RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4080
(403 letters)
>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 = 144 bits (365), Expect = 7e-43
Identities = 53/78 (67%), Positives = 66/78 (84%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
CLGVFGLS+YTTE+ + +FS+YGP+E+V+VV D KTGRSRGF FVYFES +DA AK+
Sbjct: 1 CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKER 60
Query: 241 CTGMEIDGRQIRVDFSVT 258
GMEIDGR+IRVD+S+T
Sbjct: 61 LNGMEIDGRRIRVDYSIT 78
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 116 bits (291), Expect = 5e-32
Identities = 53/87 (60%), Positives = 68/87 (78%)
Query: 173 RENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
R NP P+ CLGVFGLS+YTTE+ + +FSKYGP+ V +V D ++ RSRGF FVYFE+ D
Sbjct: 3 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62
Query: 233 DAAAAKDACTGMEIDGRQIRVDFSVTQ 259
DA AK+ GME+DGR+IRVDFS+T+
Sbjct: 63 DAKEAKERANGMELDGRRIRVDFSITK 89
>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 = 105 bits (262), Expect = 6e-28
Identities = 48/79 (60%), Positives = 62/79 (78%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
CLGVFGLS+YTTE+ + +FS+YGP+ V VV D +TGRSRGF FVYFE DD+ A +
Sbjct: 1 CLGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60
Query: 241 CTGMEIDGRQIRVDFSVTQ 259
GME+DGR+IRVD+S+T+
Sbjct: 61 ANGMELDGRRIRVDYSITK 79
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 92.3 bits (230), Expect = 2e-23
Identities = 34/70 (48%), Positives = 48/70 (68%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L TTE+++ +FSK+G VE V +V D +TG+S+GF FV FES +DA A +A G
Sbjct: 4 VGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG 63
Query: 244 MEIDGRQIRV 253
E+DGR ++V
Sbjct: 64 KELDGRPLKV 73
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 85.3 bits (212), Expect = 6e-21
Identities = 32/69 (46%), Positives = 45/69 (65%), Gaps = 1/69 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L TTE+ + +FSK+GP+E + +V D TGRS+GF FV FE +DA A +A G
Sbjct: 3 VGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEALNG 61
Query: 244 MEIDGRQIR 252
E+ GR++R
Sbjct: 62 KELGGRELR 70
>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 = 83.1 bits (206), Expect = 5e-20
Identities = 33/71 (46%), Positives = 47/71 (66%), Gaps = 1/71 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L TTE+ + +FSK+G +E V +V D K G+S+GF FV FES +DA A +A G
Sbjct: 3 VGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEALNG 61
Query: 244 MEIDGRQIRVD 254
E+DGR+++V
Sbjct: 62 KELDGRKLKVS 72
>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 = 82.7 bits (205), Expect = 9e-20
Identities = 37/73 (50%), Positives = 50/73 (68%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GLS TTE+++ +FSK+G VE V ++ D +TG SRGF FV FES +DA AA
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63
Query: 242 TGMEIDGRQIRVD 254
G E++GR I+V+
Sbjct: 64 NGKELEGRVIKVE 76
>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 = 81.0 bits (200), Expect = 4e-19
Identities = 40/73 (54%), Positives = 47/73 (64%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GLS T EQ + +FSKYG + V VV D +T RSRGF FV FE+ DDA A A
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 242 TGMEIDGRQIRVD 254
G +DGRQIRVD
Sbjct: 63 NGKSVDGRQIRVD 75
>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 = 77.2 bits (191), Expect = 8e-18
Identities = 30/69 (43%), Positives = 44/69 (63%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS YTTE+QI +FS+ G ++R+ + +D T GFCFV + +R+DA A G ++
Sbjct: 6 LSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKL 65
Query: 247 DGRQIRVDF 255
D R IRVD+
Sbjct: 66 DDRIIRVDW 74
>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 = 76.5 bits (189), Expect = 1e-17
Identities = 26/70 (37%), Positives = 39/70 (55%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L TE+ + +F ++G V V+ D +TGRSRGF FV E+ ++A AA + G
Sbjct: 4 VGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNG 63
Query: 244 MEIDGRQIRV 253
+ GR + V
Sbjct: 64 TDFGGRTLTV 73
