RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13533
(207 letters)
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 171 bits (434), Expect = 9e-56
Identities = 66/76 (86%), Positives = 74/76 (97%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
S+YVGNVDYGATAEELE+HFHGCGSVNRVTILC+KF GHPKGFAYIEF+DK+SV+TA+A+
Sbjct: 1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALAL 60
Query: 153 DESLFRGRQIKVNPKR 168
DESLFRGRQIKV PKR
Sbjct: 61 DESLFRGRQIKVMPKR 76
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 147 bits (372), Expect = 2e-46
Identities = 59/77 (76%), Positives = 69/77 (89%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
S+YVGNVDYG+TAEELE+HF GCG +NRVTILC+KF GHPKG+AYIEFA +DSV+ A+A+
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL 60
Query: 153 DESLFRGRQIKVNPKRT 169
DES FRGR IKV PKRT
Sbjct: 61 DESSFRGRVIKVLPKRT 77
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and
similar proteins. PABPs are 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. ePABP-2 is
predominantly located in the cytoplasm and PABP-2 is
located in the nucleus. In contrast to the type I PABPs
containing four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), the type II PABPs contains
a single highly-conserved RRM. This subfamily also
includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C)
gene encoding cytoplasmic mRNA-binding protein Rbp29
that binds preferentially to poly(A). Although not
essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 147 bits (372), Expect = 3e-46
Identities = 50/72 (69%), Positives = 60/72 (83%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
SI+VGNVDYG T EEL+ HF CG++NR+TILC+KF G PKGFAYIEF DK SV+ A+ +
Sbjct: 1 SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLL 60
Query: 153 DESLFRGRQIKV 164
+ES FRGRQIKV
Sbjct: 61 NESEFRGRQIKV 72
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM2 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 = 73
Score = 80.3 bits (199), Expect = 3e-20
Identities = 29/72 (40%), Positives = 43/72 (59%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
S++VGN+ + EEL HF CG V V I+ ++ G KGF Y+ F KDSV A+ +
Sbjct: 1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60
Query: 153 DESLFRGRQIKV 164
+ +GR+I+V
Sbjct: 61 NGIKLKGRKIRV 72
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 78.4 bits (194), Expect = 2e-19
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
+++VGN+ T EEL F G V V ++ +K G KGFA++EF ++ + A+ A
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 152 MDESLFRGRQIKV 164
++ GR +KV
Sbjct: 61 LNGKELDGRPLKV 73
>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 = 72.0 bits (177), Expect = 4e-17
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 2/73 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++VGN+ T E+L F G + V I+ +K DG KGFA++EF + + A+ A+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59
Query: 153 DESLFRGRQIKVN 165
+ GR++KV+
Sbjct: 60 NGKELDGRKLKVS 72
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 67.7 bits (166), Expect = 3e-15
Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R+IYVGN+D TA++L F G V V + + P +A++EFA++ SV A+
Sbjct: 5 RTIYVGNLDPTTTADQLLEFFSQAGEVKYVR-MAGD-ETQPTRYAFVEFAEQTSVINALK 62
Query: 152 MDESLFRGRQIKVN 165
++ ++F GR +KVN
Sbjct: 63 LNGAMFGGRPLKVN 76
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 66.2 bits (162), Expect = 9e-15
Identities = 26/78 (33%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R+I+VG +D + ++L+ F CG V RV + + H FA++EFAD +S +A+
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGD--RQHSARFAFVEFADAESALSALN 58
Query: 152 MDESLFRGRQIKVNPKRT 169
+ +L G ++V+P +T
Sbjct: 59 LSGTLLGGHPLRVSPSKT 76
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 65.8 bits (161), Expect = 1e-14
Identities = 26/71 (36%), Positives = 44/71 (61%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VGN+ Y TAE+L +HF G+ V +L +K G KG A++EF +++ A+ +
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62
Query: 154 ESLFRGRQIKV 164
+L +GR+I V
Sbjct: 63 HTLLKGRKINV 73
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 64.6 bits (158), Expect = 3e-14
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
+YVGN+ Y T E+L+ F G V ++ ++ G +GF ++E + A+ +
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61
Query: 153 DESLFRGRQIKVN 165
+ + F GR + VN
Sbjct: 62 NGTDFGGRTLTVN 74
>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 = 64.2 bits (157), Expect = 5e-14
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++VGN+ T E+L+ F G + + I G KGFA++EF D++ + A+ A+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRI-VRDETGRSKGFAFVEFEDEEDAEKALEAL 59
Query: 153 DESLFRGRQIK 163
+ GR+++
Sbjct: 60 NGKELGGRELR 70
>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 = 63.4 bits (155), Expect = 9e-14
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILC---NKFDGHPKGFAYIEFADKDSVQT 148
R IYV N+D+ ++L F G V + I K GFA++ F D S +
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60
Query: 149 AMAMDESLFRGRQIKVNP 166
A+ ++ + GR+I V+
Sbjct: 61 ALQLNGTELGGRKISVSL 78
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 72
Score = 62.3 bits (152), Expect = 2e-13
Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 1/72 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
+++V N+DY +EL F CG + V ++ + G KG+AY+EF +++SVQ A+ +
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLV-KNYKGKSKGYAYVEFENEESVQEALKL 59
Query: 153 DESLFRGRQIKV 164
D L +GR + V
Sbjct: 60 DRELIKGRPMFV 71
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 61.8 bits (151), Expect = 4e-13
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM- 152
+YV N+ T E+L F G V V ++ NK P+GFA++EFA + + A+
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDR--PRGFAFVEFASPEDAEAALKKL 58
Query: 153 DESLFRGRQIK 163
+ + GR ++
Sbjct: 59 NGLVLDGRTLR 69
>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 = 59.7 bits (145), Expect = 3e-12
Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMAM 152
++V N+ Y ++LE F G ++ V + +K G KGFAY+ F D +D+V+ +
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 153 DESLFRGRQIKVNP 166
D +F+GR I + P
Sbjct: 65 DGKVFQGRLIHILP 78
>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 = 59.2 bits (144), Expect = 3e-12
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++VGN+ Y AT E+L F G V ++ ++ G PKG+ + EF D ++ +A+ +
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 153 DESLFRGRQIKVNP 166
+ F GR ++V+
Sbjct: 61 NGYEFNGRALRVDF 74
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 77
Score = 58.9 bits (143), Expect = 4e-12
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
+++VGN+ + A ++LE F CG V V I + DG KGF ++EFA ++ Q A+
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEK 59
Query: 153 DESLFRGRQIKV 164
GR+I+V
Sbjct: 60 SGEELLGREIRV 71
>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 = 57.6 bits (140), Expect = 1e-11
Identities = 19/74 (25%), Positives = 36/74 (48%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
I+VG + Y T + L +F G + ++ ++ G +G+ ++ F DK+S + A
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 152 MDESLFRGRQIKVN 165
+ GR+ VN
Sbjct: 61 DPNPIIDGRKANVN 74
>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 = 57.3 bits (139), Expect = 2e-11
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++V N+ + T EEL F G ++ V + +K KGFA++ F + A +
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 153 DESLFRGRQIKV 164
D S+F+GR + V
Sbjct: 62 DGSIFQGRLLHV 73
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2 of
PHIP1. A. thaliana PHIP1 and its homologs represent a
novel class of plant-specific RNA-binding proteins that
may play a unique role in the polarized mRNA transport
to the vicinity of the cell plate. The family members
consist of multiple functional domains, including a
lysine-rich domain (KRD domain) that contains three
nuclear localization motifs (KKKR/NK), two RNA
recognition motifs (RRMs), and three CCHC-type zinc
fingers. PHIP1 is a peripheral membrane protein and is
localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 57.0 bits (138), Expect = 2e-11
Identities = 20/73 (27%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
++Y+GN+ + T +++ F + V + +K G KGF +++FAD++S+ A+ +
Sbjct: 1 TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59
Query: 153 DESLFRGRQIKVN 165
D ++ GR I++
Sbjct: 60 DGTVLCGRPIRIA 72
>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 = 57.0 bits (138), Expect = 2e-11
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAM 152
++V + + T EELE F G V V ++ N+ G PKG AY+E+ ++ S A + M
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKM 63
Query: 153 DESLFRGRQIKV---NP 166
D + + + I V NP
Sbjct: 64 DGTEIKEKTISVAISNP 80
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 61.1 bits (147), Expect = 3e-11
Identities = 26/120 (21%), Positives = 56/120 (46%), Gaps = 1/120 (0%)
Query: 50 EEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYGATAEELE 109
EE ++++ + + +K + + +++VGN+ Y T E+L
Sbjct: 74 EENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLR 133
Query: 110 SHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQIKVNPKR 168
F G V RV ++ ++ G +GFA++EF ++S + A+ ++ GR ++V +
Sbjct: 134 ELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193
>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 = 55.9 bits (135), Expect = 8e-11
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++VGN+ + E L++ F G+V ++ ++ G +GF Y++F + + A+ AM
Sbjct: 2 LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61
Query: 153 DESLFRGRQIKVN 165
D GR I V+
Sbjct: 62 DGKELDGRPINVD 74
>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ)
autosomal homologs, DAZL (DAZ-like) and BOULE. This
subfamily corresponds to the RRM domain of two Deleted
in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like)
and BOULE. BOULE is the founder member of the family and
DAZL arose from BOULE in an ancestor of vertebrates. The
DAZ gene subsequently originated from a duplication
transposition of the DAZL gene. Invertebrates contain a
single DAZ homolog, BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. The family members encode closely related
RNA-binding proteins that are required for fertility in
numerous organisms. These proteins contain an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a varying
number of copies of a DAZ motif, believed to mediate
protein-protein interactions. DAZL and BOULE contain a
single copy of the DAZ motif, while DAZ proteins can
contain 8-24 copies of this repeat. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 80
Score = 55.4 bits (134), Expect = 1e-10
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
I+VG + T EEL F GSV V I+ ++ G KG+ ++ F ++ + +AM
Sbjct: 5 IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMG 63
Query: 154 ESLFRGRQIKVNP 166
FRG+++ + P
Sbjct: 64 NLNFRGKKLNIGP 76
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 55.5 bits (134), Expect = 1e-10
Identities = 24/62 (38%), Positives = 33/62 (53%)
Query: 105 AEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKV 164
L HF CG + RV+I ++ G KGFAYIEF D V+ A+ +D S G + V
Sbjct: 17 RRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLVV 76
Query: 165 NP 166
+
Sbjct: 77 DE 78
>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 = 54.5 bits (132), Expect = 2e-10
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R++++ N+ + AT EEL+ F G V I+ +K GH KG A+++F K+S Q +
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60
Query: 152 ------MDESLFRGRQIKVNP 166
GR++ V
Sbjct: 61 AADNAEDSGLSLDGRRLIVTL 81
>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 = 54.3 bits (131), Expect = 3e-10
Identities = 20/73 (27%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++VGN+ + A + + F G ++ V + + G PKGF Y+EF+ +++ Q A+ A+
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 153 DESLFRGRQIKVN 165
+ GR ++++
Sbjct: 61 GGTDLLGRPVRLD 73
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 53.5 bits (129), Expect = 6e-10
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R+++VGN+D T E L F G + V I +G PK FA++ F + SV A+
Sbjct: 2 RTLFVGNLDARVTEEILYELFLQAGPLEGVKI-PKDPNGKPKSFAFVTFKHEVSVPYAIQ 60
Query: 152 MDE--SLFRGRQIKV 164
+ LF GR++++
Sbjct: 61 LLNGIRLF-GRELRI 74
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. hnRNP A1 is an abundant
eukaryotic nuclear RNA-binding protein that may modulate
splice site selection in pre-mRNA splicing. hnRNP A2/B1
is an RNA trafficking response element-binding protein
that interacts with the hnRNP A2 response element
(A2RE). hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. The hnRNP D
subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and
similar proteins. hnRNP D0 is a UUAG-specific nuclear
RNA binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus, plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this subfamily contain two putative RRMs and
a glycine- and tyrosine-rich C-terminus. The family also
contains DAZAP1 (Deleted in azoospermia-associated
protein 1), RNA-binding protein Musashi homolog
Musashi-1, Musashi-2 and similar proteins. They all
harbor two RRMs. .
Length = 72
Score = 52.6 bits (127), Expect = 1e-09
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
+++G + + T E L +F G V I+ + G +GF ++ FAD SV +A
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60
Query: 154 ESLFRGRQIKVNPK 167
+ GR+I +PK
Sbjct: 61 PHVLDGREI--DPK 72
>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation
initiation factor 4B (eIF-4B) and similar proteins.
This subfamily corresponds to the RRM of eIF-4B, a
multi-domain RNA-binding protein that has been primarily
implicated in promoting the binding of 40S ribosomal
subunits to mRNA during translation initiation. It
contains two RNA-binding domains; the N-terminal
well-conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), binds the 18S rRNA of the 40S ribosomal subunit
and the C-terminal basic domain (BD), including two
arginine-rich motifs (ARMs), binds mRNA during
initiation, and is primarily responsible for the
stimulation of the helicase activity of eIF-4A. eIF-4B
also contains a DRYG domain (a region rich in Asp, Arg,
Tyr, and Gly amino acids) in the middle, which is
responsible for both, self-association of eIF-4B and
binding to the p170 subunit of eIF3. Additional research
indicates that eIF-4B can interact with the poly(A)
binding protein (PABP) in mammalian cells, which can
stimulate both, the eIF-4B-mediated activation of the
helicase activity of eIF-4A and binding of poly(A) by
PABP. eIF-4B has also been shown to interact
specifically with the internal ribosome entry sites
(IRES) of several picornaviruses which facilitate
cap-independent translation initiation. .
Length = 77
Score = 52.4 bits (126), Expect = 1e-09
Identities = 21/71 (29%), Positives = 39/71 (54%)
Query: 95 YVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDE 154
Y+GN+ Y T E+++ F G + G +GF Y EF D+DS+ A+++++
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLND 64
Query: 155 SLFRGRQIKVN 165
+ R+I+V+
Sbjct: 65 ESLKNRRIRVD 75
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 52.2 bits (125), Expect = 2e-09
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
++VGN+ + E L F CG + V I+ + KGFAY++F D+++V+ A+ +
Sbjct: 1 CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLL 60
Query: 153 DESLF---RGRQIKV 164
+E F R+++V
Sbjct: 61 NEKKFPPMLPRELRV 75
>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 = 52.0 bits (125), Expect = 2e-09
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
S+YV NV ++L F G + V I + + P+GFAY++F D + A+
Sbjct: 2 SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYY 61
Query: 152 MDESLFRGRQIKV 164
+D + F GR+I++
Sbjct: 62 LDRTRFLGREIEI 74
>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 = 49.9 bits (120), Expect = 1e-08
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCG-SVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
+ + + + AT E++ F G + + I+ + DG P G AY+EFA + + A+
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDD-DGRPTGEAYVEFASPEDARRALRK 60
Query: 153 DESLFRGRQIKV 164
+ GR I+V
Sbjct: 61 HNNKMGGRYIEV 72
>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM1 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated form is predominantly nuclear and the
nonacetylated form is in cytoplasm. It also functions as
a translational regulator that activates translation in
an mRNA-specific manner. DAZAP1 was initially identified
as a binding partner of Deleted in Azoospermia (DAZ). It
also interacts with numerous hnRNPs, including hnRNP U,
hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D,
suggesting DAZAP1 might associate and cooperate with
hnRNP particles to regulate adenylate-uridylate-rich
elements (AU-rich element or ARE)-containing mRNAs.
DAZAP1 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
proline-rich domain. .
Length = 82
Score = 49.8 bits (119), Expect = 1e-08
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VG + + T E L +F G V I+ +K +GF +++F D + V T +A
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61
Query: 154 ESLFRGRQIKVNPKRTN 170
GR I +PK
Sbjct: 62 PHTLDGRTI--DPKPCT 76
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 49.9 bits (120), Expect = 1e-08
Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
+YVGN+ + T E++ F CG + R+ + ++F P GF ++E+ ++ + A+ +
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 153 DESLFRGRQIKV 164
+ + R I+V
Sbjct: 61 NGTKLDDRIIRV 72
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 53.0 bits (127), Expect = 2e-08
Identities = 29/100 (29%), Positives = 47/100 (47%), Gaps = 2/100 (2%)
Query: 84 EEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
+ E D R+++V + A +L F G V V + ++ KG AY+EF D
Sbjct: 82 LTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDV 141
Query: 144 DSVQTAMAMDESLFRGRQIKVNPKRT--NRPGISTTNRGG 181
+SV A+A+ + GR I V + NR + T++ G
Sbjct: 142 ESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPG 181
Score = 35.3 bits (81), Expect = 0.018
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
+YVGN+ + T +EL F G + V + + G KGF +I+F D + + A+
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALE 246
Query: 151 AMDESLFRGRQIKV 164
M+ GR IKV
Sbjct: 247 VMNGFELAGRPIKV 260
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 49.3 bits (118), Expect = 2e-08
Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R++YV ++D T E+L + F CG V + C + FA+IEF D++ + A++
Sbjct: 3 RTVYVSDIDQQVTEEQLAALFSNCGQVVDCRV-CGDPN-SVLRFAFIEFTDEEGARAALS 60
Query: 152 MDESLFRGRQIKVNPKRT 169
+ ++ ++V P +T
Sbjct: 61 LSGTMLGFYPVRVLPSKT 78
>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 = 48.8 bits (117), Expect = 3e-08
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
+++V N+ Y T E+LE F G + R ++ +K +GF Y+ FA ++ + A+
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60
Query: 152 MDESLFRGRQIKV 164
++ F GR+I V
Sbjct: 61 KKKTKFGGRKIHV 73
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 50.4 bits (120), Expect = 4e-08
Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 1/108 (0%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
+++G + +G L F G V ++ ++ G +GF ++ F D+ + A++ M
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96
Query: 153 DESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGY 200
D GR I+VNP GG G G G GG+
Sbjct: 97 DGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGDGGGGF 144
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein
7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S), an
oligopyrimidine-binding protein that binds to the highly
conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK
RNA. LARP7 is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP). It intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. It plays an essential role in the inhibition of
positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
LARP7 contains a La motif (LAM) and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the N-terminal region,
which mediates binding to the U-rich 3' terminus of 7SK
RNA. LARP7 also carries another putative RRM domain at
its C-terminus. .
Length = 80
Score = 48.1 bits (115), Expect = 6e-08
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM- 152
+YV + AT E L++ F G+V V++ K G KGFA+IEF + Q A
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61
Query: 153 -DESLFRGRQIKVNPKRT 169
+ + PK
Sbjct: 62 NNPPETATDKPGKFPKTV 79
>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein
interacting with the FHA domain of pKI-67 (NIFK) and
similar proteins. This subgroup corresponds to the RRM
of NIFK and Nop15p. NIFK, also termed MKI67 FHA
domain-interacting nucleolar phosphoprotein, or
nucleolar phosphoprotein Nopp34, is a putative
RNA-binding protein interacting with the forkhead
associated (FHA) domain of pKi-67 antigen in a
mitosis-specific and phosphorylation-dependent manner.
It is nucleolar in interphase but associates with
condensed mitotic chromosomes. This family also includes
Saccharomyces cerevisiae YNL110C gene encoding ribosome
biogenesis protein 15 (Nop15p), also termed nucleolar
protein 15. Both, NIFK and Nop15p, contain an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 47.6 bits (114), Expect = 7e-08
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ-TAMAM 152
+Y+G++ +G EL +F G+V R+ + +K G KG+A++EF + + A M
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 153 DESLFRGRQIKV 164
+ L R +K
Sbjct: 62 NNYLLFERLLKC 73
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding
protein 7 (RBM7). This subfamily corresponds to the RRM
of RBM7, a ubiquitously expressed pre-mRNA splicing
factor that enhances messenger RNA (mRNA) splicing in a
cell-specific manner or in a certain developmental
process, such as spermatogenesis. RBM7 interacts with
splicing factors SAP145 (the spliceosomal splicing
factor 3b subunit 2) and SRp20. It may play a more
specific role in meiosis entry and progression. Together
with additional testis-specific RNA-binding proteins,
RBM7 may regulate the splicing of specific pre-mRNA
species that are important in the meiotic cell cycle.
RBM7 contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. .
Length = 75
Score = 47.6 bits (113), Expect = 7e-08
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R+++VGN+D T E + F G V +V I +K DG PK FA++ F + SV AM
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMN 60
Query: 152 MDESL-FRGRQIKV 164
+ + GR + +
Sbjct: 61 LLNGIKLYGRPLNI 74
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 47.7 bits (114), Expect = 8e-08
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 95 YVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDE 154
+VGN+ + +L++ F SV V ++ +K KGF Y+EF D +S++ A+ D
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDG 63
Query: 155 SLFRGRQIKVN 165
+LF R ++V+
Sbjct: 64 ALFDDRSLRVD 74
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 47.4 bits (113), Expect = 1e-07
Identities = 17/73 (23%), Positives = 34/73 (46%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
I+VG + T EE + +F G V ++ + G +GF ++ F + +V+ +
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61
Query: 154 ESLFRGRQIKVNP 166
G+Q++V
Sbjct: 62 MLELGGKQVEVKR 74
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to the
RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein and
is localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 47.0 bits (112), Expect = 1e-07
Identities = 22/71 (30%), Positives = 41/71 (57%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
+YVG + Y +T +E+ S+F CG + + ++ G +G A+I F +++ + A+A+D
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60
Query: 154 ESLFRGRQIKV 164
GR +KV
Sbjct: 61 GEDMGGRFLKV 71
>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear
ribonucleoprotein 70 kDa (U1-70K) and similar proteins.
