAYRSLFQDLENKKERRVILDCERDKVNDIVDQVI--TIGKHVKGYHYI 209
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding
protein RBP1, is a putative glucose-repressible protein
that binds both, RNA and single-stranded DNA (ssDNA), in
yeast. It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the carboxyl terminus which
also harbors a methionine-rich region. The family also
includes protein NAM8, which is a putative RNA-binding
protein that acts as a suppressor of mitochondrial
splicing deficiencies when overexpressed in yeast. It
may be a non-essential component of the mitochondrial
splicing machinery. Like NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 25.6 bits (56), Expect = 7.7
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 101 YIKFRREEDAEKAVNDLNNRWFGGRPV 127
+++F E D ++A+ ++ + GGRP+
Sbjct: 48 FVRFSDENDQQRALIEMQGVYCGGRPM 74
>gnl|CDD|225131 COG2221, DsrA, Dissimilatory sulfite reductase (desulfoviridin),
alpha and beta subunits [Energy production and
conversion].
Length = 317
Score = 26.5 bits (59), Expect = 7.9
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 87 NVCDNLGDHLV-----GNVYIKFRREEDAEKAVNDLNN 119
++ + GD L+ + I EDA+ V +L
Sbjct: 52 DIAEKYGDGLIHITSRQGLEIPGISPEDADDVVEELRE 89
>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 = 25.2 bits (56), Expect = 8.0
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 101 YIKFRREEDAEKAVNDLN 118
++ F EDAE+A+ LN
Sbjct: 45 FVTFHTREDAERAIEKLN 62
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 and RRM4 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
and is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 82
Score = 25.2 bits (55), Expect = 8.7
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 53 ISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEK 112
I NV+D + + +++ ECE KYGEIE + + +I F +A
Sbjct: 7 IGNVSDVGDERNLPE--KELRKECE-KYGEIESIRILRE-----KACAFINFMNIPNAIA 58
Query: 113 AVNDLNNR 120
A+ LN +
Sbjct: 59 ALQTLNGK 66
>gnl|CDD|220150 pfam09239, Topo-VIb_trans, Topoisomerase VI B subunit, transducer.
Members of this family adopt a structure consisting of a
four-stranded beta-sheet backed by three alpha-helices,
the last of which is over 50 amino acids long and
extends from the body of the protein by several turns.
This domain has been proposed to mediate intersubunit
communication by structurally transducing signals from
the ATP binding and hydrolysis domains to the DNA
binding and cleavage domains of the gyrase holoenzyme.
Length = 160
Score = 26.0 bits (58), Expect = 8.8
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 161 LKPISRELRRYLYSRRKRSSRRSR 184
L+ +R+L+RYL +RK RR +
Sbjct: 137 LQEAARKLKRYLSRKRKAKERRKK 160
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 25.2 bits (55), Expect = 9.1
Identities = 13/53 (24%), Positives = 26/53 (49%)
Query: 67 NFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 119
+ +ED V ++ G+I E + G ++ + +E+A+ A+ LNN
Sbjct: 12 DMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILNN 64
>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 = 25.2 bits (55), Expect = 9.1
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 15/73 (20%)
Query: 55 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 114
N+T +E++E FED ++ + G YI+F+ E +AEKA+
Sbjct: 14 NITVDELKE----VFEDAV-----------DIRLPSGKDGSSKGIAYIEFKTEAEAEKAL 58
Query: 115 NDLNNRWFGGRPV 127
+ GR +
Sbjct: 59 EEKQGAEVDGRSI 71
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
0.322 0.137 0.426
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: 9,648,109
Number of extensions: 881677
Number of successful extensions: 1395
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1353
Number of HSP's successfully gapped: 180
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.4 bits)