>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 = 74.2 bits (183), Expect = 1e-16
Identities = 33/84 (39%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ L V L+ TTE ++ F +YGP++R+ +V D KTG+ RG+ F+ FE D AA
Sbjct: 2 KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61
Query: 240 ACTGMEIDGRQIRVDFSVTQRAHT 263
G +IDGR++ VD +R T
Sbjct: 62 YADGKKIDGRRVLVD---VERGRT 82
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 76.5 bits (187), Expect = 2e-15
Identities = 50/191 (26%), Positives = 78/191 (40%), Gaps = 4/191 (2%)
Query: 66 KKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYR 125
K S S K ++ + G + S+ + S P +
Sbjct: 6 LKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKK 65
Query: 126 KRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCLGVF 185
+ SS R R G+ E E E E +++ + + L V
Sbjct: 66 RLLSSERKEENEREMEEQNDGER----GYTKEFEEELFRSSESPKSRQKSKEENNTLFVG 121
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L TE+ + +F K+GPV+RV +V D +TG+SRGF FV FES + A A + G E
Sbjct: 122 NLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKE 181
Query: 246 IDGRQIRVDFS 256
++GR +RV +
Sbjct: 182 LEGRPLRVQKA 192
>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 = 70.0 bits (172), Expect = 4e-15
Identities = 32/83 (38%), Positives = 46/83 (55%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
P L V LS+ TTE+ + +FS+YG + R+ +V D TG S+G+ FV +E DA A
Sbjct: 2 PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61
Query: 238 KDACTGMEIDGRQIRVDFSVTQR 260
+ IDG +I VDF +
Sbjct: 62 YRDAHKLVIDGSEIFVDFERERT 84
>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 = 69.5 bits (171), Expect = 5e-15
Identities = 32/84 (38%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYG--PVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
P+ L + GL + TTE+ I S P++ V ++ D TG SRGF FV F S +DA
Sbjct: 1 PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60
Query: 236 AAKDA---CTGMEIDGRQIRVDFS 256
DA IDGR +RV ++
Sbjct: 61 QWMDALNNLDPFVIDGRVVRVSYA 84
>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 = 68.4 bits (168), Expect = 9e-15
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE + IF +G +E V++ D +TGRS+G+ F+ F +DA A + G E+ GR I
Sbjct: 11 TEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPI 70
Query: 252 RV 253
+V
Sbjct: 71 KV 72
>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 = 68.0 bits (167), Expect = 1e-14
Identities = 23/62 (37%), Positives = 36/62 (58%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
+ + IFS YG V+ V++ ID + RG+ +V FES +DA A G +IDG+++
Sbjct: 11 NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEV 70
Query: 252 RV 253
V
Sbjct: 71 TV 72
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 67.6 bits (166), Expect = 2e-14
Identities = 27/62 (43%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
TE+ + FS YG VE V +V + R RGF FV F S +DA AA G+ +DGR
Sbjct: 10 VTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRT 67
Query: 251 IR 252
+R
Sbjct: 68 LR 69
>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 = 67.6 bits (166), Expect = 2e-14
Identities = 26/73 (35%), Positives = 41/73 (56%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L TT++Q+ FS+ GP++R VV D + + RGF +V F +DA A +
Sbjct: 4 VRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKK 63
Query: 244 MEIDGRQIRVDFS 256
+ GR+I V+F+
Sbjct: 64 TKFGGRKIHVEFA 76
>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 = 67.4 bits (165), Expect = 2e-14
Identities = 34/73 (46%), Positives = 44/73 (60%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V LS ++ + F K+G V V+ D +TGRSRGF +V FES +DA A +A G
Sbjct: 4 VGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDG 63
Query: 244 MEIDGRQIRVDFS 256
E+DGR I VDFS
Sbjct: 64 KELDGRPINVDFS 76
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 28/66 (42%), Positives = 40/66 (60%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
TE+Q+ IFS+ GPV +V D TG+ +G+ F FE + AA+A G E +GR