This subfamily corresponds to the RRM of U1-70K, also
termed snRNP70, a key component of the U1 snRNP complex,
which is one of the key factors facilitating the
splicing of pre-mRNA via interaction at the 5' splice
site, and is involved in regulation of polyadenylation
of some viral and cellular genes, enhancing or
inhibiting efficient poly(A) site usage. U1-70K plays an
essential role in targeting the U1 snRNP to the 5'
splice site through protein-protein interactions with
regulatory RNA-binding splicing factors, such as the RS
protein ASF/SF2. Moreover, U1-70K protein can
specifically bind to stem-loop I of the U1 small nuclear
RNA (U1 snRNA) contained in the U1 snRNP complex. It
also mediates the binding of U1C, another U1-specific
protein, to the U1 snRNP complex. U1-70K contains a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by an adjacent glycine-rich region at the
N-terminal half, and two serine/arginine-rich (SR)
domains at the C-terminal half. The RRM is responsible
for the binding of stem-loop I of U1 snRNA molecule.
Additionally, the most prominent immunodominant region
that can be recognized by auto-antibodies from
autoimmune patients may be located within the RRM. The
SR domains are involved in protein-protein interaction
with SR proteins that mediate 5' splice site
recognition. For instance, the first SR domain is
necessary and sufficient for ASF/SF2 Binding. The family
also includes Drosophila U1-70K that is an essential
splicing factor required for viability in flies, but its
SR domain is dispensable. The yeast U1-70k doesn't
contain easily recognizable SR domains and shows low
sequence similarity in the RRM region with other U1-70k
proteins and therefore not included in this family. The
RRM domain is dispensable for yeast U1-70K function.
Length = 91
Score = 47.2 bits (113), Expect = 1e-07
Identities = 21/78 (26%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
++++V ++Y T +L F G + R+ ++ +K G P+G+A+IEF + ++ A
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61
Query: 151 AMDESLFRGRQIKVNPKR 168
D GR++ V+ +R
Sbjct: 62 YADGKKIDGRRVLVDVER 79
>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 = 46.9 bits (112), Expect = 1e-07
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
+YVGN+ + T ++L F G + V + + G KG+ +I+FAD + + A+ +
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60
Query: 153 DESLFRGRQIKVN 165
+ GR IKV
Sbjct: 61 NGFELAGRPIKVG 73
>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage
stimulation factor subunit 2 (CSTF2), cleavage
stimulation factor subunit 2 tau variant (CSTF2T) and
similar proteins. This subgroup corresponds to the RRM
domain of CSTF2, its tau variant and eukaryotic
homologs. CSTF2, also termed cleavage stimulation factor
64 kDa subunit (CstF64), is the vertebrate conterpart of
yeast mRNA 3'-end-processing protein RNA15. It is
expressed in all somatic tissues and is one of three
cleavage stimulatory factor (CstF) subunits required for
polyadenylation. CstF64 contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
CstF77-binding domain, a repeated MEARA helical region
and a conserved C-terminal domain reported to bind the
transcription factor PC-4. During polyadenylation, CstF
interacts with the pre-mRNA through the RRM of CstF64 at
U- or GU-rich sequences within 10 to 30 nucleotides
downstream of the cleavage site. CSTF2T, also termed
tauCstF64, is a paralog of the X-linked cleavage
stimulation factor CstF64 protein that supports
polyadenylation in most somatic cells. It is expressed
during meiosis and subsequent haploid differentiation in
a more limited set of tissues and cell types, largely in
meiotic and postmeiotic male germ cells, and to a lesser
extent in brain. The loss of CSTF2T will cause male
infertility, as it is necessary for spermatogenesis and
fertilization. Moreover, CSTF2T is required for
expression of genes involved in morphological
differentiation of spermatids, as well as for genes
having products that function during interaction of
motile spermatozoa with eggs. It promotes germ
cell-specific patterns of polyadenylation by using its
RRM to bind to different sequence elements downstream of
polyadenylation sites than does CstF64. .
Length = 75
Score = 46.7 bits (111), Expect = 1e-07
Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
++VGN+ Y AT E+L+ F G V ++ ++ G PKG+ + E+ D+++ +AM +
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 153 DESLFRGRQIKVN 165
+ GRQ++V+
Sbjct: 61 NGYELNGRQLRVD 73
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 46.4 bits (111), Expect = 2e-07
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
+YVG + + L + F G + + I + +GFA++EF + + A+ M
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 153 DESLFRGRQIKVN 165
+ES GR I+VN
Sbjct: 61 NESELFGRTIRVN 73
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 46.4 bits (111), Expect = 2e-07
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPK-----GFAYIEFADKDSV 146
+++V N+++ T E L+ HF CG V VTI K P G+ ++EF K++
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60
Query: 147 QTAM 150
Q A+
Sbjct: 61 QKAL 64
>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 = 46.2 bits (110), Expect = 3e-07
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
++YV N+ + T +L F G V +VTI+ +K KG A+I F D++ + A
Sbjct: 3 TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62
Query: 152 MDESLFRGRQIKV 164
++ GR +K
Sbjct: 63 LNNKELFGRTLKC 75
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 45.9 bits (109), Expect = 3e-07
Identities = 18/57 (31%), Positives = 34/57 (59%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++VGN+ + T +EL +HF G + RV ++ + G KGFA+++F + + A+
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57
>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 = 46.1 bits (110), Expect = 3e-07
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
+YVGN+ AT ELE F G + V + N P GFA++EF D + A+ A+
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRAL 56
Query: 153 DESLFRGRQIKV 164
D G +++V
Sbjct: 57 DGRRICGNRVRV 68
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 45.7 bits (109), Expect = 4e-07
Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
+ V NV + AT +EL F G V V L KFDG +GFA++EF K Q AM A+
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61
Query: 153 DESLFRGRQIKVNP 166
+ GR + +
Sbjct: 62 KSTHLYGRHLVLEY 75
>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM3 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. hnRNP M functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 72
Score = 44.9 bits (107), Expect = 7e-07
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
I+V N+ + T ++L+ F CG+V R + + DG KGF + F + Q A+
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRAIEMF 59
Query: 153 DESLFRGRQIKV 164
+ GR+++V
Sbjct: 60 NGYDLEGRELEV 71
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of RBM23
remains unclear, it shows high sequence homology to
RBM39 and contains two RRMs. It may possibly function as
a pre-mRNA splicing factor. .
Length = 73
Score = 44.9 bits (107), Expect = 7e-07
Identities = 20/72 (27%), Positives = 34/72 (47%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
+++V + +L F G V V I+ ++ KG AY+EF D++SV A+ +
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60
Query: 153 DESLFRGRQIKV 164
G+ I V
Sbjct: 61 TGQRLLGQPIMV 72
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 45.0 bits (106), Expect = 8e-07
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R+++VGN++ E L F G + +VTI C +G PK F ++ F +SV A+A
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTI-CKDKEGKPKSFGFVCFKHSESVPYAIA 60
Query: 152 MDESL-FRGRQIKVN 165
+ + GR IKV+
Sbjct: 61 LLNGIRLYGRPIKVH 75
>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 = 44.5 bits (106), Expect = 1e-06
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
++YVGN+ +G T EEL+ F G++ V + KG+A++ F ++ TA+ A
Sbjct: 2 TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVF------KDKGYAFVRFDTHEAAATAIVA 55
Query: 152 MDESLFRGRQIKV 164
++ + G+ +K
Sbjct: 56 VNGTSINGQTVKC 68
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 44.3 bits (105), Expect = 1e-06
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
++Y G +++ F CG V +VT+L H A+I F + ++ Q A+
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPH----AFITFENLEAAQLAIET 56
Query: 152 MDESLFRGRQIKV 164
++ + G IKV
Sbjct: 57 LNGASVDGNCIKV 69
>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 = 43.7 bits (104), Expect = 1e-06
Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 6/57 (10%)
Query: 111 HFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQIKVNP 166
F G+V ++ +L K GFA++EF+ +++ + A+ ++ LF GR ++V+
Sbjct: 4 LFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 43.9 bits (104), Expect = 2e-06
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
RS++V G + E+L +F G V V + +K G +A +EF K+ V +
Sbjct: 2 ERSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIM--DKDKGV---YAIVEFDSKEGVDKVL 56
Query: 151 AMDESLFRGRQIKVNPK 167
+ + G +++V P+
Sbjct: 57 SEPQHTLNGHRLRVRPR 73
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3' processing
machinery that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. Structurally related CFIm68 and
CFIm59, also termed cleavage and polyadenylation
specificity factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59), are functionally redundant. Both contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a central proline-rich region, and a C-terminal RS-like
domain. Their N-terminal RRM mediates the interaction
with CFIm25, and also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 76
Score = 43.8 bits (104), Expect = 2e-06
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 94 IYVGNVDYGATAEELESHFHGCG--SVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
+YVGN+ + T E+LE G V + +K +G KGFAY+EFA + +
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60
Query: 151 AMDESLFRGRQIKVNP 166
++ F G++ V
Sbjct: 61 KLEGREFNGKKCVVTY 76
>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 = 43.8 bits (104), Expect = 2e-06
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 96 VGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDE 154
V N+ Y T ++L F G V V I +++ +GFA++ F DK + AM AMD
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 155 SLFRGRQIKV 164
GR+++V
Sbjct: 63 KELDGRELRV 72
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the RRM
of SLIRP, a widely expressed small steroid receptor RNA
activator (SRA) binding protein, which binds to STR7, a
functional substructure of SRA. SLIRP is localized
predominantly to the mitochondria and plays a key role
in modulating several nuclear receptor (NR) pathways. It
functions as a co-repressor to repress SRA-mediated
nuclear receptor coactivation. It modulates SHARP- and
SKIP-mediated co-regulation of NR activity. SLIRP
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is required for SLIRP's corepression activities. .
Length = 73
Score = 43.4 bits (103), Expect = 2e-06
Identities = 17/71 (23%), Positives = 40/71 (56%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VGN+ + ++EL+ +F G V + +K G KG+ ++ F+ +D ++ A+
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61
Query: 154 ESLFRGRQIKV 164
+ + G +++V
Sbjct: 62 KHILEGNKLQV 72
>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 = 43.3 bits (103), Expect = 3e-06
Identities = 16/59 (27%), Positives = 31/59 (52%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
+I V N+ A ++L F G ++RV + +K G +GFA++ F ++ + A+
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59
>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 = 43.3 bits (102), Expect = 4e-06
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
+++G + + + LE F G ++ V ++ ++ +GF ++ F + D + AM AM
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 153 DESLFRGRQIKVN 165
+ GRQI+V+
Sbjct: 63 NGKSVDGRQIRVD 75
>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras
GTPase-activating protein-binding protein G3BP1, G3BP2
and similar proteins. This subfamily corresponds to the
RRM domain in the G3BP family of RNA-binding and SH3
domain-binding proteins. G3BP acts at the level of RNA
metabolism in response to cell signaling, possibly as
RNA transcript stabilizing factors or an RNase. Members
include G3BP1, G3BP2 and similar proteins. These
proteins associate directly with the SH3 domain of
GTPase-activating protein (GAP), which functions as an
inhibitor of Ras. They all contain an N-terminal nuclear
transfer factor 2 (NTF2)-like domain, an acidic domain,
a domain containing PXXP motif(s), an RNA recognition
motif (RRM), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif).
Length = 81
Score = 42.8 bits (101), Expect = 5e-06
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
D ++VGN+ + T +EL+ F G+V V I G F ++ F D ++VQ
Sbjct: 2 DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61
Query: 150 MAMDESLFRGRQ-IKVNPKR 168
+A FRG + V K+
Sbjct: 62 LANKPIYFRGDHRLNVEEKK 81
>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM3 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 42.8 bits (101), Expect = 6e-06
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
+++ N+ Y T E+LE F G ++ V + +K PKGFA++ + + A A +
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64
Query: 153 DESLFRGRQIKVNP 166
D ++F+GR + + P
Sbjct: 65 DGTVFQGRLLHLLP 78
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 42.2 bits (100), Expect = 6e-06
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 4/73 (5%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
++ V N+ T ++ F CG + V I + A IEF +D A+
Sbjct: 2 TVKVKNLPKDTTENKIRQFFKDCGEIREVKI----VESEGGLVAVIEFETEDEALAALTK 57
Query: 153 DESLFRGRQIKVN 165
D G +I V+
Sbjct: 58 DHKRLGGNEISVS 70
>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 = 42.6 bits (101), Expect = 6e-06
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA---M 150
+YVGN+D T E L F G V V I ++ +G+ ++EF ++ A M
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 151 AMDESLFRGRQIKVN 165
M L+ G+ I+VN
Sbjct: 61 NM-IKLY-GKPIRVN 73
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 42.5 bits (101), Expect = 7e-06
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF--ADKDSVQTAMA 151
++VG + T +LE F G+V+ V I+ K G +GFAYI+ ++ +
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61
Query: 152 MDESLFRGRQIKV 164
++ + ++G +K+
Sbjct: 62 LNGTKWKGSVLKI 74
>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 = 42.3 bits (100), Expect = 7e-06
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
D SI+VG + T EEL F G + V ++ K H FA+I+F + + A
Sbjct: 2 DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARA 59
Query: 150 M-AMDESLFRGRQIKV 164
+ + + S+ + + + V
Sbjct: 60 VESENHSMLKNKTMHV 75
>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM2 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 77
Score = 41.5 bits (98), Expect = 1e-05
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
IYV +V + ++++S F G + ++ + G KG+ +IE+ + S Q A+A M
Sbjct: 3 IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62
Query: 153 DESLFRGRQIKVN 165
+ G+Q++V
Sbjct: 63 NLFDLGGQQLRVG 75
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 77
Score = 41.4 bits (97), Expect = 1e-05
Identities = 17/54 (31%), Positives = 28/54 (51%)
Query: 96 VGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
V N+ T EE E G++ R ++ ++ GH KG+ ++E+ KDS A
Sbjct: 4 VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKA 57
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 42.2 bits (99), Expect = 1e-05
Identities = 18/59 (30%), Positives = 29/59 (49%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
+++V N+ Y AT E L HF GSV + +K G KG ++ F D+ + +
Sbjct: 3 TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 41.4 bits (97), Expect = 2e-05
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VG + + T ++L+ +F G V TI + G +GF ++ F D SV+ +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 154 ESLFRGRQIKVNPKR 168
E GR I +PKR
Sbjct: 61 EHKLDGRVI--DPKR 73
>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 = 41.1 bits (97), Expect = 2e-05
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNK---FDGHPKGFAYIEFADKDSVQTAM 150
+++GN+D T L F G + + L +K G P+G+ ++ F K+ + A+
Sbjct: 2 LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61
Query: 151 A-MDESLFRGRQIKVNPKR 168
++ G+++ V
Sbjct: 62 KSLNGKTALGKKLVVRWAH 80
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by YNL110C
from Saccharomyces cerevisiae, and localizes to the
nucleoplasm and nucleolus. Nop15p has been identified as
a component of a pre-60S particle. It interacts with RNA
components of the early pre-60S particles. Furthermore,
Nop15p binds directly to a pre-rRNA transcript in vitro
and is required for pre-rRNA processing. It functions as
a ribosome synthesis factor required for the 5' to 3'
exonuclease digestion that generates the 5' end of the
major, short form of the 5.8S rRNA as well as for
processing of 27SB to 7S pre-rRNA. Nop15p also play a
specific role in cell cycle progression. Nop15p contains
an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 40.9 bits (96), Expect = 2e-05
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
IY+G++ +G +EL+ +F G+V V + +K G+ K + +I+F + + A +M
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 153 DESLFRGRQIKV 164
+ L G+ ++V
Sbjct: 62 NNYLLMGKVLQV 73
>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in
(U)-binding-splicing factor PUF60 and similar proteins.
This subfamily corresponds to the RRM1 of PUF60, also
termed FUSE-binding protein-interacting repressor
(FBP-interacting repressor or FIR), or Ro-binding
protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1).
PUF60 is an essential splicing factor that functions as
a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins.
Research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 76
Score = 40.9 bits (96), Expect = 2e-05
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
+YVG++ + + + F G + + + + KGFA++E+ ++ Q A+ M
Sbjct: 3 VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62
Query: 153 DESLFRGRQIKVN 165
+ + GR IKV
Sbjct: 63 NGVMLGGRNIKVG 75
>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 = 40.6 bits (96), Expect = 2e-05
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++VG + + L+ F G+V V + ++ P+G+AY+EF + + A+ M
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 153 DESLFRGRQIKV 164
D G+++ V
Sbjct: 61 DGGQIDGQEVTV 72
>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 = 41.0 bits (96), Expect = 3e-05
Identities = 15/74 (20%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
+++V N+ + T E+L F + ++ + G +G+ ++ FA + Q A+A
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAK 60
Query: 152 MDESLFRGRQIKVN 165
+ GR ++++
Sbjct: 61 LKNKKLHGRILRLD 74
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 75
Score = 40.7 bits (95), Expect = 3e-05
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VG + + + ++L+ +F G V TI + G +GF +I F D SV+ +
Sbjct: 2 MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61
Query: 154 ESLFRGRQIKVNPKR 168
E GR I +PK+
Sbjct: 62 EHRLDGRLI--DPKK 74
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 73
Score = 40.3 bits (95), Expect = 3e-05
Identities = 21/71 (29%), Positives = 36/71 (50%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VG + T E+L +F G+V V I+ +K G +GFA++ F D D V +
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61
Query: 154 ESLFRGRQIKV 164
G +++V
Sbjct: 62 YHTINGHRVEV 72
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 40.0 bits (94), Expect = 5e-05
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 10/80 (12%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNR--------VTILCNKFDGHPKGFAYIEFADKDS 145
IY+ + T + L F G G + R + I +K + PKG A + + D +
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDK-ETEPKGEATVTYDDPSA 59
Query: 146 VQTAMAM-DESLFRGRQIKV 164
Q A+ + FRG +IKV
Sbjct: 60 AQAAIEWFNGYEFRGNKIKV 79
>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM2 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 82
Score = 40.2 bits (94), Expect = 5e-05
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 92 RSIYVGNVDYGATAEELESHFHG-CGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
R+IY N+D T +++ F CG V+R+ +L + H A++EFA +S A+
Sbjct: 5 RTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYH--HSTRIAFVEFAMAESAIAAL 62
Query: 151 AMDESLFRGRQIKVNPKRT 169
++ I+V+P +T
Sbjct: 63 NCSGAVLGSLPIRVSPSKT 81
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM1 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 81
Score = 39.9 bits (94), Expect = 5e-05
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD 142
++++G+++ + S F CG V V I+ NK G G+ ++EFA
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFAT 50
>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 = 40.0 bits (94), Expect = 6e-05
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 93 SIYVGNVDYGATAEELESHFHG-CGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
SI+VG++ T L+ F SV ++ + G KG+ ++ F D+D A+
Sbjct: 3 SIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALT 62
Query: 152 -MDESLFRGRQIKVNP 166
M+ R ++V+P
Sbjct: 63 EMNGVYCSSRPMRVSP 78
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 39.6 bits (93), Expect = 6e-05
Identities = 16/56 (28%), Positives = 28/56 (50%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
+ VGN+ T E+ G+V R ++ ++ G KG+ ++E+A K S A
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 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 = 82
Score = 39.8 bits (94), Expect = 6e-05
Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 17/84 (20%)
Query: 92 RSIYVGNVDYGATAEELESHFHGC-----------GSVNRVTILCNKFDGHPKGFAYIEF 140
R +YVGN+ G T EEL F+ V V I K FA++EF
Sbjct: 2 RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQI------NPEKNFAFVEF 55
Query: 141 ADKDSVQTAMAMDESLFRGRQIKV 164
+ A+A+D +F+G+ +K+
Sbjct: 56 RTVEEATAALALDGIIFKGQPLKI 79
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both, Nop12p and Nop13p, are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 85
Score = 39.8 bits (93), Expect = 8e-05
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 11/80 (13%)
Query: 94 IYVGNVDYGATAEELESHF-------HGCGSVNRVTI--LCNKFDGHP--KGFAYIEFAD 142
+++GN+ + T E L F + RV + K G KGFAY++F
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60
Query: 143 KDSVQTAMAMDESLFRGRQI 162
+++ + A+A+ E + GR++
Sbjct: 61 QEATKAAIALSEKILNGRKL 80
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that 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. 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. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its median
region, 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 = 77
Score = 39.2 bits (91), Expect = 9e-05
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMAM 152
+YVGN+ GA ELE F G + V I N P GFA++EF D +D+ +
Sbjct: 2 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 56
Query: 153 DESLFRGRQIKV 164
D + G +++V
Sbjct: 57 DGKVICGSRVRV 68
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 39.2 bits (91), Expect = 1e-04
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
+++G + + T ++L+ +F G V T+ + G +GF ++ F + +SV M
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 154 ESLFRGRQIKVNPKR 168
E G+ I +PKR
Sbjct: 61 EHKLNGKVI--DPKR 73
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 39.3 bits (91), Expect = 1e-04
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
LR +++G + + T E L SHF G++ ++ + +GF ++ ++ + V AM
Sbjct: 2 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61
Query: 151 AMDESLFRGRQIKVNPKR 168
GR V PKR
Sbjct: 62 NARPHKVDGRV--VEPKR 77
>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 = 39.2 bits (92), Expect = 1e-04
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 21/93 (22%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSV----------------NRVTILCNKFDGHPKG- 134
R+++VGN+ ++L+ F G + +V + KF H K
Sbjct: 1 RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKF--HDKKD 58
Query: 135 --FAYIEFADKDSVQTAMAMDESLFRGRQIKVN 165
AY+ F +++S + A+ ++ + F G I+V+
Sbjct: 59 NVNAYVVFKEEESAEKALKLNGTEFEGHHIRVD 91
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
++++G++ T E+L++ F G + + ++ P+G AY+ + A+
Sbjct: 3 TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRALQ 56
Query: 151 AMDESLFRGRQIKV 164
+ G++IKV
Sbjct: 57 KLRNVKLAGKKIKV 70
>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 = 38.8 bits (90), Expect = 1e-04
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMA 151
S++V N+ +E+L F G + V + + + P+GFAY++F D +D+
Sbjct: 2 SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN 61
Query: 152 MDESLFRGRQIKVNPKRTNR 171
+D GRQI++ + +R
Sbjct: 62 LDRKWICGRQIEIQFAQGDR 81
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
+ V N+ + T +L+ F G V VTI K DG KGFA+++F K + A+ +
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIP-RKPDGKKKGFAFVQFTSKADAEKAIKGV 60
Query: 153 DESLFRGRQIKV 164
+ +GR + V
Sbjct: 61 NGKKIKGRPVAV 72
>gnl|CDD|240947 cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, G-rich sequence factor 1 (GRSF-1) and
similar proteins. This subfamily corresponds to the
RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein
family includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3
(also termed hnRNP 2H9), which represent a group of
nuclear RNA binding proteins that are involved in
pre-mRNA processing. These proteins have similar RNA
binding affinities and specifically recognize the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. hnRNP H and
hnRNP H2 are almost identical; both have been found to
bind nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements downstream
of the 5' splice site in the transcripts of c-src, human
immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and
myelin. It silences exons when bound to exonic elements
in the transcripts of beta-tropomyosin, HIV-1, and
alpha-tropomyosin. hnRNP H2 has been implicated in
pre-mRNA 3' end formation. hnRNP H3 may be involved in
splicing arrest induced by heat shock. Most family
members contain three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and play an
important role in efficiently silencing the exon.
Members in this family can regulate the alternative
splicing of fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced silencing
activity within hnRNP H3. Members in this family have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. They also
include a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. They may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 contains three
potential RRMs responsible for the RNA binding, and two
auxiliary domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 77
Score = 38.5 bits (90), Expect = 1e-04
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 103 ATAEELESHFHGC---GSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRG 159
ATAE++ + F C G N + ++ +G P G A+IE ++ V+ A+
Sbjct: 11 ATAEDVLNFFSDCRIKGGENGIHFTYSR-EGRPSGEAFIELESEEDVEKALEKHNEHMGH 69
Query: 160 RQIKV 164
R I+V
Sbjct: 70 RYIEV 74
>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM2 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 = 74
Score = 38.1 bits (89), Expect = 2e-04
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 103 ATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDE 154
T E+L F G + V+I+ +K G KGF Y++F K S Q A+A++
Sbjct: 12 YTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFH-KPS-QAAVALEN 61
>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 = 38.5 bits (90), Expect = 2e-04
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG------HPKGFAYIEFADKDSV 146
+Y+ N+ Y ++ E+LE F V I G P G AY EF+ +
Sbjct: 1 RVYISNLSYSSSEEDLEE-FLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59
Query: 147 QTAM-AMDESLFRGRQIKV 164
+ + ++ +F+ R++ V
Sbjct: 60 EKVVKDLNGKVFKNRKLFV 78
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 38.1 bits (89), Expect = 2e-04
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAM 152
+YVGN+D T + L F G + ++ + +A++E+ D S A M
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLI---REHGNDPYAFVEYYDHRSAAAALQTM 57
Query: 153 DESLFRGRQIKVN 165
+ L G++IKVN
Sbjct: 58 NGRLILGQEIKVN 70
>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl
cis-trans isomerase-like 4 (PPIase) and similar
proteins. This subfamily corresponds to the RRM of
PPIase, also termed cyclophilin-like protein PPIL4, or
rotamase PPIL4, a novel nuclear RNA-binding protein
encoded by cyclophilin-like PPIL4 gene. The precise role
of PPIase remains unclear. PPIase contains a conserved
N-terminal peptidyl-prolyl cistrans isomerase (PPIase)
motif, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a lysine rich
domain, and a pair of bipartite nuclear targeting
sequences (NLS) at the C-terminus.
Length = 83
Score = 38.4 bits (90), Expect = 2e-04
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAMDESLFRGRQI 162
T E+LE F G + ++ +K G +A+IEF K+ + A MD L R+I
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75
Query: 163 KV 164
V
Sbjct: 76 HV 77
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma
Protein (EWS). This subgroup corresponds to the RRM of
EWS, also termed Ewing sarcoma breakpoint region 1
protein, a member of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the FET
family, EWS contains an N-terminal Ser, Gly, Gln and
Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U RNA.
It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor gene.
.
Length = 84
Score = 38.3 bits (89), Expect = 2e-04
Identities = 28/82 (34%), Positives = 41/82 (50%), Gaps = 9/82 (10%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSV--NR------VTILCNKFDGHPKGFAYIEFADKD 144
+IYV ++ T EEL F CG V N+ V I +K G PKG A + + D
Sbjct: 2 TIYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPP 61
Query: 145 SVQTAMAM-DESLFRGRQIKVN 165
S + A+ D F+G ++KV+
Sbjct: 62 SAKAAVEWFDGKDFQGSKLKVS 83
>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 = 38.0 bits (89), Expect = 3e-04
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++V + T +ELE+ F G V V ++ + G +GF ++ F + A+ +
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 153 DESLFRGRQIKV 164
+ GR IKV
Sbjct: 64 NGKELEGRVIKV 75
>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 = 40.9 bits (96), Expect = 3e-04
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 2/87 (2%)
Query: 80 NLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIE 139
L E K +A ++YV N+D T E+L F CG + ++ ++ G +GF ++
Sbjct: 274 ELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVC 332
Query: 140 FADKDSVQTAMA-MDESLFRGRQIKVN 165
F++ + A+ M + G+ + V
Sbjct: 333 FSNPEEANRAVTEMHGRMLGGKPLYVA 359
Score = 32.1 bits (73), Expect = 0.21
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
S+YVG++D T +L F G V V + + G+ Y+ F + + A+
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61
Query: 152 MDESLFRGRQIKV 164
M+ G+ I++
Sbjct: 62 MNFKRLGGKPIRI 74
Score = 29.8 bits (67), Expect = 1.2
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 2/72 (2%)
Query: 84 EEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
E ++YV N+D ++L F G + + G +GFA++ F
Sbjct: 171 EAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAV-MKDGSGRSRGFAFVNFEKH 229
Query: 144 DSVQTAM-AMDE 154
+ A+ M+
Sbjct: 230 EDAAKAVEEMNG 241
Score = 29.0 bits (65), Expect = 2.2
Identities = 16/88 (18%), Positives = 39/88 (44%), Gaps = 4/88 (4%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
I+V N+D + L F G++ + ++ +G +G+ ++ F ++S + A+ +
Sbjct: 91 IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKV 149
Query: 153 DESLFRGRQIKVNP--KRTNRPGISTTN 178
+ L +++ V K+ R
Sbjct: 150 NGMLLNDKEVYVGRFIKKHEREAAPLKK 177
>gnl|CDD|241174 cd12730, RRM1_GRSF1, RNA recognition motif 1 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM1 of GRSF-1, a cytoplasmic
poly(A)+ mRNA binding protein which interacts with RNA
in a G-rich element-dependent manner. It may function in
RNA packaging, stabilization of RNA secondary structure,
or other macromolecular interactions. GRSF-1 contains
three potential RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which are responsible for
the RNA binding. In addition, GRSF-1 has two auxiliary
domains, an acidic alpha-helical domain and an
N-terminal alanine-rich region, that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 79
Score = 37.5 bits (87), Expect = 4e-04
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 4/67 (5%)
Query: 101 YGATAEELESHFHGC---GSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLF 157
+ TAE++ + F C N V L N+ DG P+G A IE ++ VQ A+
Sbjct: 11 WSCTAEDVMNFFDDCRIRNGENGVHFLLNR-DGKPRGDALIELESEEDVQKALEQHRHYM 69
Query: 158 RGRQIKV 164
R ++V
Sbjct: 70 GQRYVEV 76
>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding
protein 25 and similar proteins. This subfamily
corresponds to the RRM of RBM25, also termed
Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein
S164, or RNA-binding region-containing protein 7, an
evolutionary-conserved splicing coactivator SRm160
(SR-related nuclear matrix protein of 160 kDa,
)-interacting protein. RBM25 belongs to a family of
RNA-binding proteins containing a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
N-terminus, a RE/RD-rich (ER) central region, and a
C-terminal proline-tryptophan-isoleucine (PWI) motif. It
localizes to the nuclear speckles and associates with
multiple splicing components, including splicing
cofactors SRm160/300, U snRNAs, assembled splicing
complexes, and spliced mRNAs. It may play an important
role in pre-mRNA processing by coupling splicing with
mRNA 3'-end formation. Additional research indicates
that RBM25 is one of the RNA-binding regulators that
direct the alternative splicing of apoptotic factors. It
can activate proapoptotic Bcl-xS 5'ss by binding to the
exonic splicing enhancer, CGGGCA, and stabilize the
pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1
snRNP-associated factor. .
Length = 84
Score = 37.6 bits (88), Expect = 4e-04
Identities = 19/84 (22%), Positives = 35/84 (41%), Gaps = 7/84 (8%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSV---NRVTILCNKFDGHPKGFAYIEFADKDSVQT 148
+++VGN+ G + + + CG V RV + G K F + EF D +
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVK---DPSTGKLKAFGFCEFEDPEGALR 57
Query: 149 AM-AMDESLFRGRQIKVNPKRTNR 171
A+ ++ G+++ V R
Sbjct: 58 ALRLLNGLELGGKKLLVKVDAKTR 81
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog of
DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 37.5 bits (87), Expect = 5e-04
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
+++VG +D E+ S F GSV V I+ ++ G KG+ ++ F D VQ +
Sbjct: 7 TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVES 65
Query: 153 DESLFRGRQIKVNP 166
+ F G+++K+ P
Sbjct: 66 QIN-FHGKKLKLGP 78
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 37.3 bits (87), Expect = 5e-04
Identities = 19/71 (26%), Positives = 35/71 (49%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
I+VG + T +L +F G+V V ++ + P+GF +I F +DSV +
Sbjct: 5 IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64
Query: 154 ESLFRGRQIKV 164
G++++V
Sbjct: 65 FHDINGKKVEV 75
>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 = 37.0 bits (86), Expect = 5e-04
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
I+VG++ E L + F G ++ ++ + G KG+ ++ F K+ + A+ M
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 153 DESLFRGRQIKVN 165
+ GR I+ N
Sbjct: 62 NGQWLGGRAIRTN 74
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 37.3 bits (86), Expect = 6e-04
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMA 151
S++V NV E+L F G + V + + + P+GFAYI+F D +D+
Sbjct: 2 SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYN 61
Query: 152 MDESLFRGRQIKVNPKRTNR 171
++ GRQI++ + +R
Sbjct: 62 LNRKWVCGRQIEIQFAQGDR 81
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family. This
subfamily corresponds to the RRM of the ist3 family that
includes fungal U2 small nuclear ribonucleoprotein
(snRNP) component increased sodium tolerance protein 3
(ist3), X-linked 2 RNA-binding motif proteins (RBMX2)
found in Metazoa and plants, and similar proteins. Gene
IST3 encoding ist3, also termed U2 snRNP protein SNU17
(Snu17p), is a novel yeast Saccharomyces cerevisiae
protein required for the first catalytic step of
splicing and for progression of spliceosome assembly. It
binds specifically to the U2 snRNP and is an intrinsic
component of prespliceosomes and spliceosomes. Yeast
ist3 contains an atypical RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In the yeast pre-mRNA
retention and splicing complex, the atypical RRM of ist3
functions as a scaffold that organizes the other two
constituents, Bud13p (bud site selection 13) and Pml1p
(pre-mRNA leakage 1). Fission yeast Schizosaccharomyces
pombe gene cwf29 encoding ist3, also termed cell cycle
control protein cwf29, is an RNA-binding protein
complexed with cdc5 protein 29. It also contains one
RRM. The biological function of RBMX2 remains unclear.
It shows high sequence similarity to yeast ist3 protein
and harbors one RRM as well. .
Length = 89
Score = 37.2 bits (87), Expect = 7e-04
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
IY+G + Y T ++ F G + + ++ +K G KGFA++ + D+ S T +A+D
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS--TILAVD 69
Query: 154 E---SLFRGRQIKV 164
GR I+V
Sbjct: 70 NLNGIKLLGRTIRV 83
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 36.9 bits (86), Expect = 7e-04
Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 14/80 (17%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
+ ++YVG + T ++L HF+ G + +T++ + A++ F +++ + A
Sbjct: 1 ITTLYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAA 54
Query: 151 AMDESLF-----RGRQIKVN 165
E LF GR++K+
Sbjct: 55 ---ERLFNKLIINGRRLKLK 71
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 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 = 36.6 bits (85), Expect = 7e-04
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
R++++GN++ T +L F G + + I K G +A+I++AD SV AM
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDI---KKQGGNPAYAFIQYADIASVVKAMR 59
Query: 151 AMDESLFRGRQIKV 164
MD ++K+
Sbjct: 60 KMDGEYLGNNRVKL 73
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 36.8 bits (85), Expect = 8e-04
Identities = 17/71 (23%), Positives = 33/71 (46%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VG + +L HF G V + ++ +K G +GF ++ F + DS A +
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVK 61
Query: 154 ESLFRGRQIKV 164
G +++V
Sbjct: 62 FHPINGHRVEV 72
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 36.5 bits (84), Expect = 8e-04
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
+++G + + + ++L + G V TI + G +GF ++ F D SV + +
Sbjct: 2 MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61
Query: 154 ESLFRGRQIKVNPKR 168
E G+ I +PKR
Sbjct: 62 EHKLDGKLI--DPKR 74
>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 = 36.4 bits (84), Expect = 9e-04
Identities = 17/69 (24%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
++YV N+ T +EL F G++ + +L +K G P+G A++ + ++ Q A+ +
Sbjct: 2 NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61
Query: 152 MDESLFRGR 160
++ ++ G
Sbjct: 62 LNGTIPPGS 70
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM1
of hnRNP A2/B1 which is an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Moreover, the
overexpression of hnRNP A2/B1 has been described in many
cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 81
Score = 36.2 bits (83), Expect = 0.001
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
R +++G + + T E L +++ G + ++ + +GF ++ F+ + V AM
Sbjct: 2 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61
Query: 151 AMDESLFRGRQIKVNPKR 168
A GR V PKR
Sbjct: 62 AARPHTIDGRV--VEPKR 77
>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly
[ADP-ribose] polymerase PARP-10, RNA recognition motif 2
in PARP-14, RNA recognition motif in N-myc-interactor
(Nmi), interferon-induced 35 kDa protein (IFP 35),
RNA-binding protein 43 (RBM43) and similar proteins.
This subfamily corresponds to the RRM1 and RRM2 of
PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi),
interferon-induced 35 kDa protein (IFP 35) and
RNA-binding protein 43 (RBM43). PARP-10 is a novel
oncoprotein c-Myc-interacting protein with
poly(ADP-ribose) polymerase activity. It is localized to
the nuclear and cytoplasmic compartments. In addition to
PARP activity, PARP-10 is also involved in the control
of cell proliferation by inhibiting c-Myc- and
E1A-mediated cotransformation of primary cells. PARP-10
may also play a role in nuclear processes including the
regulation of chromatin, gene transcription, and
nuclear/cytoplasmic transport. PARP-10 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two overlapping C-terminal domains composed of
a glycine-rich region and a region with homology to
catalytic domains of PARP enzymes (PARP domain). In
addition, PARP-10 contains two ubiquitin-interacting
motifs (UIM). PARP-14, also termed aggressive lymphoma
protein 2, is a member of the B aggressive lymphoma
(BAL) family of macrodomain-containing PARPs. Like
PARP-10, PARP-14 also includes two RRMs at the
N-terminus. Nmi, also termed N-myc and STAT interactor,
is an interferon inducible protein that interacts with
c-Myc, N-Myc, Max and c-Fos, and other transcription
factors containing bHLH-ZIP, bHLH or ZIP domains.
Besides binding Myc proteins, Nmi also associates with
all the Stat family of transcription factors except
Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma)
stimulation, Nmi can enhance Stat-mediated
transcriptional activity through recruiting the Stat1
and Stat5 transcriptional coactivators, CREB-binding
protein (CBP) and p300. IFP 35 is an interferon-induced
leucine zipper protein that can specifically form
homodimers. Distinct from known bZIP proteins, IFP 35
lacks a basic domain critical for DNA binding. In
addition, IFP 35 may negatively regulate other bZIP
transcription factors by protein-protein interaction.
For instance, it can form heterodimers with B-ATF, a
member of the AP1 transcription factor family. Both Nmi
and IFP35 harbor one RRM. RBM43 is a putative
RNA-binding protein containing one RRM, but its
biological function remains unclear. .
Length = 74
Score = 35.7 bits (83), Expect = 0.001
Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 11/80 (13%)
Query: 92 RSIYVGNVDYGATAEELESHF-----HGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
R + V + + ++LE +F G G V RV L KG A + FAD
Sbjct: 1 RCVLVAGLPETVSDDKLELYFENKRRSGGGDVTRVQYL------REKGSALVTFADFKVA 54
Query: 147 QTAMAMDESLFRGRQIKVNP 166
+ + + G Q+ V P
Sbjct: 55 ERVVKQKKHPLNGTQLSVRP 74
>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 = 38.5 bits (89), Expect = 0.001
Identities = 31/138 (22%), Positives = 62/138 (44%), Gaps = 11/138 (7%)
Query: 31 SKCTDEAELAAMKARVREMEEEAEK--LKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKE 88
K + E + KA+ ME+ ++ LKQ ++ +Q+ N ++
Sbjct: 53 PKLSSEQKDDIQKAKKYAMEQSIKQVLLKQTKAHQQQQLE--------NQQRQQQRQQAL 104
Query: 89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQT 148
A + +YVG++ + + + F G + + + + G KGFA++E+ ++ Q
Sbjct: 105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQL 164
Query: 149 AM-AMDESLFRGRQIKVN 165
A+ M+ + GR IKV
Sbjct: 165 ALEQMNGQMLGGRNIKVG 182
Score = 32.7 bits (74), Expect = 0.13
Identities = 14/58 (24%), Positives = 27/58 (46%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
IYV +V + +++S F G + + + KG+ +IE+ + S A+A
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 71
Score = 35.7 bits (83), Expect = 0.001
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 11/65 (16%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPK---GFAYIEFADKDSVQT 148
R ++VG + T E+L +F G V V I PK FA++ FAD + Q+
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI--------PKPFRAFAFVTFADPEVAQS 52
Query: 149 AMAMD 153
D
Sbjct: 53 LCGED 57
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 35.6 bits (82), Expect = 0.002
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
++VGN+ T EE+ F G + F KGF +I + + A A +
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEI------FIHKDKGFGFIRLETRTLAEIAKAEL 57
Query: 153 DESLFRGRQIKV 164
D RG+Q++V
Sbjct: 58 DNMPLRGKQLRV 69
>gnl|CDD|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage
factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar
proteins. This subgroup corresponds to the RRM of
CFIm68. Cleavage factor Im (CFIm) is a highly conserved
component of the eukaryotic mRNA 3' processing machinery
that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. Two separate genes, CPSF6
and CPSF7, code for two isoforms of the large subunit,
CFIm68 and CFIm59. The family includes CFIm68, also
termed cleavage and polyadenylation specificity factor
subunit 6 (CPSF6), or cleavage and polyadenylation
specificity factor 68 kDa subunit (CPSF68), or protein
HPBRII-4/7. CFIm68 contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a central
proline-rich region, and a C-terminal RS-like domain.
The N-terminal RRM of CFIm68 mediates the interaction
with CFIm25. It also serves to enhance RNA binding and
facilitate RNA looping. .
Length = 77
Score = 35.9 bits (83), Expect = 0.002
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNR---VTILCNKFDGHPKGFAYIEFADKDSVQTA 149
++YVGN+ + T ++L G VN + N+ +G KGFA I + S +
Sbjct: 1 ALYVGNLTWWTTDQDLTEAIQSIG-VNDLLEIKFFENRANGQSKGFALIVLGSESSSRKL 59
Query: 150 M 150
M
Sbjct: 60 M 60
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, an abundant eukaryotic nuclear RNA-binding protein
that may modulate splice site selection in pre-mRNA
splicing. hnRNP A1 has been characterized as a splicing
silencer, often acting in opposition to an activating
hnRNP H. It silences exons when bound to exonic elements
in the alternatively spliced transcripts of c-src, HIV,
GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle
between the nucleus and the cytoplasm. Thus, it may be
involved in transport of cellular RNAs, including the
packaging of pre-mRNA into hnRNP particles and transport
of poly A+ mRNA from the nucleus to the cytoplasm. The
cytoplasmic hnRNP A1 has high affinity with AU-rich
elements, whereas the nuclear hnRNP A1 has high affinity
with a polypyrimidine stretch bordered by AG at the 3'
ends of introns. hnRNP A1 is also involved in the
replication of an RNA virus, such as mouse hepatitis
virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 35.7 bits (82), Expect = 0.002
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
+ I+VG + L +F G + + I+ ++ G +GFA++ F D DSV
Sbjct: 1 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSV 55
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal Rrp7 domain. .
Length = 102
Score = 36.5 bits (85), Expect = 0.002
Identities = 20/76 (26%), Positives = 29/76 (38%), Gaps = 15/76 (19%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCN-------------KFDGHPKGF--A 136
R+++V NV T E L+ F CG V V + KGF A
Sbjct: 1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVA 60
Query: 137 YIEFADKDSVQTAMAM 152
Y+ F S+ A+ +
Sbjct: 61 YVVFKKPSSLSRALKL 76
>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 = 35.7 bits (83), Expect = 0.002
Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
+ +YV N+ T E+L F G V RV K +A++ F ++D AM
Sbjct: 2 KVLYVRNLPLSTTEEQLRELFSEYGEVERVKK--------IKDYAFVHFEERDDAVKAME 53
Query: 151 AMDESLFRGRQIKV 164
M+ G I+V
Sbjct: 54 EMNGKELEGSPIEV 67
>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 = 35.8 bits (83), Expect = 0.002
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 102 GATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLF--R 158
T ++L F G + + ++ +K KG AY++FA S AM M+
Sbjct: 13 SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72
Query: 159 GRQIKV 164
+ +KV
Sbjct: 73 TKPLKV 78
>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 = 35.2 bits (81), Expect = 0.002
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
+I+VG++ T L + F S + ++ + G +G+ ++ F + + A+
Sbjct: 1 NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60
Query: 152 MDESLFRGRQIKVN 165
M+ R I+ N
Sbjct: 61 MNGKWLGSRPIRCN 74
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 35.4 bits (82), Expect = 0.002
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
+++G + Y T + L+++F G + ++ + +GF ++ FA V AM
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61
Query: 154 ESLFRGRQIKVNPKR 168
GR+ V PKR
Sbjct: 62 PHKVDGRE--VEPKR 74
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition, steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway. It binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 76
Score = 35.3 bits (81), Expect = 0.003
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
+++G +++ T + L +F G V T++ + G +GF ++ F SV M
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMK-K 59
Query: 154 ESLFRGRQIKVNPKR 168
E + G+ I +PKR
Sbjct: 60 EHILDGKII--DPKR 72
>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in
heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0)
and similar proteins. This subfamily corresponds to the
RRM1 of hnRNP A0 which is a low abundance hnRNP protein
that has been implicated in mRNA stability in mammalian
cells. It has been identified as the substrate for
MAPKAP-K2 and may be involved in the lipopolysaccharide
(LPS)-induced post-transcriptional regulation of tumor
necrosis factor-alpha (TNF-alpha), cyclooxygenase 2
(COX-2) and macrophage inflammatory protein 2 (MIP-2).
hnRNP A0 contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 79
Score = 35.2 bits (81), Expect = 0.003
Identities = 17/76 (22%), Positives = 31/76 (40%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
L ++VG ++ + L HF G + ++ + +GF +I F+ D AM
Sbjct: 2 LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61
Query: 151 AMDESLFRGRQIKVNP 166
G QI++
Sbjct: 62 EAQPHSIDGNQIELKR 77
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 35.5 bits (81), Expect = 0.003
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
LR +++G + + T + L HF G++ ++ + +GF ++ ++ + V AM
Sbjct: 2 LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61
Query: 151 AMDESLFRGRQIKVNPKR 168
+ GR V PKR
Sbjct: 62 SARPHKVDGRV--VEPKR 77
>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the RRM1
of yeast protein PUB1, also termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein. PUB1 has been identified as
both, a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP),
which may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. It is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is
one of the major cellular proteins cross-linked by UV
light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there is
no strong evidence implicating PUB1 in the mechanism of
DNA replication. PUB1 contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a GAR motif
(glycine and arginine rich stretch) that is located
between RRM2 and RRM3. .
Length = 74
Score = 34.8 bits (80), Expect = 0.003
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNK-FDGHPKGFAYIEFADKDSVQTAMAM 152
+YVGN+D T + L+ F G V V I+ +K G GF +E+ + A+
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGF--VEYHQSHDAEIAL-- 56
Query: 153 DESLFRGRQIKVNPKRTN 170
GRQI+ N R N
Sbjct: 57 --QTLNGRQIENNEIRVN 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 = 35.3 bits (82), Expect = 0.003
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 106 EELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQIKV 164
++L G V +V + FD HP G A ++F + + + A++ F GRQ++
Sbjct: 27 DDLREECEKFGQVKKVVV----FDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEA 82
>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 = 34.5 bits (80), Expect = 0.004
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 96 VGNVDYGATAEELESHFHGCGSVNRVTILCNKFD--GHPKGFAYIEFADKDSVQTAMA-M 152
V N+ Y T E+LE F G V +V I +D G +G A + F ++ + A+
Sbjct: 5 VSNLHYDVTEEDLEELFGRVGEVKKVKI---NYDRSGRSEGTADVVFEKREDAERAIKQF 61
Query: 153 DESLFRGRQIKVN 165
+ L G+ ++V
Sbjct: 62 NGVLLDGQPMQVE 74
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to the
RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contain
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. On the other
hand, both RRM1 and RRM2 of CELF-4 can activate cardiac
troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in
brain, is also known as bruno-like protein 5 (BRUNOL-5),
or CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, strongly
expressed in kidney, brain, and testis, is also known as
bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in an muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In additiona to three highly conserved RRMs,
CELF-6 also possesses numerous potential phosphorylation
sites, a potential nuclear localization signal (NLS) at
the C terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 35.1 bits (81), Expect = 0.004
Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 4/84 (4%)
Query: 87 KEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
K+ D ++VG + ++L F G + +T+L +K+ G KG A++ + ++S
Sbjct: 1 KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60
Query: 147 QTAMAM--DESLFRG--RQIKVNP 166
A + ++ G R I+V P
Sbjct: 61 LKAQSALHEQKTLPGMNRPIQVKP 84
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 34.4 bits (79), Expect = 0.004
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMAM 152
+YVGN+ E+E F+ G + + + K P G+A+IEF D +D+
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRGR 58
Query: 153 DESLFRGRQIKV 164
D F G++++V
Sbjct: 59 DGYDFDGQRLRV 70
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM2
of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Overexpression of hnRNP
A2/B1 has been described in many cancers. It functions
as a nuclear matrix protein involving in RNA synthesis
and the regulation of cellular migration through
alternatively splicing pre-mRNA. It may play a role in
tumor cell differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 80
Score = 34.7 bits (79), Expect = 0.004
Identities = 13/55 (23%), Positives = 27/55 (49%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
+ ++VG + L +F G ++ + I+ ++ G +GF ++ F D D V
Sbjct: 1 KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPV 55
>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 = 34.4 bits (79), Expect = 0.004
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
D R+++V N+ Y T +EL+ F + + DG KG AYIEF + + A
Sbjct: 2 DARTLFVKNLPYNITVDELKEVFEDAVDIRLPS----GKDGSSKGIAYIEFKTEAEAEKA 57
Query: 150 MA-MDESLFRGRQIKVN 165
+ + GR I V+
Sbjct: 58 LEEKQGAEVDGRSIVVD 74
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor 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. 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 = 34.6 bits (79), Expect = 0.005
Identities = 19/65 (29%), Positives = 29/65 (44%)
Query: 107 ELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNP 166
+LE F G V V ++ ++ KG AY+EF D SV A+ + G I V
Sbjct: 17 DLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQA 76
Query: 167 KRTNR 171
+ +
Sbjct: 77 SQAEK 81
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of specific
mRNAs during gametogenesis. .
Length = 81
Score = 34.4 bits (79), Expect = 0.006
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
I+VG +D+ +L F G+V V I+ ++ G KG+ ++ F ++ Q +
Sbjct: 5 IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQEA 63
Query: 154 ESL-FRGRQIKVNP 166
L FR +++ +
Sbjct: 64 NRLCFRDKKLNIGQ 77
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM3
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 72
Score = 34.3 bits (79), Expect = 0.006
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKG-FAYIEFADKDSVQTA 149
I V N YG TAEEL F G + RV + P G A +EFA+ + A
Sbjct: 3 ILVKNFPYGTTAEELRDLFEPHGKLTRVLM-------PPAGTIAIVEFANPQQARLA 52
>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 = 36.5 bits (84), Expect = 0.006
Identities = 17/59 (28%), Positives = 34/59 (57%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
++YV N+ T ++L++ F G + + IL +K G P+G A++ F ++ Q A++
Sbjct: 195 NLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS 253
Score = 29.2 bits (65), Expect = 1.3
Identities = 30/119 (25%), Positives = 53/119 (44%), Gaps = 8/119 (6%)
Query: 68 SMGSPPN--SNNLLNL-----SIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNR 120
SMG+ N S N LN S + ++ V + T EL + F G +N
Sbjct: 77 SMGNMANMASTNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINT 136
Query: 121 VTILCNKFDGHPKGFAYIEF-ADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 178
I+ + G+ G+A+++F ++ DS + ++ R +++KV+ R I TN
Sbjct: 137 CRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTN 195
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the nucleus
and can accumulate in the perinucleolar compartment, a
dynamic nuclear substructure that harbors PTB. Raver-1
also modulates focal adhesion assembly by binding to the
cytoskeletal proteins, including alpha-actinin,
vinculin, and metavinculin (an alternatively spliced
isoform of vinculin) at adhesion complexes, particularly
in differentiated muscle tissue. Raver-1 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
through the PTB-binding motifs at its C-terminal half,
and binds to other partners, such as RNA having the
sequence UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the sequence
UCAUGCAGUCUG with micromolar affinity is found in
vinculin mRNA. Additional research indicates that the
RRM1 of raver-1 directs its interaction with the tail
domain of activated vinculin. Then the raver1/vinculin
tail (Vt) complex binds to vinculin mRNA, which is
permissive for vinculin binding to F-actin. .
Length = 77
Score = 34.2 bits (78), Expect = 0.006
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 96 VGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDES 155
+ N+ T ++ E G++ R ++ ++ GH KG+ ++E+ KDS A +S
Sbjct: 4 IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARA----KS 59
Query: 156 LFRGRQI 162
G+Q+
Sbjct: 60 DLLGKQL 66
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 34.3 bits (79), Expect = 0.006
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNR--------VTILCNKFDGHPKGFAYIEFADKDS 145
++V N+ T ++L HF G + + + +K G PKG A + + D +
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60
Query: 146 VQTAMA-MDESLFRGRQIKV 164
A+ + F G IKV
Sbjct: 61 ASAAIEWFNNKDFMGNTIKV 80
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 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 = 92
Score = 34.4 bits (80), Expect = 0.007
Identities = 20/82 (24%), Positives = 40/82 (48%), Gaps = 11/82 (13%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVN--------RVTILCNKFDGHPKGFAYIEFADKD 144
++YV + T EE F CG + ++ + ++ +G+ KG A + ++
Sbjct: 3 NVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDE-NGNLKGDALCCYLKEE 61
Query: 145 SVQTAMAM-DESL-FRGRQIKV 164
SV+ A+ + D + RG ++KV
Sbjct: 62 SVELAIQLLDGTEIGRGYKMKV 83
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM3 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 33.8 bits (78), Expect = 0.008
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 116 GSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQIKVNPKR 168
G V RV IL NK D A I+ AD QTA+ ++ G++++V +
Sbjct: 25 GDVVRVKILFNKKDT-----ALIQMADPQQAQTALTHLNGIRLHGKKLRVTLSK 73
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 33.8 bits (77), Expect = 0.009
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
D ++VGN+ + EL+ F G+V + I G F ++ F D + VQ
Sbjct: 4 DSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRI 63
Query: 150 MAMDESLFRGRQIKVN 165
+ +FRG ++++N
Sbjct: 64 LGAKPIMFRG-EVRLN 78
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 33.7 bits (78), Expect = 0.009
Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 94 IYVGNVDYGATAEELESHF--HGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
+ + +D T E++ + V ++ +K G +GFA++EF S++ A
Sbjct: 5 LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEF---PSLEDATQ 61
Query: 152 MDESLFRGRQIKVNPKR 168
++L ++ +
Sbjct: 62 WMDALNNLDPFVIDGRV 78
>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 = 33.9 bits (77), Expect = 0.010
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
++VG++ T E+++S F G ++ ++ + G KG+ ++ F +K + A+ M
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 153 DESLFRGRQIKVN 165
GRQI+ N
Sbjct: 64 GGQWLGGRQIRTN 76
>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 = 33.7 bits (78), Expect = 0.012
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 106 EELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQI 162
EE G V + + P+G Y++F ++ Q + A++ F GRQI
Sbjct: 30 EECSKF----GPVEHIKV----DKNSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQI 79
>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 = 35.7 bits (82), Expect = 0.012
Identities = 27/98 (27%), Positives = 40/98 (40%), Gaps = 4/98 (4%)
Query: 82 SIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFA 141
S + K A+L YV + T ELES F G + IL + G KG +I F
Sbjct: 83 SSDSIKGANL---YVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFD 139
Query: 142 DKDSVQTAM-AMDESLFRGRQIKVNPKRTNRPGISTTN 178
+D A+ ++ + G + K N P S +
Sbjct: 140 KRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSK 177
>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 = 33.5 bits (76), Expect = 0.013
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
++VG++ T +++++ F G ++ ++ + G KG+ ++ F +K + A+ M
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 153 DESLFRGRQIKVN 165
GRQI+ N
Sbjct: 64 GGQWLGGRQIRTN 76
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1) and has been implicated in the maintenance of
the stem-cell state, differentiation, and tumorigenesis.
It translationally regulates the expression of a
mammalian numb gene by binding to the 3'-untranslated
region of mRNA of Numb, encoding a membrane-associated
inhibitor of Notch signaling, and further influences
neural development. It represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 74
Score = 33.1 bits (75), Expect = 0.014
Identities = 14/54 (25%), Positives = 29/54 (53%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
I+VG + T E+++ +F G V+ ++ +K +GF ++ F +D V+
Sbjct: 2 IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVE 55
>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 = 33.1 bits (76), Expect = 0.014
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQI 162
T EEL S F G + I+ ++ G G+ ++++ D++ Q A+ ++ R +++
Sbjct: 13 TQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRL 72
Query: 163 KV 164
KV
Sbjct: 73 KV 74
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. hnRNP M is able to interact
with early spliceosomes, further influencing splicing
patterns of specific pre-mRNAs. It functions as the
receptor of carcinoembryonic antigen (CEA) that contains
the penta-peptide sequence PELPK signaling motif. In
addition, hnRNP M and another splicing factor Nova-1
work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 33.1 bits (76), Expect = 0.015
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEF 140
I+V N+DY ++L+ F G V R I +K +G +G ++F
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQF 46
>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 = 33.0 bits (75), Expect = 0.017
Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
+ + V N+ Y A+ + L+ F +I + +G PKG+A++EF + + A+
Sbjct: 2 KVLVVNNLSYSASEDSLQEVFE-----KATSIRIPQNNGRPKGYAFVEFESAEDAKEALN 56
Query: 151 AMDESLFRGRQIKV 164
+ + + GR I++
Sbjct: 57 SCNNTEIEGRSIRL 70
>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 = 33.0 bits (75), Expect = 0.019
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++YV + T +ELE F G + IL ++ G +G +I F + + A+
Sbjct: 2 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAI 59
>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in
RRM-containing coactivator activator/modulator (CoAA)
and similar proteins. This subfamily corresponds to the
RRM in CoAA (also known as RBM14 or PSP2) and
RNA-binding protein 4 (RBM4). CoAA is a heterogeneous
nuclear ribonucleoprotein (hnRNP)-like protein
identified as a nuclear receptor coactivator. It
mediates transcriptional coactivation and RNA splicing
effects in a promoter-preferential manner, and is
enhanced by thyroid hormone receptor-binding protein
(TRBP). CoAA contains two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a TRBP-interacting
domain. RBM4 is a ubiquitously expressed splicing factor
with two isoforms, RBM4A (also known as Lark homolog)
and RBM4B (also known as RBM30), which are very similar
in structure and sequence. RBM4 may also function as a
translational regulator of stress-associated mRNAs as
well as play a role in micro-RNA-mediated gene
regulation. RBM4 contains two N-terminal RRMs, a
CCHC-type zinc finger, and three alanine-rich regions
within their C-terminal regions. This family also
includes Drosophila RNA-binding protein lark (Dlark), a
homolog of human RBM4. It plays an important role in
embryonic development and in the circadian regulation of
adult eclosion. Dlark shares high sequence similarity
with RBM4 at the N-terminal region. However, Dlark has
three proline-rich segments instead of three
alanine-rich segments within the C-terminal region. .
Length = 66
Score = 32.2 bits (74), Expect = 0.021
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++VGN+ T+EEL + F G+V ++ K + ++ +++ + A+ A+
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKAL 53
Query: 153 DESLFRGRQIKV 164
+ F G++I V
Sbjct: 54 NGYEFMGKRINV 65
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM5
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 32.5 bits (74), Expect = 0.021
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
I V N+ + AT +++ + F G + V + KFD +GFA++EF+ AM
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRV-PKKFDQSARGFAFVEFSTAKEALNAM 58
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal
(SXL) and similar proteins. This subfamily corresponds
to the RRM1 of SXL which governs sexual differentiation
and X chromosome dosage compensation in Drosophila
melanogaster. It induces female-specific alternative
splicing of the transformer (tra) pre-mRNA by binding to
the tra uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 32.8 bits (75), Expect = 0.022
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESL-FRGRQI 162
T EE S F G V I+ +K G+ GF ++++ + Q A+ L + ++I
Sbjct: 13 TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72
Query: 163 KV 164
KV
Sbjct: 73 KV 74
>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM1 of hnRNP R, which
is a ubiquitously expressed nuclear RNA-binding protein
that specifically binds mRNAs with a preference for
poly(U) stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. It is predominantly located in
axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with wild
type of survival motor neuron (SMN) proteins directly,
further providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, and in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; it binds RNA
through its RRM domains. .
Length = 79
Score = 32.6 bits (74), Expect = 0.022
Identities = 14/62 (22%), Positives = 32/62 (51%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VG + +EL F G + + ++ + G +G+A+I F K++ Q A+ +
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63
Query: 154 ES 155
++
Sbjct: 64 DN 65
>gnl|CDD|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM1 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa,which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 74
Score = 32.4 bits (74), Expect = 0.022
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R++Y+GN+ T +EL SH G + V IL K A+I F D S TA
Sbjct: 2 RTVYLGNLPPNTTVKELLSHVR-SGPIENVRILPEKN------CAFISFLD-PSAATAFH 53
Query: 152 MDESL----FRGRQIKV 164
D L +G ++K+
Sbjct: 54 SDAILKRLSIKGVELKI 70
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable
RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 32.7 bits (74), Expect = 0.022
Identities = 19/65 (29%), Positives = 29/65 (44%)
Query: 107 ELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNP 166
+LE F G V V I+ ++ KG AY+EF + SV A+ + G I V
Sbjct: 17 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA 76
Query: 167 KRTNR 171
+ +
Sbjct: 77 SQAEK 81
>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 = 32.5 bits (74), Expect = 0.023
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 12/81 (14%)
Query: 93 SIYVGNVDYGATAEE------LESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
SI+VG D E +S F C S I+ + G +G+ ++ F+D++
Sbjct: 3 SIFVG--DLSPEVNESDLVSLFQSRFPSCKSAK---IMTDPVTGVSRGYGFVRFSDENDQ 57
Query: 147 QTAMA-MDESLFRGRQIKVNP 166
Q A+ M GR ++++
Sbjct: 58 QRALIEMQGVYCGGRPMRIST 78
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that 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.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains 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 = 81
Score = 32.7 bits (74), Expect = 0.023
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTAMAM 152
+YVGN+ ELE F G + V + N P GFA++EF D +D+ +
Sbjct: 7 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 61
Query: 153 DESLFRGRQIKV 164
D G +++V
Sbjct: 62 DGRTLCGCRVRV 73
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is
a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 75
Score = 32.4 bits (74), Expect = 0.023
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
+++G + + TAE L +F G + ++ + +GF ++ F+D SV +A
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60
Query: 154 ESLFRGRQIKVNPK 167
G+ K++PK
Sbjct: 61 PHELDGK--KIDPK 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 = 32.4 bits (74), Expect = 0.024
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
IYVGN+ ++E F+ G + + + N+ G P FA++EF D + A+
Sbjct: 2 IYVGNLPGDIRERDIEDLFYKYGPIKAIDLK-NRRRGPP--FAFVEFEDPRDAEDAVRGR 58
Query: 153 DESLFRGRQIKV 164
D F G +++V
Sbjct: 59 DGYDFDGYRLRV 70
>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 = 32.6 bits (74), Expect = 0.024
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++VG+V T +E+ F G+V V I+ +K GH +G +++++ +D A+
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also termed
TARDBP), a ubiquitously expressed pathogenic protein
whose normal function and abnormal aggregation are
directly linked to the genetic disease cystic fibrosis,
and two neurodegenerative disorders: frontotemporal
lobar degeneration (FTLD) and amyotrophic lateral
sclerosis (ALS). TDP-43 binds both DNA and RNA, and has
been implicated in transcriptional repression, pre-mRNA
splicing and translational regulation. TDP-43 is a
dimeric protein with two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
glycine-rich domain. The RRMs are responsible for DNA
and RNA binding; they bind to TAR DNA and RNA sequences
with UG-repeats. The glycine-rich domain can interact
with the hnRNP family proteins to form the hnRNP-rich
complex involved in splicing inhibition. It is also
essential for the cystic fibrosis transmembrane
conductance regulator (CFTR) exon 9-skipping activity. .
Length = 77
Score = 32.4 bits (74), Expect = 0.026
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 96 VGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDES 155
V + + T ++L+ +F G + V + + G KGF ++ FAD + ++
Sbjct: 4 VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ-RH 62
Query: 156 LFRGRQIKVNPKR 168
+ GR V
Sbjct: 63 MIDGRWCDVKIPN 75
>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 = 32.1 bits (74), Expect = 0.032
Identities = 15/75 (20%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VG + +EL F G + + ++ + F G +G+A++ + +K++ Q A+
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAVKQL 62
Query: 154 ESLFR--GRQIKVNP 166
+ G+++ V
Sbjct: 63 HNYEIRPGKRLGVCI 77
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM, but
unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might share
similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 31.9 bits (73), Expect = 0.037
Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 1/73 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA- 151
+++V + A +L+ F G V I+ N + F ++ A + +
Sbjct: 1 NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60
Query: 152 MDESLFRGRQIKV 164
+ + GR I V
Sbjct: 61 LHRTELHGRVISV 73
>gnl|CDD|216246 pfam01017, STAT_alpha, STAT protein, all-alpha domain. STAT
proteins (Signal Transducers and Activators of
Transcription) are a family of transcription factors
that are specifically activated to regulate gene
transcription when cells encounter cytokines and growth
factors. STAT proteins also include an SH2 domain
pfam00017.
Length = 182
Score = 33.4 bits (77), Expect = 0.037
Identities = 11/59 (18%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 35 DEAELAAMKARVREMEEEAEKLKQLQSEVDKQM----SMGSPPNSNNLLNLSIEEKKEA 89
++++ ++ V++ E++ ++L+ LQ E D + S+ P + L ++++K
Sbjct: 7 IDSKVEDLRNSVQDTEQDIKQLEDLQDEFDFRYKTLQSLIETPANGTSLKEHLKQEKLT 65
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 32.3 bits (73), Expect = 0.037
Identities = 16/73 (21%), Positives = 32/73 (43%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
+ I+VG + L +F G + + ++ ++ G +GFA++ F D D+V +
Sbjct: 1 KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60
Query: 152 MDESLFRGRQIKV 164
G +V
Sbjct: 61 QKYHTINGHNCEV 73
>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 = 31.8 bits (73), Expect = 0.046
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFA 141
+YV N+D E L F G++ ++ ++ G KGF ++ F+
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFS 50
>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins
family. This subfamily corresponds to the RRM2 of Hu
proteins family which represents a group of RNA-binding
proteins involved in diverse biological processes. Since
the Hu proteins share high homology with the Drosophila
embryonic lethal abnormal vision (ELAV) protein, the Hu
family is sometimes referred to as the ELAV family.
Drosophila ELAV is exclusively expressed in neurons and
is required for the correct differentiation and survival
of neurons in flies. The neuronal members of the Hu
family include Hu-antigen B (HuB or ELAV-2 or Hel-N1),
Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D
(HuD or ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Moreover, HuR has an anti-apoptotic
function during early cell stress response. It binds to
mRNAs and enhances the expression of several
anti-apoptotic proteins, such as p21waf1, p53, and
prothymosin alpha. HuR also has pro-apoptotic function
by promoting apoptosis when cell death is unavoidable.
Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 79
Score = 31.5 bits (72), Expect = 0.051
Identities = 16/58 (27%), Positives = 27/58 (46%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
+YV + T +ELE+ F G + ILC+ G +G +I F + + A+
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK 60
>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 = 31.4 bits (71), Expect = 0.055
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
I+VGNV T++EL F G V + C+K K +A++ ++ A+ A+
Sbjct: 3 IFVGNVSATCTSDELRGLFEEFGRV----VECDKV----KDYAFVHMEREEEALAAIEAL 54
Query: 153 DESLFRGRQIKV 164
+ +GR+I V
Sbjct: 55 NGKEVKGRRINV 66
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM2 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 31.6 bits (72), Expect = 0.057
Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
R++Y+GN+ + EEL G ++++ I+ K A++ F S+ A+
Sbjct: 4 RNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHFL---SIANAI 53
>gnl|CDD|240948 cd12504, RRM2_hnRNPH_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein (hnRNP) H protein family.
This subfamily corresponds to the RRM2 of hnRNP H
protein family which 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). They
represent a group of nuclear RNA binding proteins that
are involved in pre-mRNA processing, having similar RNA
binding affinities and specifically recognizing the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation. hnRNP
H3 may be involved in the splicing arrest induced by
heat shock. Most family members contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. .
Length = 77
Score = 31.2 bits (71), Expect = 0.062
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 101 YGATAEELESHFHGCGSV-NRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
+G + EE+ F G V N +T+ + G G AY++FA ++S + A+
Sbjct: 10 FGCSKEEIAQFFSGLEIVPNGITLPMDY-RGRSTGEAYVQFASQESAERAL 59
>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM1 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP,
a dual functional protein participating in both viral
RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains.
Length = 79
Score = 31.5 bits (71), Expect = 0.068
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM- 152
I+VG + +EL F G + + ++ + G +G+A++ F K++ Q A+ +
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63
Query: 153 -DESLFRGRQIKV 164
+ + G+ I V
Sbjct: 64 NNHEIRPGKHIGV 76
>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 = 30.9 bits (70), Expect = 0.071
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R ++ GN +Y A E+E F G V+RV + GFA++ D+ + A+
Sbjct: 1 RPVFCGNFEYDARQSEIERLFGKYGRVDRVDM--------KSGFAFVYMEDERDAEDAIR 52
Query: 152 MDESLFRGRQ 161
++ GRQ
Sbjct: 53 GLDNFEFGRQ 62
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM1 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1). Musashi-1 has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover, it
represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 77
Score = 31.1 bits (70), Expect = 0.079
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
+++G + + T E L +F G V ++ + +GF ++ F D+ V +A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
>gnl|CDD|240952 cd12508, RRM2_ESRPs_Fusilli, RNA recognition motif 2 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM2 of ESRPs and Fusilli.
ESRP1 (also termed RBM35A) and ESRP2 (also termed
RBM35B) are epithelial-specific RNA binding proteins
that promote splicing of the epithelial variant of the
fibroblast growth factor receptor 2 (FGFR2), ENAH (also
termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. They are highly conserved
paralogs and specifically bind to GU-rich binding site.
ESRP1 and ESRP2 contain three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes
Drosophila fusilli (fus) gene encoding RNA-binding
protein Fusilli.Loss of fusilli activity causes
lethality during embryogenesis in flies. Drosophila
Fusilli can regulate endogenous FGFR2 splicing and
functions as a splicing factor. It shows high sequence
homology to ESRPs and contains three RRMs as well. It
also has an N-terminal domain with unknown function and
a C-terminal domain particularly rich in alanine,
glutamine, and serine. .
Length = 80
Score = 31.1 bits (71), Expect = 0.081
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 101 YGATAEELESHFHGCGSVNRVT---ILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLF 157
Y ATA ++ + F G V + DG P G A++ F ++ Q A+ +
Sbjct: 11 YSATAADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRALGKHKENL 70
Query: 158 RGRQIKV 164
R I++
Sbjct: 71 GSRYIEL 77
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 31.1 bits (70), Expect = 0.088
Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
+++V N+DY ++L+ F G V R IL +K DG +G + F + ++ A+
Sbjct: 2 TVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDK-DGKSRGIGTVTF--EQPIEAVQAI 58
Query: 153 DESLFRGR 160
S+F G+
Sbjct: 59 --SMFNGQ 64
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, being highly expressed
throughout the brain and in glandular tissues,
moderately expressed in heart, skeletal muscle, and
liver, is also known as bruno-like protein 4 (BRUNOL-4),
or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4
also contain three highly conserved RRMs. The splicing
activation or repression activity of CELF-4 on some
specific substrates is mediated by its RRM1/RRM2. On the
other hand, both RRM1 and RRM2 of CELF-4 can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
being strongly expressed in kidney, brain, and testis,
is also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in a muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element, MSE2.
CELF-6 also promotes skipping of exon 11 of insulin
receptor, a known target of CELF activity that is
expressed in kidney. In addition to three highly
conserved RRMs, CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 30.9 bits (70), Expect = 0.096
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
R ++VG + T +++ F G++ TIL DG+ KG A+++F+ Q A+
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGP-DGNSKGCAFVKFSSHAEAQAAIN 60
>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 = 31.0 bits (71), Expect = 0.098
Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
+YV N+ E+L+ F G + ++ + +G KGF ++ F + ++ Q A+ +
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEEL 62
Query: 153 DESLFRGRQIKV 164
+ G+++ V
Sbjct: 63 NGKEVNGKKLYV 74
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 30.7 bits (69), Expect = 0.10
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 4/81 (4%)
Query: 90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
D ++VGN+ + EL+ F G+V + I G F ++ F D + VQ
Sbjct: 2 DSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQKI 58
Query: 150 MAMDESLFRGR-QIKVNPKRT 169
++ +FRG ++ V K+T
Sbjct: 59 LSNRPIMFRGDVRLNVEEKKT 79
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 30.5 bits (69), Expect = 0.11
Identities = 13/53 (24%), Positives = 27/53 (50%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSV 146
I+VG + T ++++ +F G V ++ +K +GF ++ F +D V
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVV 54
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, 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. .
Length = 84
Score = 30.8 bits (70), Expect = 0.11
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 121 VTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
V I+ NK G P G+ ++EFAD+ + + +
Sbjct: 30 VKIIRNKLTGGPAGYCFVEFADEATAERCL 59
>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM2 of CPEB family of proteins that
bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins has been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to the high sequence similarity, members
in this subfamily may share similar expression patterns
and functions. CPEB-2 is an RNA-binding protein that is
abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation. It directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 81
Score = 30.8 bits (70), Expect = 0.12
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 92 RSIYVGNVDYGATAEELESHF-HGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
R+++VG + TA EL + G V V I ++F +P G A + F ++ S A+
Sbjct: 1 RTVFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKAV 60
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 30.4 bits (69), Expect = 0.14
Identities = 14/75 (18%), Positives = 33/75 (44%), Gaps = 7/75 (9%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
+Y+GN+ +L F + ++L K G+A+++ D+ A+ +
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHK-IPVSSVLVKK-----GGYAFVDCPDQSWADKAIEKL 54
Query: 153 DESLFRGRQIKVNPK 167
+ + +G+ I+V
Sbjct: 55 NGKILQGKVIEVEHS 69
>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 = 30.6 bits (70), Expect = 0.15
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
I+V V A E++ F G + + + ++ G KG+A IE+ K Q A+ +
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68
Query: 153 DESLFRGRQIKVN 165
+ G+ I V+
Sbjct: 69 NGKELLGQTISVD 81
>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. This
subfamily also includes some p54nrb/PSF/PSP1 homologs
from invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior, and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contain a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 71
Score = 29.9 bits (68), Expect = 0.15
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAM 152
++VGN+ T EE + F G V+ V + NK KGF +I + + + A +
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFL--NK----EKGFGFIRLDTRTNAEKAKAEL 57
Query: 153 DESLFRGRQIKV 164
D + +GRQ++V
Sbjct: 58 DGIMRKGRQLRV 69
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a role
in the pre-mRNA splicing process, but is not essential
for growth. Srp1p is closely related to the SR protein
family found in Metazoa. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a glycine
hinge and a RS domain in the middle, and a C-terminal
domain. The family also includes a novel group of
arginine/serine (RS) or serine/arginine (SR) splicing
factors existing in plants, such as A. thaliana RSp31,
RSp35, RSp41 and similar proteins. Like vertebrate RS
splicing factors, these proteins function as plant
splicing factors and play crucial roles in constitutive
and alternative splicing in plants. They all contain two
RRMs at their N-terminus and an RS domain at their
C-terminus.
Length = 70
Score = 30.1 bits (68), Expect = 0.15
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 93 SIYVGNVDYGAT-AEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
+++V D G T E++E F G + R I K FA++EF D + A+
Sbjct: 1 TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALE 52
Query: 151 AMDESLFRGRQIKV 164
A+ S G + V
Sbjct: 53 ALHGSRIDGSVLTV 66
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 2 (Musashi-2) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 79
Score = 30.0 bits (67), Expect = 0.17
Identities = 13/56 (23%), Positives = 29/56 (51%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
+ I+VG + E+++ +F G V ++ +K +GF ++ F ++D V+
Sbjct: 4 KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVE 59
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional and
post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 30.0 bits (67), Expect = 0.18
Identities = 11/54 (20%), Positives = 28/54 (51%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
++VG + T E+++ +F G + + + + +GF ++ + D++ VQ
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQ 55
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 29.9 bits (68), Expect = 0.19
Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 22/91 (24%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
++V N+ T EEL F R+ + G P ++EF D V A A+
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKG--GGP--VCFVEFED---VSFATQAL 57
Query: 153 DESLFRGRQIKVNPKRTNRPGISTTNRGGPR 183
+ +G +S+++RGG R
Sbjct: 58 NS--LQGAV------------LSSSDRGGIR 74
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 2 (Musashi-2 ) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 76
Score = 30.0 bits (67), Expect = 0.21
Identities = 12/58 (20%), Positives = 28/58 (48%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
+++G + + + + L +F G + ++ + +GF ++ FAD SV +A
Sbjct: 2 MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLA 59
>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein M (hnRNP M) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein M (hnRNP M),
myelin expression factor 2 (MEF-2 or MyEF-2 or MST156)
and similar proteins. hnRNP M is pre-mRNA binding
protein that may play an important role in the pre-mRNA
processing. It also preferentially binds to poly(G) and
poly(U) RNA homopolymers. 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). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 29.7 bits (67), Expect = 0.22
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 94 IYVGNVDYGATAEELESHFHG-CGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
+++ N+ Y ++L+ F G V V L +G +G +EF DK+SVQ A+
Sbjct: 2 VFISNIPYDLKWQDLKDLFREKVGEVTYVE-LFKDEEGKSRGCGVVEFKDKESVQKALET 60
Query: 152 MDESLFRGRQIKV 164
M+ +GR++ V
Sbjct: 61 MNRYELKGRKLVV 73
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end)
protein family. This subfamily corresponds to the RRM2
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and component of the NXF1
pathway. It binds to NXF1 and serves as receptor for the
RNA export element RTE. It also possess mRNA export
activity and can facilitate the access of DEAD-box
protein DBP5 to mRNA at the nuclear pore complex (NPC).
RNA-binding protein 15B (RBM15B), also termed one
twenty-two 3 (OTT3), is a paralog of RBM15 and therefore
has post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 29.7 bits (67), Expect = 0.22
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKG--FAYIEFADKDSVQTA 149
R+++VGN++ T EEL F G V V I K +G +A+++F + D A
Sbjct: 3 RTLFVGNLEITITEEELRRAFERYGVVEDVDI---KRPPRGQGNAYAFVKFLNLDMAHRA 59
Query: 150 -MAMDESLFRGRQIKV 164
+AM QIK+
Sbjct: 60 KVAMSGQYIGRNQIKI 75
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 29.9 bits (68), Expect = 0.22
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
R+++V N++ EEL + F G + + C GF + + D + + A
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHR-----GFIMVSYYDIRAARRAKR 56
Query: 151 AMDESLFRGRQIKV 164
A+ + GR++ +
Sbjct: 57 ALQGTELGGRKLDI 70
>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 = 29.8 bits (68), Expect = 0.23
Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
S+YVG++ T L F G V + + + G+AY+ F + + A+
Sbjct: 1 SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDT 60
Query: 152 MDESLFRGRQIKV 164
++ + +G+ I++
Sbjct: 61 LNFDVIKGKPIRI 73
>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 = 29.6 bits (67), Expect = 0.23
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNR-VTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
I + N+ + T E+ + F G + + IL +K G G AY+EF ++ A +
Sbjct: 2 IKIKNIPFDVTKGEVLAFFAGIAIAEQGIHILYDK-TGKTLGEAYVEFVSEEDAMRAERL 60
Query: 153 DESLFRGRQIKV 164
+GR+I +
Sbjct: 61 HRKKLKGREILL 72
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4
(THOC4) and similar proteins. This subgroup corresponds
to the RRM of THOC4, also termed transcriptional
coactivator Aly/REF, or ally of AML-1 and LEF-1, or
bZIP-enhancing factor BEF, an mRNA transporter protein
with a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It is involved in RNA
transportation from the nucleus. THOC4 was initially
identified as a transcription coactivator of LEF-1 and
AML-1 for the TCRalpha enhancer function. In addition,
THOC4 specifically binds to rhesus (RH) promoter in
erythroid. It might be a novel transcription cofactor
for erythroid-specific genes. .
Length = 75
Score = 29.5 bits (67), Expect = 0.24
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFD--GHPKGFAYIEFADKDSVQTAM 150
+ V N+D+G + ++++ F G++ + + +D G G A + F + AM
Sbjct: 3 LLVSNLDFGVSDDDIKELFAEFGALKKAAV---HYDRSGRSLGTADVVFERRADALKAM 58
>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 = 29.8 bits (68), Expect = 0.26
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 12/67 (17%)
Query: 98 NVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGF-AYIEFADKDSVQTA-MAMDES 155
N+ Y T + L F G+V ++ I K G A ++F DSV++A A
Sbjct: 8 NLLYPVTVDVLHQVFSPYGAVEKILIF-EKN----TGVQALVQF---DSVESAENAK--K 57
Query: 156 LFRGRQI 162
GR I
Sbjct: 58 ALNGRNI 64
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein
19 (RBM19) and similar proteins. This subfamily
corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 72
Score = 29.3 bits (66), Expect = 0.31
Identities = 8/36 (22%), Positives = 20/36 (55%)
Query: 129 DGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKV 164
G GFA+++ ++ ++ A+ ++ GR I++
Sbjct: 36 HGRKTGFAFVDLKSEEDLKKALKRNKDYMGGRYIEL 71
>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 = 29.3 bits (65), Expect = 0.35
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESL-FRGRQI 162
T +EL S F G V ++ +K GH G+ ++ + + + A+ L + + I
Sbjct: 14 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTI 73
Query: 163 KVNPKR 168
KV+ R
Sbjct: 74 KVSYAR 79
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 29.3 bits (66), Expect = 0.37
Identities = 15/71 (21%), Positives = 36/71 (50%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
I+VG + T E++ +F G++ + + +K +GF +I F ++ V+ +
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61
Query: 154 ESLFRGRQIKV 164
+ G++++V
Sbjct: 62 FHVIGGKKVEV 72
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which 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 = 84
Score = 29.4 bits (66), Expect = 0.37
Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 16/83 (19%)
Query: 93 SIYVGNVDYGATAEELESHFHGCG--SVNRVTILCNKFDGHPK--------GFAYIEFAD 142
+++V N+++ T + L F RV K PK GF ++ F
Sbjct: 2 TLFVKNLNFSTTNQHLTDAFKHLDGFVFARV-----KTKPDPKRPGQTLSMGFGFVGFKT 56
Query: 143 KDSVQTAM-AMDESLFRGRQIKV 164
K+ Q A+ AMD + G + V
Sbjct: 57 KEQAQAALKAMDGFVLDGHTLVV 79
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 29.1 bits (66), Expect = 0.42
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 129 DGHPKGFAYIEFADKDSVQTAM 150
G KG+A++EFA + + A+
Sbjct: 46 TGKTKGYAFVEFATPEEAKEAV 67
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 28.9 bits (65), Expect = 0.43
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNK 127
R++Y+GN+D T E+L + F G + V L K
Sbjct: 4 RNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREK 39
>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 = 28.8 bits (65), Expect = 0.44
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK 143
+Y+G + Y A ++E F G G + + + GF ++EF D
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDP 43
>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 = 29.1 bits (66), Expect = 0.45
Identities = 18/56 (32%), Positives = 34/56 (60%)
Query: 95 YVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
+VG + AT E++ + F G++ VTI+ +K G KG A+++F+ ++ Q A+
Sbjct: 3 FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAI 58
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 30.8 bits (70), Expect = 0.49
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 36 EAELAAMKARVREMEEEAEKLKQLQSEV 63
EAE+A+++ARV E+ E+L+ L +
Sbjct: 323 EAEIASLEARVAELTARIERLESLLRTI 350
>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM2 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 is a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 83
Score = 28.8 bits (65), Expect = 0.52
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGS-VNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-A 151
+++GN+D + L F G + I+ + G+ KGFA+I + ++ A+ A
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 152 MDESLFRGRQIKV 164
M+ R I V
Sbjct: 64 MNGQYLCNRPITV 76
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair
protein alkB homolog 8 (ALKBH8) and similar proteins.
This subfamily corresponds to the RRM of ALKBH8, also
termed alpha-ketoglutarate-dependent dioxygenase ABH8,
or S-adenosyl-L-methionine-dependent tRNA
methyltransferase ABH8, expressed in various types of
human cancers. It is essential in urothelial carcinoma
cell survival mediated by NOX-1-dependent ROS signals.
ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation of
tRNA modification. ALKBH8 localizes to the cytoplasm. It
contains the characteristic AlkB domain that is composed
of a tRNA methyltransferase motif, a motif homologous to
the bacterial AlkB DNA/RNA repair enzyme, and a
dioxygenase catalytic core domain encompassing
cofactor-binding sites for iron and 2-oxoglutarate. In
addition, unlike other AlkB homologs, ALKBH8 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal S-adenosylmethionine (SAM)-dependent
methyltransferase (MT) domain. .
Length = 80
Score = 28.7 bits (65), Expect = 0.52
Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 8/61 (13%)
Query: 92 RSIYVGNV--DYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
+ + V N G + EEL F G+V + + K + ++ ++ + A
Sbjct: 2 QHLVVANGGLGNGVSREELLRVFEKYGTVEDLVMPPG------KPYCFVSYSSIEDAAAA 55
Query: 150 M 150
Sbjct: 56 Y 56
>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 = 0.56
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-M 152
I+VGNVD + EEL + F G+V ++ + FA++ + + A+ +
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEEL 54
Query: 153 DESLFRGRQIKV 164
+ GR++ V
Sbjct: 55 NGRELHGRKLVV 66
>gnl|CDD|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53
and similar proteins. This subfamily corresponds to the
RRM domain of nucleoporin Nup53, also termed mitotic
phosphoprotein 44 (MP-44), or nuclear pore complex
protein Nup53, required for normal cell growth and
nuclear morphology in vertebrate. It tightly associates
with the nuclear envelope membrane and the nuclear
lamina where it interacts with lamin B. It may also
interact with a group of nucleoporins including Nup93,
Nup155, and Nup205 and play a role in the association of
the mitotic checkpoint protein Mad1 with the nuclear
pore complex (NPC). The family also includes
Saccharomyces cerevisiae Nup53p, an ortholog of
vertebrate nucleoporin Nup53. A unique property of yeast
Nup53p is that it contains an additional Kap121p-binding
domain and interacts specifically with the karyopherin
Kap121p, which is involved in the assembly of Nup53p
into NPCs. Both, vertebrate Nup35 and yeast Nup53p,
contain an atypical RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a C-terminal amphipathic
alpha-helix and several FG repeats. This family
corresponds to the RRM domain which lacks the conserved
residues that typically bind RNA in canonical RRM
domains.
Length = 73
Score = 28.3 bits (64), Expect = 0.60
Identities = 9/70 (12%), Positives = 26/70 (37%), Gaps = 10/70 (14%)
Query: 101 YGATAEELES---HFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLF 157
+G L F CG++ + +++++ + + A++ + ++
Sbjct: 7 FGFPPSALNLVLREFSSCGTI------LEVRYPPGANWIHLKYSSRLEAERALSKNGTII 60
Query: 158 RGR-QIKVNP 166
G + V P
Sbjct: 61 NGGVMVGVKP 70
>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 = 28.4 bits (64), Expect = 0.63
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 10/61 (16%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHP--KGFAYIEFADKDSVQTAM 150
+++VG +D T +EL S F G + V I P KG +++F + + + A+
Sbjct: 3 TVFVGGLDPAVTEDELRSLFGPFGEIVYVKI--------PPGKGCGFVQFVHRAAAEAAI 54
Query: 151 A 151
Sbjct: 55 Q 55
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 28.8 bits (65), Expect = 0.65
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 11/57 (19%)
Query: 129 DGHPKGFAYIEFA---DKDSVQTAMAMDESLFRGRQIKV---NPKRTNRPGISTTNR 179
+G P+GFA++E+A D + Q A++ +G I+V NP RPG S N
Sbjct: 40 NGQPRGFAFVEYATAEDAEEAQQ--ALNGHSLQGSPIRVSFGNP---GRPGASLLNA 91
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface
Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX)
proteins. This subgroup corresponds to the conserved
RNA recognition motif (RRM) in ECTO-NOX proteins (also
termed ENOX), comprising a family of plant and animal
NAD(P)H oxidases exhibiting both, oxidative and protein
disulfide isomerase-like, activities. They are
growth-related and drive cell enlargement, and may play
roles in aging and neurodegenerative diseases. ENOX
proteins function as terminal oxidases of plasma
membrane electron transport (PMET) through catalyzing
electron transport from plasma membrane quinones to
extracellular oxygen, forming water as a product. They
are also hydroquinone oxidases that oxidize externally
supplied NADH, hence NOX. ENOX proteins harbor a
di-copper center that lack flavin. ENOX proteins display
protein disulfide interchange activity that is also
possessed by protein disulfide isomerase. In contrast to
the classic protein disulfide isomerases, ENOX proteins
lack the double CXXC motif. This family includes two
ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed
candidate growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous and
refractory to drugs. ENOX2, also termed APK1 antigen, or
cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role in
cell proliferation and tumor progression. In contrast to
ENOX1, ENOX2 is drug-responsive and harbors a drug
binding site to which the cancer-specific S-peptide
tagged pan-ENOX2 recombinant (scFv) is directed.
Moreover, ENOX2 is specifically inhibited by a variety
of quinone site inhibitors that have anticancer activity
and is unique to the surface of cancer cells. ENOX
proteins contain many functional motifs.
Length = 84
Score = 28.5 bits (64), Expect = 0.65
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
++++VG + AT E + F CG + + I +K K F +I FA++ +V A+
Sbjct: 7 KTVFVGGLPENATEEIIREVFEQCGEI--IAIRMSK-----KNFCHIRFAEEFAVDKAIY 59
Query: 152 M 152
+
Sbjct: 60 L 60
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 28.4 bits (64), Expect = 0.66
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQI 162
T ++L F G+V + +K G K F ++ + + +S Q A+ AM+ G+++
Sbjct: 11 TDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70
Query: 163 KVN 165
KV
Sbjct: 71 KVQ 73
>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused
in Ewing's sarcoma protein (FUS), TATA-binding
protein-associated factor 15 (TAF15) and similar
proteins. This subgroup corresponds to the RRM of FUS
and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed
75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS
(Translocated in liposarcoma), is a member of the FET
(previously TET) (FUS/TLS, EWS, TAF15) family of RNA-
and DNA-binding proteins whose expression is altered in
cancer. It is a multi-functional protein and has been
implicated in pre-mRNA splicing, chromosome stability,
cell spreading, and transcription. FUS was originally
identified in human myxoid and round cell liposarcomas
as an oncogenic fusion with the stress-induced
DNA-binding transcription factor CHOP (CCAAT
enhancer-binding homologous protein) and later as hnRNP
P2, a component of hnRNP H complex assembled on
pre-mRNA. It can form ternary complexes with hnRNP A1
and hnRNP C1/C2. Additional research indicates that FUS
binds preferentially to GGUG-containing RNAs. In the
presence of Mg2+, it can bind both single- and
double-stranded DNA (ssDNA/dsDNA) and promote
ATP-independent annealing of complementary ssDNA and
D-loop formation in superhelical dsDNA. FUS has been
shown to be recruited by single stranded noncoding RNAs
to the regulatory regions of target genes such as cyclin
D1, where it represses transcription by disrupting
complex formation. TAF15 (TAFII68), also termed
TATA-binding protein-associated factor 2N (TAF2N), or
RNA-binding protein 56 (RBP56), originally identified as
a TAF in the general transcription initiation TFIID
complex, is a novel RNA/ssDNA-binding protein with
homology to the proto-oncoproteins FUS and EWS (also
termed EWSR1), belonging to the FET family as well.
TAF15 likely functions in RNA polymerase II (RNAP II)
transcription by interacting with TFIID and subunits of
RNAP II itself. TAF15 is also associated with U1 snRNA,
chromatin and RNA, in a complex distinct from the
Sm-containing U1 snRNP that functions in splicing. Like
other members in the FET family, both FUS and TAF15
contain an N-terminal Ser, Gly, Gln and Tyr-rich region
composed of multiple copies of a degenerate hexapeptide
repeat motif. The C-terminal region consists of a
conserved nuclear import and retention signal (C-NLS), a
C2/C2 zinc-finger motif, a conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and at least 1
arginine-glycine-glycine (RGG)-repeat region. .
Length = 86
Score = 28.8 bits (64), Expect = 0.66
Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 90 DLRSIYVGNVDYGATAEELESHFHGCG--SVNRVT------ILCNKFDGHPKGFAYIEFA 141
D +I+V + T E + +F G N+ T + ++ G KG A + F
Sbjct: 1 DNNTIFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 60
Query: 142 DKDSVQTAMA-MDESLFRGRQIKVN 165
D S + A+ D F G IKV+
Sbjct: 61 DPPSAKAAIDWFDGKEFSGNPIKVS 85
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA binding
motif protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. RBM15B belongs to the Spen (split end) protein
family, which shares a domain architecture comprising of
three N-terminal RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 28.4 bits (63), Expect = 0.71
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-M 150
R++++GN+D+ + EL F G + V I G +A+++F + D A +
Sbjct: 9 RNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIK-RPARGQGGAYAFLKFQNLDMAHRAKV 67
Query: 151 AMDESLFRGRQIKV 164
AM + IK+
Sbjct: 68 AMSGRVIGRNPIKI 81
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 of MRD1. RBM19, also termed RNA-binding
domain-1 (RBD-1), is a nucleolar protein conserved in
eukaryotes involved in ribosome biogenesis by processing
rRNA and is essential for preimplantation development.
It has a unique domain organization containing 6
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). MRD1 is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well conserved in
yeast and its homologues exist in all eukaryotes. MRD1
is present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 28.3 bits (64), Expect = 0.72
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 10/58 (17%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHP--KGFAYIEFADKDSVQTA 149
I V N+ +G T EEL F GS+ R+ + P + A +EF + + A
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSLGRLLL--------PPSRTIALVEFLEPSDARKA 52
>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator. DivIC from B.
subtilis is necessary for both vegetative and
sporulation septum formation. These proteins are mainly
composed of an amino terminal coiled-coil.
Length = 80
Score = 28.3 bits (64), Expect = 0.78
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 36 EAELAAMKARVREMEEEAEKLKQLQSEVDKQ 66
+AELA +KA E+E E + LK ++++
Sbjct: 30 QAELAKLKAENEELEAEVKDLKSDPDYIEER 60
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 28.3 bits (64), Expect = 0.81
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 88 EADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSV 146
E D R I+VG++ T E L F S + ++ +K G KG+ ++ F+D D +
Sbjct: 4 ENDFR-IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62
Query: 147 QTAMAMDESLFRGRQIKVNP 166
+ M+ R IK+
Sbjct: 63 KAMKEMNGKYVGNRPIKLRK 82
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb or NonO or
NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in vertebrates.
p54nrb is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and circadian
rhythm maintenance. PSF is also a multi-functional
protein that binds RNA, single-stranded DNA (ssDNA),
double-stranded DNA (dsDNA) and many factors, and
mediates diverse activities in the cell. PSP1 is a novel
nucleolar factor that accumulates within a new
nucleoplasmic compartment, termed paraspeckles, and
diffusely distributes in the nucleoplasm. The cellular
function of PSP1 remains unknown currently. The family
also includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65. D.
melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 28.0 bits (63), Expect = 0.92
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
++ V N+ + E LE F G V R ++ + G G +EF+ K Q A+
Sbjct: 1 ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDD-RGRSTGEGIVEFSRKPGAQAAIKR 59
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 27.9 bits (63), Expect = 0.93
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 92 RSIYVGNVDYGA-TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++ V N+ +L HF G++ + + + +P+ A ++F+ + + A
Sbjct: 2 TTLEVRNIPPELNNITKLNEHFSKFGTIVNIQV-----NYNPES-ALVQFSTSEEAKKAY 55
Query: 151 AMDESLFRGRQIKV 164
E++F R IKV
Sbjct: 56 RSPEAVFNNRFIKV 69
>gnl|CDD|212670 cd10228, HSPA4_like_NDB, Nucleotide-binding domain of 105/110 kDa
heat shock proteins including HSPA4 and similar
proteins. This subgroup includes the human proteins,
HSPA4 (also known as 70-kDa heat shock protein 4, APG-2,
HS24/P52, hsp70 RY, and HSPH2; the human HSPA4 gene maps
to 5q31.1), HSPA4L (also known as 70-kDa heat shock
protein 4-like, APG-1, HSPH3, and OSP94; the human
HSPA4L gene maps to 4q28), and HSPH1 (also known as heat
shock 105kDa/110kDa protein 1, HSP105; HSP105A; HSP105B;
NY-CO-25; the human HSPH1 gene maps to 13q12.3),
Saccharomyces cerevisiae Sse1p and Sse2p, and a sea
urchin sperm receptor. It belongs to the 105/110 kDa
heat shock protein (HSP105/110) subfamily of the
HSP70-like family, and includes proteins believed to
function generally as co-chaperones of HSP70 chaperones,
acting as nucleotide exchange factors (NEFs), to remove
ADP from their HSP70 chaperone partners during the ATP
hydrolysis cycle. HSP70 chaperones assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Like HSP70
chaperones, HSP105/110s have an N-terminal
nucleotide-binding domain (NBD) and a C-terminal
substrate-binding domain (SBD). For HSP70 chaperones,
the nucleotide sits in a deep cleft formed between the
two lobes of the NBD. The two subdomains of each lobe
change conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is also
regulated by J-domain proteins.
Length = 381
Score = 29.8 bits (68), Expect = 0.97
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 14/42 (33%)
Query: 43 KARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIE 84
KAR+R + EKLK K +S +N L+IE
Sbjct: 259 KARLR-LLAACEKLK-------KVLS------ANTEAPLNIE 286
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 29.6 bits (67), Expect = 0.98
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 89 ADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQT 148
+R++ V NV AT +++ F G + V + + AY+ F D +T
Sbjct: 2 MQVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQS---ENERSQIAYVTFKDPQGAET 58
Query: 149 AM 150
A+
Sbjct: 59 AL 60
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing 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. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 27.9 bits (63), Expect = 1.0
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 22/64 (34%)
Query: 98 NVDYGATAEELESHFHGCGSVNRVTILCNKFDGH-------PKGFAYIEFADKDSVQTAM 150
N+ T E LE F N+F G +G A++EF ++ Q +
Sbjct: 9 NLPEETTKEMLEMLF-------------NQFPGFKEVRLVPRRGIAFVEFETEE--QATV 53
Query: 151 AMDE 154
A+
Sbjct: 54 ALQA 57
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 28.1 bits (62), Expect = 1.1
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADK-DSVQTAMA 151
+I+V N+D+ ++L+ F G+V R I +K DG +G + F ++VQ
Sbjct: 2 TIFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDK-DGKSRGMGTVTFEQPIEAVQAISM 60
Query: 152 MDESLFRGRQIKV 164
+ R + V
Sbjct: 61 FNGQFLFDRPMHV 73
>gnl|CDD|240962 cd12518, RRM_SRSF11, RNA recognition motif in serine/arginine-rich
splicing factor 11 (SRSF11) and similar proteins. This
subgroup corresponds to the RRM of SRSF11, also termed
arginine-rich 54 kDa nuclear protein (SRp54 or p54),
which belongs to a family of proteins containing regions
rich in serine-arginine dipeptides (SR proteins family).
It is involved in bridge-complex formation and splicing
by mediating protein-protein interactions across either
introns or exons. SRSF11 has been identified as a tau
exon 10 splicing repressor. It interacts with a
purine-rich element in exon 10, and suppresses exon 10
inclusion by antagonizing Tra2beta, an
SR-domain-containing protein that enhances exon 10
inclusion. SRSF11 is a unique SR family member and may
regulate the alternative splicing in a tissue- and
substrate-dependent manner. It can directly interact
with the U2 auxiliary factor 65-kDa subunit (U2AF65), a
protein associated with the 3' splice site. In addition,
unlike the typical SR proteins, SRSF11 associates with
other SR proteins but not with the U1 small nuclear
ribonucleoprotein U1-70K or the U2 auxiliary factor
35-kDa subunit (U2AF35). SREK1 has unique properties in
regulating alternative splicing of different pre-mRNAs;
it promotes the use of the distal 5' splice site in E1A
pre-mRNA alternative splicing. It also inhibits cryptic
splice site selection on the beta-globin pre-mRNA
containing competing 5' splice sites. SREK1 contains an
RNA recognition motif (RRM), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and one serine-arginine (SR)-rich domains (SR domains).
.
Length = 80
Score = 28.1 bits (62), Expect = 1.1
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHP----KGFAYIEFADKDSVQTA 149
I V NV A++E++ + F G ++ + + D P +++F D DS +
Sbjct: 2 IQVTNVSPSASSEQMRTLFGFLGKIDELRLF--PPDDSPLPVTSRVCFVKFHDPDSAVVS 59
Query: 150 MAMDESLFRGRQIKVNP 166
+ ++F R + V P
Sbjct: 60 QHLTNTVFVDRALIVVP 76
>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 = 27.9 bits (63), Expect = 1.2
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 4/63 (6%)
Query: 106 EELESHFHGCGSVNRVTILCNKFDGHPK---GFAYIEFADKDSVQTAM-AMDESLFRGRQ 161
E+++ G V V I + +G G ++EFAD + Q A A+ F GR
Sbjct: 26 EDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRT 85
Query: 162 IKV 164
+
Sbjct: 86 VVA 88
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 27.8 bits (62), Expect = 1.2
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
I+V N+ T E++ +H G + V + F+ + K A +EFA ++ A+A
Sbjct: 10 IHVSNLPSDVTEEDVINHLAEHGVIVNVKV----FESNGKKQALVEFATEEQATEALA 63
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 27.5 bits (61), Expect = 1.2
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++VGN+ AT +E+ S F G V I+ K + ++ DK + A+
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAI 51
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 27.7 bits (61), Expect = 1.2
Identities = 13/57 (22%), Positives = 27/57 (47%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
I+VG + E++ +F G V + + + +GF +I F +++ V+ M
Sbjct: 2 IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time
control protein FCA and similar proteins. This subgroup
corresponds to the RRM2 of FCA, a gene controlling
flowering time in Arabidopsis, which encodes a flowering
time control protein that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. The flowering time control
protein FCA contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNP
(ribonucleoprotein domains), and a WW protein
interaction domain. .
Length = 80
Score = 27.9 bits (62), Expect = 1.2
Identities = 14/58 (24%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
++VG ++ AT +E+E F G V + ++ ++ +G A+++++ K+ Q A+
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIK 58
>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin.
This subfamily corresponds to the RRM1 of ubiquitously
expressed protein nucleolin, also termed protein C23.
Nucleolin 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. RRM1,
together with RRM2, binds specifically to RNA stem-loops
containing the sequence (U/G)CCCG(A/G) in the loop. .
Length = 75
Score = 27.8 bits (62), Expect = 1.2
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
S++VGN++ +EL++ S + + + G K F Y++F + ++ A+ +
Sbjct: 2 SLFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRI-GSSKKFGYVDFESAEDLEKALEL 60
Query: 153 DESLFRGRQIKV 164
G +IK+
Sbjct: 61 TGKKLLGNEIKL 72
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms oligomers,
most probably dimers. hnRNP R has been implicated in
mRNA processing and mRNA transport, and also acts as a
regulator to modify binding to ribosomes and RNA
translation. hnRNP R is predominantly located in axons
of motor neurons and to a much lower degree in sensory
axons. In axons of motor neurons, it also functions as a
cytosolic protein and interacts with wild type of
survival motor neuron (SMN) proteins directly, further
providing a molecular link between SMN and the
spliceosome. Moreover, hnRNP R plays an important role
in neural differentiation and development, as well as in
retinal development and light-elicited cellular
activities. hnRNP R contains an acidic auxiliary
N-terminal region, followed by two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RGG motif; hnRNP R binds RNA
through its RRM domains. .
Length = 72
Score = 27.7 bits (61), Expect = 1.2
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++ ++V N+ T E LE F G + RV L K +A++ F ++D+ AM
Sbjct: 1 VKVLFVRNLATTVTEEILEKSFSEFGKLERVKKL--------KDYAFVHFEERDAAVRAM 52
Query: 151 -AMDESLFRGRQIKV 164
M+ G +I++
Sbjct: 53 DEMNGKEIEGEEIEI 67
>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 = 29.5 bits (66), Expect = 1.3
Identities = 23/102 (22%), Positives = 37/102 (36%), Gaps = 18/102 (17%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDG---------HPKGFAYIEFAD 142
R +YVG + E + F+ + T DG K FA++EF
Sbjct: 176 RRLYVGGIPPEFVEEAVVDFFN---DLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRT 232
Query: 143 KDSVQTAMAMDESLFRGRQIKV------NPKRTNRPGISTTN 178
+ AMA+D ++ +K+ P P +S N
Sbjct: 233 VEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKN 274
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 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 shows 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 = 27.4 bits (61), Expect = 1.3
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
+++ + Y A +++ FHG V V I + +G G A ++FA + A+
Sbjct: 2 VFLHGLPYTADEHDVKEFFHGL-DVEDV-IFLKRHNGRNNGNAIVKFATFQDAKEALKRH 59
Query: 154 ESLFRGRQIKVNP 166
L R I++
Sbjct: 60 RELMGSRYIELML 72
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM2 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 27.7 bits (61), Expect = 1.4
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++ V N+ + E LE F G V R ++ + G P G +EFA K S + A+
Sbjct: 1 ALTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDD-RGRPTGKGIVEFAGKPSARKAL 57
>gnl|CDD|179427 PRK02471, PRK02471, bifunctional glutamate--cysteine
ligase/glutathione synthetase; Provisional.
Length = 752
Score = 29.5 bits (67), Expect = 1.5
Identities = 19/46 (41%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 132 PKGFAYIEFADKDSVQTAMAMDESLFRGRQIKVNPKRTN-RPGIST 176
P G EF + A+A D SLF + I V PK TN GIS
Sbjct: 504 PAG---DEFTSLEE---ALA-DYSLFADKAIVVKPKSTNFGLGISI 542
>gnl|CDD|240908 cd12462, RRM_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subgroup corresponds to the RRM of SCAF8 (also
termed CDC5L complex-associated protein 7, or
RNA-binding motif protein 16, or CTD-binding SR-like
protein RA8), 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.
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, together with SCAF4,
represents a new class of SCAFs (SR-like CTD-associated
factors). They contain a conserved N-terminal
CTD-interacting domain (CID), an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and
serine/arginine-rich motifs.
Length = 79
Score = 27.3 bits (60), Expect = 1.6
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 16/69 (23%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
+++VG VD AT ++L + F G + + ++ P+G AY+ M
Sbjct: 4 TLWVGQVDKKATQQDLTNLFEEFGQIESINMI------PPRGCAYV----------CMVH 47
Query: 153 DESLFRGRQ 161
+ +R Q
Sbjct: 48 RQDAYRALQ 56
>gnl|CDD|233791 TIGR02231, TIGR02231, conserved hypothetical protein. This family
consists of proteins over 500 amino acids long in
Caenorhabditis elegans and several bacteria (Pseudomonas
aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans,
etc.). The function is unknown.
Length = 525
Score = 29.3 bits (66), Expect = 1.6
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 36 EAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNN----LLNLSIEEKKEADL 91
+E+ + RE E +L++ SE+ +++ S L+ L E EA+L
Sbjct: 137 GSEIERLLTEDREAERRIRELEKQLSELQNELNALLTGKSQRSHTVLVRLEAPEDAEAEL 196
Query: 92 RSIY-VGNV 99
Y VGN
Sbjct: 197 NLTYQVGNA 205
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome
proliferator-activated receptor gamma coactivator 1A
(PGC-1alpha) family of regulated coactivators. This
subfamily corresponds to the RRM of PGC-1alpha,
PGC-1beta, and PGC-1-related coactivator (PRC), which
serve as mediators between environmental or endogenous
signals and the transcriptional machinery governing
mitochondrial biogenesis. They play an important
integrative role in the control of respiratory gene
expression through interacting with a number of
transcription factors, such as NRF-1, NRF-2, ERR, CREB
and YY1. All family members are multi-domain proteins
containing the N-terminal activation domain, an LXXLL
coactivator signature, a tetrapeptide motif (DHDY)
responsible for HCF binding, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In contrast to PGC-1alpha
and PRC, PGC-1beta possesses two glutamic/aspartic
acid-rich acidic domains, but lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 89
Score = 27.7 bits (62), Expect = 1.6
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTI 123
R IYVG + T EL F G + +T+
Sbjct: 3 RVIYVGKIPIDTTRSELRQRFQPFGEIEEITL 34
>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 = 27.2 bits (60), Expect = 1.6
Identities = 13/57 (22%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++VG + +EL F G + + ++ + FDG +G+A++ + K + A+
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAV 59
>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of
uncharacterized plant proteins similar to fission yeast
Vip1. This subfamily corresponds to the Vip1-like,
uncharacterized proteins found in plants. Although their
biological roles remain unclear, these proteins show
high sequence similarity to the fission yeast Vip1. Like
Vip1 protein, members in this family contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 69
Score = 27.0 bits (60), Expect = 1.7
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
+ V N+ AT ++ F G + V I G AY+ F D + +TA+ +
Sbjct: 1 VEVTNLSPKATERDIYDFFSFSGDIEYVEIQR---SGEQSQTAYVTFKDPQAQETALLL 56
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44
(RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 27.2 bits (60), Expect = 1.7
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 10/79 (12%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-- 151
++VG + + +L SHF V+ +++ C + Y + +A
Sbjct: 2 VHVGGLSPSVSEGDLRSHFQKY-QVSVISL-CKL-----SNYRYASLHFDRASDALLAVK 54
Query: 152 -MDESLFRGRQIKVNPKRT 169
M+ + G IKV +
Sbjct: 55 KMNGGVLSGLSIKVRMVKA 73
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small
nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K)
and similar proteins. This subfamily corresponds to the
RRM of U11/U12-35K, also termed protein HM-1, or U1
snRNP-binding protein homolog, and is one of the
components of the U11/U12 snRNP, which is a subunit of
the minor (U12-dependent) spliceosome required for
splicing U12-type nuclear pre-mRNA introns. U11/U12-35K
is highly conserved among bilateria and plants, but
lacks in some organisms, such as Saccharomyces
cerevisiae and Caenorhabditis elegans. Moreover,
U11/U12-35K shows significant sequence homology to U1
snRNP-specific 70 kDa protein (U1-70K or snRNP70). It
contains a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5' splice
site recognition in the minor spliceosome and play a
role in exon bridging, interacting with components of
the major spliceosome bound to the pyrimidine tract of
an upstream U2-type intron. The family corresponds to
the RRM of U11/U12-35K that may directly contact the U11
or U12 snRNA through the RRM domain.
Length = 93
Score = 27.6 bits (62), Expect = 1.7
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFAD-KDSVQTA 149
+++VG + T E L F G + R+ ++ + G KG+A++E+ +D+++
Sbjct: 3 YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62
Query: 150 MAMDESLFRGRQIKV 164
+ + G +I V
Sbjct: 63 RDAHKLVIDGSEIFV 77
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 27.3 bits (60), Expect = 1.8
Identities = 14/57 (24%), Positives = 31/57 (54%)
Query: 91 LRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQ 147
++ I+VG ++ AT E++ +F G + + + + +GF +I F ++D V+
Sbjct: 4 VKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVK 60
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 29.1 bits (65), Expect = 2.0
Identities = 22/52 (42%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 41 AMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEE-KKEADL 91
A+K VRE+E E EKLK+ + + S P LN IE+ KKE DL
Sbjct: 426 AVKTPVRELEGEVEKLKEQILKAKE--SSSKPSEL--ALNEMIEKLKKEIDL 473
>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 77
Score = 27.3 bits (60), Expect = 2.0
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAM 152
I+V N+ + T ++L+ F CG V I +G KG + F +S + A M
Sbjct: 2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKACRLM 59
Query: 153 DESLFRGRQIKVNPKR 168
+ GR+I V R
Sbjct: 60 NGIKINGREIDVRLDR 75
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (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. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 27.1 bits (60), Expect = 2.1
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AM 152
IYVGN+ +++E F+ G++ + L N+ G P FA++EF D + A+
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAIRDID-LKNR-RGPP--FAFVEFEDPRDAEDAVYGR 57
Query: 153 DESLFRGRQIKVNPKR 168
D + G +++V R
Sbjct: 58 DGYDYDGYRLRVEFPR 73
>gnl|CDD|240950 cd12506, RRM3_hnRNPH_CRSF1_like, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1) and similar
proteins. This subfamily corresponds to the RRM3 of
hnRNP H proteins and GRSF-1. The hnRNP H protein family
includes hnRNP H (also termed mcs94-1), hnRNP H2 (also
termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also
termed hnRNP 2H9), which represent a group of nuclear
RNA binding proteins that are involved in pre-mRNA
processing. These proteins have similar RNA binding
affinities and specifically recognize the sequence GGGA.
They can either stimulate or repress splicing upon
binding to a GGG motif. hnRNP H binds to the RNA
substrate in the presence or absence of these proteins,
whereas hnRNP F binds to the nuclear mRNA only in the
presence of cap-binding proteins. hnRNP H and hnRNP H2
are almost identical; both have been found to bind
nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements downstream
of the 5' splice site in the transcripts of c-src, human
immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and
myelin. It silences exons when bound to exonic elements
in the transcripts of beta-tropomyosin, HIV-1, and
alpha-tropomyosin. hnRNP H2 has been implicated in
pre-mRNA 3' end formation. hnRNP H3 may be involved in
the splicing arrest induced by heat shock. Most family
members contain three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and they
play an important role in efficiently silencing the
exon. For instance, members in this family can regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, the family members have an extensive
glycine-rich region near the C-terminus, which may allow
them to homo- or heterodimerize. The family also
includes a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. It may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 also contains
three potential RRMs responsible for the RNA binding,
and two auxiliary domains (an acidic alpha-helical
domain and an N-terminal alanine-rich region) that may
play a role in protein-protein interactions and provide
binding specificity. .
Length = 75
Score = 26.9 bits (60), Expect = 2.3
Identities = 21/62 (33%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 101 YGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGR 160
Y AT ++ F VN V I N DG G A +EFA + AM+ D R
Sbjct: 10 YRATENDIFEFFSPLNPVN-VRIEYNA-DGRATGEADVEFATHEDAVAAMSKDREHMGHR 67
Query: 161 QI 162
I
Sbjct: 68 YI 69
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 26.9 bits (59), Expect = 2.3
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++ V N+ + E LE F G V R ++ + G P G ++EFA K + + A+
Sbjct: 1 ALTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDD-RGRPTGKGFVEFAAKPAARKAL 57
>gnl|CDD|197544 smart00150, SPEC, Spectrin repeats.
Length = 101
Score = 27.3 bits (61), Expect = 2.5
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 3 DQENSFIHEEENF----ENGDHIENGDMEADQSKCTD-EAELAAMKARVREMEEEAEKLK 57
D+ +++ E+E + G +E+ +EA K EAEL A + RV + E E+L
Sbjct: 8 DELEAWLEEKEQLLASEDLGKDLES--VEALLKKHEAFEAELEAHEERVEALNELGEQLI 65
Query: 58 QLQSE 62
+
Sbjct: 66 EEGHP 70
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 28.4 bits (64), Expect = 2.6
Identities = 16/52 (30%), Positives = 29/52 (55%)
Query: 37 AELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKE 88
EL ++ ++E+EEE EK+K+L ++ K+ PP L +E K++
Sbjct: 334 EELKELEEELKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEK 385
>gnl|CDD|241175 cd12731, RRM2_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM2 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; both have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 83
Score = 26.9 bits (59), Expect = 2.8
Identities = 16/64 (25%), Positives = 29/64 (45%)
Query: 101 YGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGR 160
+G + EE+ F G V L F G G A+++FA ++ + A+ + R
Sbjct: 11 FGCSKEEIVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHR 70
Query: 161 QIKV 164
I++
Sbjct: 71 YIEI 74
>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 = 26.8 bits (59), Expect = 2.8
Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA 151
++VG + +EL F G + ++ +F G +G+A++ + K+ Q A+
Sbjct: 2 CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMM-EFSGENRGYAFVMYTTKEEAQLAIR 60
Query: 152 M 152
+
Sbjct: 61 I 61
>gnl|CDD|240416 PTZ00432, PTZ00432, falcilysin; Provisional.
Length = 1119
Score = 28.6 bits (64), Expect = 2.8
Identities = 21/99 (21%), Positives = 42/99 (42%), Gaps = 11/99 (11%)
Query: 43 KARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSIYVGNVDYG 102
K +V EME+ EK K+ + D P + ++ LS+ + + + Y
Sbjct: 600 KEQVDEMEKAYEKFKKEREADD------DPEHLDSFPILSLSDLNKETEE---IPTKLYK 650
Query: 103 ATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFA 141
+++ L+ + VT+L + + G Y++FA
Sbjct: 651 LSSDSLKENMDLDSDGGSVTVLVHPIESR--GILYLDFA 687
>gnl|CDD|241176 cd12732, RRM2_hnRNPH3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H') and hnRNP F. This family
is involved in mRNA processing and exhibit extensive
sequence homology. Currently, little is known about the
functions of hnRNP H3 except for its role in the
splicing arrest induced by heat shock. In addition, the
typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and play an important role in efficiently silencing the
exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, like other hnRNP H protein family members,
hnRNP H3 has an extensive glycine-rich region near the
C-terminus, which may allow it to homo- or
heterodimerize. .
Length = 96
Score = 26.9 bits (59), Expect = 3.0
Identities = 16/64 (25%), Positives = 29/64 (45%)
Query: 101 YGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGR 160
+G + EE+ F G V L + G G A+++FA K+ + A+ + R
Sbjct: 28 FGCSKEEIVQFFSGLEIVPNGITLTMDYQGRSTGEAFVQFASKEIAENALGKHKERIGHR 87
Query: 161 QIKV 164
I++
Sbjct: 88 YIEI 91
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein
homolog alpha (TRA-2 alpha) and similar proteins. This
subgroup corresponds to the RRM of TRA2-alpha or
TRA-2-alpha, also termed transformer-2 protein homolog
A, a mammalian homolog of Drosophila transformer-2
(Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR)
protein (SRp40) that specifically binds to
gonadotropin-releasing hormone (GnRH) exonic splicing
enhancer on exon 4 (ESE4) and is necessary for enhanced
GnRH pre-mRNA splicing. It strongly stimulates GnRH
intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-alpha contains a well conserved
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
flanked by the N- and C-terminal arginine/serine
(RS)-rich regions. .
Length = 79
Score = 26.5 bits (58), Expect = 3.1
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESL-FRGRQI 162
T +L F G + V ++ ++ G +GFA++ F D + AM + GR+I
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRI 71
Query: 163 KVN 165
+V+
Sbjct: 72 RVD 74
>gnl|CDD|217469 pfam03276, Gag_spuma, Spumavirus gag protein.
Length = 582
Score = 28.3 bits (63), Expect = 3.2
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 7/50 (14%)
Query: 158 RGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGYRPVRRAR 207
RG+ I+ P+ + +S RGRGRG+ + R R R
Sbjct: 431 RGQSIRFLPQSDQQRPVS-------RGRGRGQRGPRSQPQNQRRQQNRGR 473
Score = 27.6 bits (61), Expect = 5.6
Identities = 13/44 (29%), Positives = 18/44 (40%)
Query: 158 RGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGYR 201
+GR+ NP R + G S + P RG + G G R
Sbjct: 523 QGRRWNPNPYRQSGQGRSQQQQPQPEARGNQSRTPGPGRGQGGR 566
>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM3 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 77
Score = 26.5 bits (58), Expect = 3.4
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 3/76 (3%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-MAM 152
I+V N+ + T + L+ F+ CG V I +G KG + F + + A M
Sbjct: 2 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERACRMM 59
Query: 153 DESLFRGRQIKVNPKR 168
+ GR+I V R
Sbjct: 60 NGYKLNGREIDVRIDR 75
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM2 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed
BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-1 is strongly expressed in all adult
and fetal tissues tested. Human CELF-1 is a nuclear and
cytoplasmic RNA-binding protein that regulates multiple
aspects of nuclear and cytoplasmic mRNA processing, with
implications for onset of type 1 myotonic dystrophy
(DM1), a neuromuscular disease associated with an
unstable CUG triplet expansion in the 3'-UTR
(3'-untranslated region) of the DMPK (myotonic dystrophy
protein kinase) gene; it preferentially targets UGU-rich
mRNA elements. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
binds specifically to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contains three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it preferentially binds
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contains three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are also
important for localization in the cytoplasm. The
splicing activation or repression activity of CELF-2 on
some specific substrates is mediated by RRM1/RRM2. Both,
RRM1 and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 26.6 bits (58), Expect = 3.4
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM- 150
R +++G V ++ F G + IL DG +G A++ F + QTA+
Sbjct: 2 RKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIK 60
Query: 151 AMDES 155
AM ++
Sbjct: 61 AMHQA 65
>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
Length = 371
Score = 28.2 bits (64), Expect = 3.6
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 180 GGPRGRGRGRVSRGA 194
GG RG GR R RGA
Sbjct: 102 GGGRGGGRQRARRGA 116
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM2 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 26.1 bits (57), Expect = 3.7
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFA-DKDSVQTAMAM 152
++VGN+ T +EL + F G V I+ K +A++ +D+V+ +
Sbjct: 3 LHVGNISSSCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGL 54
Query: 153 DESLFRGRQIKV 164
D + F+G+++ V
Sbjct: 55 DNTEFQGKRMHV 66
>gnl|CDD|178359 PLN02759, PLN02759, Formate--tetrahydrofolate ligase.
Length = 637
Score = 28.2 bits (63), Expect = 3.7
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 79 LNLSIEEKKEADLRSIY-VGNVDYGATAEE 107
L++SI+EK EA + Y V+Y AE
Sbjct: 520 LDISIKEKIEAIAKESYGADGVEYSEQAEA 549
>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein
(TBPIP). This family consists of several eukaryotic
TBP-1 interacting protein (TBPIP) sequences. TBP-1 has
been demonstrated to interact with the human
immunodeficiency virus type 1 (HIV-1) viral protein Tat,
then modulate the essential replication process of HIV.
In addition, TBP-1 has been shown to be a component of
the 26S proteasome, a basic multiprotein complex that
degrades ubiquitinated proteins in an ATP-dependent
fashion. Human TBPIP interacts with human TBP-1 then
modulates the inhibitory action of human TBP-1 on
HIV-Tat-mediated transactivation.
Length = 169
Score = 27.7 bits (62), Expect = 3.7
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 37 AELAAMKARVREMEEEAEKLKQLQSEVDKQM-SMGSPPNSNNLLNLSIEEKKE 88
EL + + E+ EE + LKQ S ++ ++ S+ S + L E KKE
Sbjct: 72 EELNKLDMEIEELREEVQLLKQDCSTLEIELKSLTSDLTTEELQEEIQELKKE 124
>gnl|CDD|240960 cd12516, RRM1_RBM26, RNA recognition motif 1 of vertebrate
RNA-binding protein 26 (RBM26). This subgroup
corresponds to the RRM1 of RBM26, also known as
cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2,
which represents a cutaneous lymphoma (CL)-associated
antigen. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The RRMs may play some
functional roles in RNA-binding or protein-protein
interactions. .
Length = 76
Score = 26.2 bits (57), Expect = 3.9
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 107 ELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFRGRQIKV 164
+L HF G++ + + + G P+G A I+FA + + A++ E++ R IKV
Sbjct: 18 KLNEHFSKFGTLVNLQV---AYKGDPEG-ALIQFATHEEAKKAISSTEAVLNNRFIKV 71
>gnl|CDD|215918 pfam00435, Spectrin, Spectrin repeat. Spectrin repeat-domains
are found in several proteins involved in cytoskeletal
structure. These include spectrin, alpha-actinin and
dystrophin. The sequence repeat used in this family is
taken from the structural repeat in reference. The
spectrin domain- repeat forms a three helix bundle. The
second helix is interrupted by proline in some
sequences. The repeats are defined by a characteristic
tryptophan (W) residue at position 17 in helix A and a
leucine (L) at 2 residues from the carboxyl end of
helix C. Although the domain occurs in ultiple repeats
along sequences, the domains are actually stable on
their own - ie they act, biophysically, like domains
rather than repeats that along function when
aggregated.
Length = 105
Score = 26.9 bits (60), Expect = 4.0
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 3 DQENSFIHEEENF----ENGDHIENGDMEADQSKCTD-EAELAAMKARVREMEEEAEKLK 57
D S+I E+E + G +E+ ++A K EAELAA + RV + E AEKL
Sbjct: 11 DDLESWIEEKEALLSSEDYGKDLES--VQALLKKHKALEAELAAHQDRVEALNELAEKLI 68
Query: 58 Q 58
Sbjct: 69 A 69
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 28.1 bits (63), Expect = 4.1
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 36 EAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEADLR 92
E EL ++A +R++E LK+ + E++ Q+ L IE+K++
Sbjct: 867 EEELEELEAALRDLESRLGDLKKERDELEAQLR--ELERKIEELEAQIEKKRKRLSE 921
>gnl|CDD|115307 pfam06637, PV-1, PV-1 protein (PLVAP). This family consists of
several PV-1 (PLVAP) proteins which seem to be specific
to mammals. PV-1 is a novel protein component of the
endothelial fenestral and stomatal diaphragms. The
function of this family is unknown.
Length = 442
Score = 28.1 bits (62), Expect = 4.2
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 28/92 (30%)
Query: 30 QSKCTDEAELA-----AMKAR----VREMEEEAEKLKQLQSEVDKQMS------------ 68
Q++C + +LA A++A +E+E + + +QL+ E+ ++S
Sbjct: 337 QAECARQTQLALEEKAALRAERDNLAKELEAKKREAEQLRMELAIRISALDTCIKAKSLP 396
Query: 69 -------MGSPPNSNNLLNLSIEEKKEADLRS 93
MG PPN + S+EE K+ L S
Sbjct: 397 AMPPSRPMGPPPNPPPIDPASLEEFKKKILES 428
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 28.0 bits (63), Expect = 4.3
Identities = 23/93 (24%), Positives = 36/93 (38%), Gaps = 14/93 (15%)
Query: 2 SDQENSFIHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQS 61
E + EE + + E + K E EL+ + + E EEE E+L Q
Sbjct: 79 QRLERRLLQREETLDRKMESLDKKEENLEKK---EKELSNKEKNLDEKEEELEELIAEQR 135
Query: 62 EVDKQMSMGSPPNSNNLLNLSIEEKKEADLRSI 94
E +++S L+ EE KE L +
Sbjct: 136 EELERIS-----------GLTQEEAKEILLEEV 157
>gnl|CDD|149906 pfam08988, DUF1895, Protein of unknown function (DUF1895). The
YscE protein, produced by the pathogen Yersinia,
assumes a secondary structure composed of two
anti-parallel alpha-helices separated by a flexible
loop. The function of this protein is, as yet, unknown.
Length = 68
Score = 26.0 bits (57), Expect = 4.6
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 44 ARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEAD 90
A + E +L+Q Q++V +Q+ +G P L +K+AD
Sbjct: 11 ADPETVREITMQLEQAQTDVKRQLDLGGDPQQYQLW------QKQAD 51
>gnl|CDD|129266 TIGR00162, TIGR00162, TIGR00162 family protein. This model
represents one out of two closely related ortholgous
sets of proteins that, so far, are found only in but are
universal among the Archaea. This ortholog set includes
MJ1210 from Methanococcus jannaschii and AF0525 from
Archaeoglobus fulgidus while excluding MJ0106 and AF1251
[Hypothetical proteins, Conserved].
Length = 188
Score = 27.5 bits (61), Expect = 4.7
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 36 EAELAAMKARVREMEEEAEKLKQLQSEVDKQM 67
E + A++ R +EME+ K+K+++ E+ +Q
Sbjct: 144 EVSVEALEERAKEMEKIIAKIKEMEEEMVQQW 175
>gnl|CDD|181731 PRK09257, PRK09257, aromatic amino acid aminotransferase;
Provisional.
Length = 396
Score = 27.8 bits (63), Expect = 4.7
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 36 EAELAAMKARVREMEEE-AEKLKQ 58
EAEL M+ R++ M + E LK
Sbjct: 308 EAELEEMRERIKAMRQLLVEALKA 331
>gnl|CDD|225471 COG2919, COG2919, Septum formation initiator [Cell division and
chromosome partitioning].
Length = 117
Score = 26.5 bits (59), Expect = 4.8
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 36 EAELAAMKARVREMEEEAEKLKQLQSEVDKQ 66
+AEL + AR +E E + LK + ++++
Sbjct: 63 QAELEKLSARNTALEAEIKDLKDGRDYIEER 93
>gnl|CDD|198438 cd10288, prolactin_like, Prolactin (PRL or PRL1), chorionic
somatomammotropin, and related pituitary gland hormones.
Prolactin is primarily responsible for stimulating milk
production and breast development in mammals. Aside from
roles in reproduction, various functions have been
attributed to prolactin, more than for other pituitary
gland hormones combined. These are roles in growth and
development, metamorphosis, metabolism of lipids,
carbohydrates, and steroids, brain biochemistry and even
immunoregulation, among others. Most of these roles are
poorly understood, but it has become clear that many
prolactin-like hormones are actually produced in the
placenta and not the pituitary.
Length = 199
Score = 27.2 bits (61), Expect = 4.9
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 12/64 (18%)
Query: 37 AELAAMK-------ARVREMEEEAEKLKQLQSEVDKQMSMGSPPNSNNLLNLSIEEKKEA 89
EL++MK ++ +E+EE K K+L + + +S P N
Sbjct: 100 TELSSMKGAPDTILSKAKEIEE---KNKELLEGLKRILSRVQPGIEENEDYPVWSGL--P 154
Query: 90 DLRS 93
L+S
Sbjct: 155 SLQS 158
>gnl|CDD|184060 PRK13453, PRK13453, F0F1 ATP synthase subunit B; Provisional.
Length = 173
Score = 27.2 bits (60), Expect = 5.0
Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 27 EADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQM 67
E D ++ D+AE A + A+ E EE +KLK+ Q EV K +
Sbjct: 51 ERDINRDIDDAEQAKLNAQKLE-EENKQKLKETQEEVQKIL 90
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 27.4 bits (61), Expect = 5.2
Identities = 11/54 (20%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 5 ENSFIHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQ 58
E+ E+ FE + E + + +E ++ +K +++EE +KL+
Sbjct: 26 EDKGKEEDLEFEEIEKEEIIEDSEES----NEVKIEELKDENNKLKEENKKLEN 75
>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM3 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 107
Score = 26.5 bits (58), Expect = 5.2
Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMA-MDESLFRGRQI 162
T + L + F G V RV IL NK D A I+ AD + Q AM+ ++ G+ I
Sbjct: 27 TPQSLFTLFGVYGDVQRVKILYNKKDS-----ALIQMADGNQSQLAMSHLNGQKMYGKII 81
Query: 163 KV 164
+V
Sbjct: 82 RV 83
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 25.7 bits (57), Expect = 5.6
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKF--DGHPKGFAYIEFADKDSVQTAMA 151
+ V N+ G ++L F + +T + K+ DG + F ++ + ++ Q A+
Sbjct: 3 LIVKNLPKGIKEDKLRKLF---EAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALK 59
Query: 152 -MDESLFRGRQIKVNP 166
+ S +I V
Sbjct: 60 HFNNSFIDTSKITVEI 75
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 85
Score = 26.2 bits (57), Expect = 5.6
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 103 ATAEELESHFHGCGSVNR-VTILCNKFDGHPKGFAYIEF 140
AT ++ G R V ++ NK G +GFA++EF
Sbjct: 14 ATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEF 52
>gnl|CDD|179868 PRK04612, argD, acetylornithine transaminase protein; Provisional.
Length = 408
Score = 27.6 bits (61), Expect = 5.7
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 132 PKGFAYIEFADKDSVQTAMA 151
P GF Y++F D ++++ AMA
Sbjct: 165 PGGFRYVDFNDVEALEAAMA 184
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 25.7 bits (57), Expect = 6.3
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 104 TAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMDESLFR-GRQI 162
T +L F G + +V ++ ++ G +GF ++ F + + A + GR+I
Sbjct: 12 TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRI 71
Query: 163 KV 164
+V
Sbjct: 72 RV 73
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 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 and also
regulates 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 = 81
Score = 25.8 bits (56), Expect = 6.5
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++YV + T +ELE F G + IL ++ G +G +I F + + A+
Sbjct: 4 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is an integral part of the U2
small nuclear ribonucleoprotein (snRNP) and the U11/U12
di-snRNP. SF3B is essential for the accurate excision of
introns from pre-messenger RNA and has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 25.7 bits (57), Expect = 6.6
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 90 DLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
R +YV N+ + ++EEL F G++ ++ I K +G A++ + D + A
Sbjct: 1 VNRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTK---ETRGTAFVVYEDIYDAKNA 57
Query: 150 M 150
Sbjct: 58 C 58
>gnl|CDD|227880 COG5593, COG5593, Nucleic-acid-binding protein possibly involved in
ribosomal biogenesis [Translation, ribosomal structure
and biogenesis].
Length = 821
Score = 27.3 bits (60), Expect = 7.0
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 9/89 (10%)
Query: 1 MSDQENSFIHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQL- 59
++ E++F D +D D + K+ + ++ E L ++
Sbjct: 703 DDSDDSELDFAEDDFS--------DSTSDDEPKLDAIDDEDAKSEGSQESDQEEGLDEIF 754
Query: 60 QSEVDKQMSMGSPPNSNNLLNLSIEEKKE 88
S +Q + S S+ S EEK+E
Sbjct: 755 YSFDGEQDNSDSFAESSEEDESSEEEKEE 783
>gnl|CDD|218126 pfam04520, Senescence_reg, Senescence regulator. This protein
regulates the expression of proteins associated with
leaf senescence in plants.
Length = 146
Score = 26.6 bits (59), Expect = 7.1
Identities = 16/66 (24%), Positives = 23/66 (34%)
Query: 139 EFADKDSVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYG 198
E + D A ++ L R KR R +++ R P+ GR G A
Sbjct: 4 ELDESDVWWVASSVPGPLARSSGSSPAFKRGLRGPPTSSARTIPKIPKGGRAGAGGAKAA 63
Query: 199 GYRPVR 204
PV
Sbjct: 64 SSAPVN 69
>gnl|CDD|220635 pfam10221, DUF2151, Cell cycle and development regulator. This is
a set of proteins conserved from worms to humans. The
proteins are a PAN GU kinase substrate, Mat89Bb,
essential for S-M cycles of early Drosophila
embryogenesis, Xenopus embryonic cell cycles and
morphogenesis, and cell division in cultured mammalian
cells.
Length = 692
Score = 27.1 bits (60), Expect = 7.4
Identities = 19/77 (24%), Positives = 26/77 (33%), Gaps = 8/77 (10%)
Query: 11 EEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMG 70
EE+ E GD + E K A+ + + E LK+ + D S
Sbjct: 572 LEEDDEAGDKMF--VKEPFFEKTRGTADTEEGEG---SGDREKNMLKEFEKYTD---SPD 623
Query: 71 SPPNSNNLLNLSIEEKK 87
SP N IEE
Sbjct: 624 SPEPLEKKKNAKIEELL 640
>gnl|CDD|203875 pfam08206, OB_RNB, Ribonuclease B OB domain. This family includes
the N-terminal OB domain found in ribonuclease B
proteins in one or two copies.
Length = 58
Score = 25.2 bits (56), Expect = 7.4
Identities = 18/72 (25%), Positives = 26/72 (36%), Gaps = 22/72 (30%)
Query: 127 KFDGHPKGFAY--IEFADKD----SVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRG 180
GH KGF + + + D Q AM G ++ V + +R
Sbjct: 2 TVRGHKKGFGFLIPDDEEDDIFIPPEQMKKAMH-----GDRVLVRITKGDR--------- 47
Query: 181 GPRGRGRGRVSR 192
RGR GR+ R
Sbjct: 48 --RGRREGRIVR 57
>gnl|CDD|241173 cd12729, RRM1_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM1 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F. These represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical. Both of them
have been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 79
Score = 25.6 bits (56), Expect = 7.7
Identities = 14/66 (21%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 101 YGATAEELESHFHGCGSVNRVTILCNKF--DGHPKGFAYIEFADKDSVQTAMAMDESLFR 158
+ + +E++ F C N + + + +G P G A++E ++ V+ A+ D
Sbjct: 11 WSCSVDEVQRFFSDCKIANGASGIHFIYTREGRPSGEAFVELESEEDVKLALKKDRETMG 70
Query: 159 GRQIKV 164
R ++V
Sbjct: 71 HRYVEV 76
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 25.2 bits (56), Expect = 7.7
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 94 IYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAMD 153
++VG + + ELE F G++ R+ +D + +AYIE+ ++ Q A
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRI-----DYDPG-RNYAYIEYESIEAAQAAKEAL 54
Query: 154 ESLF---RGRQIKV 164
GR+++V
Sbjct: 55 RGFPLGGPGRRLRV 68
>gnl|CDD|240716 cd12270, RRM_MTHFSD, RNA recognition motif in vertebrate
methenyltetrahydrofolate synthetase domain-containing
proteins. This subfamily corresponds to
methenyltetrahydrofolate synthetase domain (MTHFSD), a
putative RNA-binding protein found in various vertebrate
species. It contains an N-terminal
5-formyltetrahydrofolate cyclo-ligase domain and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The biological role of MTHFSD remains unclear. .
Length = 74
Score = 25.4 bits (56), Expect = 7.9
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 10/80 (12%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAMAM 152
++ VGN+ +L+S V L + G +G A++ F DKD+
Sbjct: 1 TVKVGNISRNLRVSDLKSALR----ERGVKPLRITWQGA-RGKAFLHFPDKDAAD----A 51
Query: 153 DESLFRGRQIKVNPKRTNRP 172
D +L +Q+ + T
Sbjct: 52 DSALASLQQLSIGGN-TLTV 70
>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 = 25.7 bits (57), Expect = 8.0
Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 116 GSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQI 162
G + + + N D H G Y++F ++ + A+ A++ + GR +
Sbjct: 50 GEIEDLVVCDNLGD-HLLGNVYVKFETEEDAEAALQALNGRYYAGRPL 96
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, a novel
mRNA export factor and component of the NXF1 pathway. It
binds to NXF1 and serves as receptor for the RNA export
element RTE. It also possesses mRNA export activity and
can facilitate the access of DEAD-box protein DBP5 to
mRNA at the nuclear pore complex (NPC). RBM15 belongs to
the Spen (split end) protein family, which contain three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 25.7 bits (56), Expect = 8.0
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 92 RSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA-M 150
R++++GN+D T +L F G + V I G + +++F + D A +
Sbjct: 8 RTLFLGNLDITVTETDLRRAFDRFGVITEVDIK-RPGRGQTSTYGFLKFENLDMAHRAKL 66
Query: 151 AMDESLFRGRQIKV 164
AM + R IK+
Sbjct: 67 AMSGKVLRRNPIKI 80
>gnl|CDD|233311 TIGR01208, rmlA_long, glucose-1-phosphate thymidylylransferase,
long form. The family of known and putative
glucose-1-phosphate thymidyltransferase (also called
dTDP-glucose synthase) shows a deep split into a short
form (see TIGR01207) and a long form described by this
model. The homotetrameric short form is found in
numerous bacterial species that incorporate
dTDP-L-rhamnose, which it helps synthesize, into the
cell wall. It is subject to feedback inhibition. This
form, in contrast, is found in many species for which it
serves as a sugar-activating enzyme for antibiotic
biosynthesis and or other, unknown pathways, and in
which dTDP-L-rhamnose is not necessarily produced.
Alternate name: dTDP-D-glucose synthase.
Length = 353
Score = 27.0 bits (60), Expect = 8.2
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 5 ENSFIHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVRE 48
ENS+I + G I + ++E S DE+ + ++AR+ +
Sbjct: 281 ENSYIGPYTSIGEGVVIRDAEVE--HSIVLDESVIEGVQARIVD 322
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Raver-2 contains three N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two [SG][IL]LGxxP motifs.
Raver-2 binds to PTB through the SLLGEPP motif only, and
binds to RNA through its RRMs. .
Length = 98
Score = 25.6 bits (56), Expect = 8.2
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 129 DGHPKGFAYIEFADKDSVQTAM-AMDESLFRGRQIKVNPKRTNRPGIST 176
GFA +E+ + + AMD + +G +I+++ PG ST
Sbjct: 40 GSCVGGFAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSFCAPGAPGRST 88
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 27.1 bits (61), Expect = 8.3
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 35 DEAELAAMKARVREMEEEAEKLKQLQSEVDKQ 66
+ EL + RV ++E+E ++LK V +
Sbjct: 367 YDTELEVLLQRVEQLEQELKQLKAQPVGVAPE 398
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 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. It 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 = 90
Score = 25.5 bits (55), Expect = 8.3
Identities = 15/58 (25%), Positives = 27/58 (46%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTAM 150
++YV + T +ELE F G + IL ++ G +G +I F + + A+
Sbjct: 7 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64
>gnl|CDD|241164 cd12720, RRM_SYNJ2, RNA recognition motif in synaptojanin-2 and
similar proteins. This subgroup corresponds to the RRM
of synaptojanin-2, also termed synaptic
inositol-1,4,5-trisphosphate 5-phosphatase 2, an
ubiquitously expressed central regulatory enzyme in the
phosphoinositide-signaling cascade. As a novel Rac1
effector regulating the early step of clathrin-mediated
endocytosis, synaptojanin-2 acts as a
polyphosphoinositide phosphatase directly and
specifically interacting with Rac1 in a GTP-dependent
manner. It mediates the inhibitory effect of Rac1 on
endocytosis and plays an important role in the
Rac1-mediated control of cell growth. Synaptojanin-2
shows high sequence homology to the N-terminal Sac1p
homology domain, the central inositol 5-phosphatase
domain, the putative RNA recognition motif (RRM) of
synaptojanin-1, but differs in the proline-rich region.
.
Length = 78
Score = 25.5 bits (56), Expect = 8.4
Identities = 20/91 (21%), Positives = 30/91 (32%), Gaps = 19/91 (20%)
Query: 77 NLLNLSIEEKKEADLRSIYVGNVDYGATAEELESHFHGCGSVNRVTILCNKFDGHPKGFA 136
+L + + EEK E EL G G V V I +
Sbjct: 7 SLDSPTAEEKNEFP-----------EDLRTELLQTLEGYGDVVLVRIAGGQM-------- 47
Query: 137 YIEFADKDSVQTAMAMDESLFRGRQIKVNPK 167
+ FAD S + +D G+ +K+ K
Sbjct: 48 IVTFADSRSALEVLDLDGIKVLGKTVKIRLK 78
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 26.5 bits (59), Expect = 8.7
Identities = 9/40 (22%), Positives = 22/40 (55%)
Query: 36 EAELAAMKARVREMEEEAEKLKQLQSEVDKQMSMGSPPNS 75
+ ELA ++ + E++E+ +L+Q E+ +++S
Sbjct: 72 QQELAELQEELAELQEQLAELQQENQELKQELSTLEAELE 111
>gnl|CDD|237622 PRK14140, PRK14140, heat shock protein GrpE; Provisional.
Length = 191
Score = 26.5 bits (59), Expect = 8.9
Identities = 11/58 (18%), Positives = 28/58 (48%)
Query: 1 MSDQENSFIHEEENFENGDHIENGDMEADQSKCTDEAELAAMKARVREMEEEAEKLKQ 58
M ++ E E E + +E+ E + ++ L +A++ E+E + ++L++
Sbjct: 1 MEEKNEQVEEEVEETEVEEAVEDEVEEETVEEESEAELLDEEQAKIAELEAKLDELEE 58
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 26.7 bits (60), Expect = 9.0
Identities = 13/36 (36%), Positives = 25/36 (69%), Gaps = 7/36 (19%)
Query: 42 MKARVREMEEEAEKLKQ----LQSEVDKQMSMGSPP 73
++ ++R++E E EKL++ L+SE++K + SPP
Sbjct: 20 LELKLRDLEAENEKLERELERLKSELEK---LKSPP 52
>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage
factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar
proteins. This subgroup corresponds to the RRM of
CFIm59. Cleavage factor Im (CFIm) is a highly conserved
component of the eukaryotic mRNA 3' processing machinery
that functions in UGUA-mediated poly(A) site
recognition, the regulation of alternative poly(A) site
selection, mRNA export, and mRNA splicing. It is a
complex composed of a small 25 kDa (CFIm25) subunit and
a larger 59/68/72 kDa subunit. The two separate genes,
CPSF6 and CPSF7, code for two isoforms of the large
subunit, CFIm68 and CFIm59. The family includes CFIm59,
also termed cleavage and polyadenylation specificity
factor subunit 6 (CPSF7), or cleavage and
polyadenylation specificity factor 59 kDa subunit
(CPSF59). CFIm59 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. The N-terminal
RRM of CFIm59 mediates the interaction with CFIm25. It
also serves to enhance RNA binding and facilitate RNA
looping. .
Length = 90
Score = 25.3 bits (55), Expect = 9.6
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 93 SIYVGNVDYGATAEELESHFHGCGSVNRVTILC--NKFDGHPKGFAYIEFADKDSVQ 147
++YVGN + T ++L G + V + N+ +G KG+A + A ++SV
Sbjct: 3 AVYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVH 59
>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 = 25.1 bits (55), Expect = 9.7
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 1/34 (2%)
Query: 116 GSVNRVTILCNKFDGHPKGFAYIEFADKDSVQTA 149
G + RV + N+ G G A I F A
Sbjct: 25 GPIKRVLLSYNE-GGKSTGIANITFKRAGDATKA 57
>gnl|CDD|216402 pfam01268, FTHFS, Formate--tetrahydrofolate ligase.
Length = 557
Score = 26.6 bits (60), Expect = 9.9
Identities = 26/88 (29%), Positives = 36/88 (40%), Gaps = 14/88 (15%)
Query: 34 TD-EAELAAMKARVREMEEEA----------EKLKQLQSEVDKQMSMGSPPNSNNL--LN 80
TD +AELA ++ E EA E +L V + P N L L
Sbjct: 383 TDTDAELALVRELCEEAGAEAAVSEHWAKGGEGAIELAEAVVEACIEEQPSNFKPLYDLE 442
Query: 81 LSIEEKKEADLRSIY-VGNVDYGATAEE 107
LS+EEK E IY V++ A++
Sbjct: 443 LSLEEKIETIATEIYGADGVEFSPKAKK 470
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
0.312 0.130 0.368
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,539,983
Number of extensions: 973592
Number of successful extensions: 1903
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1823
Number of HSP's successfully gapped: 420
Length of query: 207
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 115
Effective length of database: 6,857,034
Effective search space: 788558910
Effective search space used: 788558910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.6 bits)