Sbjct: 10 ATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRA 69
Query: 251 IRVDFS 256
+RVDF+
Sbjct: 70 LRVDFA 75
>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 = 66.1 bits (162), Expect = 6e-14
Identities = 28/72 (38%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAK-TGRSRGFCFVYFESRDDAAAAKDACTGME 245
L TE + +FS +G V EV I K G+ +GF FV F S+ DA A G +
Sbjct: 7 LPFKCTEADLKKLFSPFGFV--WEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKK 64
Query: 246 IDGRQIRVDFSV 257
I GR + VD++V
Sbjct: 65 IKGRPVAVDWAV 76
>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 = 65.4 bits (160), Expect = 1e-13
Identities = 26/66 (39%), Positives = 41/66 (62%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
TT++ + IFS++G ++ EV+ D KTG S + F+ FE+++D A + ID R+
Sbjct: 15 TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRR 74
Query: 251 IRVDFS 256
I VDFS
Sbjct: 75 IHVDFS 80
>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 = 64.9 bits (159), Expect = 2e-13
Identities = 27/70 (38%), Positives = 42/70 (60%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GL+ E+ ++ F +G ++ +++ +D +T + RGF FV FE +DAAAA D
Sbjct: 3 VGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNE 62
Query: 244 MEIDGRQIRV 253
E+ GR IRV
Sbjct: 63 SELFGRTIRV 72
>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 = 64.9 bits (159), Expect = 2e-13
Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 3/65 (4%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG---MEIDG 248
TE+ + +F +YG +E V ++ D TG+S+G FV F SR++A A +A G M
Sbjct: 12 TEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPGAS 71
Query: 249 RQIRV 253
R ++V
Sbjct: 72 RPLQV 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 = 64.2 bits (157), Expect = 3e-13
Identities = 32/73 (43%), Positives = 40/73 (54%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L+ TT + +F KYG V V + D T SRGF FV F + DA A DA
Sbjct: 1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60
Query: 242 TGMEIDGRQIRVD 254
G E+DGR++RV
Sbjct: 61 DGKELDGRELRVQ 73
>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 = 63.3 bits (155), Expect = 7e-13
Identities = 22/51 (43%), Positives = 31/51 (60%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
LS E + +F +GP+ RV + D +TG+SRGF FV F +R+DA A
Sbjct: 7 LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERA 57
>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 = 63.0 bits (154), Expect = 7e-13
Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 8/67 (11%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
L + TTE+Q+ +FS+YG VERV+ + D + FV+FE RDDA A + G E+
Sbjct: 9 LPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEMNGKEL 60
Query: 247 DGRQIRV 253
+G I V
Sbjct: 61 EGSPIEV 67
>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 = 63.0 bits (154), Expect = 1e-12
Identities = 28/69 (40%), Positives = 41/69 (59%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GL TE I +FS+YG + + +V D KTG+S+GF F+ +E + A D G++
Sbjct: 16 GLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIK 75
Query: 246 IDGRQIRVD 254
+ GR IRVD
Sbjct: 76 LLGRTIRVD 84
>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 = 62.6 bits (153), Expect = 1e-12
Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 5/75 (6%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA-----AAAKDAC 241
L TE+++ +FS++G V+ +V D TG S+G FV F++++ A AA
Sbjct: 8 LPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAED 67
Query: 242 TGMEIDGRQIRVDFS 256
+G+ +DGR++ V +
Sbjct: 68 SGLSLDGRRLIVTLA 82
>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 = 61.9 bits (151), Expect = 2e-12
Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 5/72 (6%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC-- 241
V GL +TT+ + FS++G +E V+ D +TG+SRG+ FV F+ ++ +A+ AC
Sbjct: 5 VGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKE---SAERACKD 61
Query: 242 TGMEIDGRQIRV 253
IDGR+ V
Sbjct: 62 PNPIIDGRKANV 73
>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 = 62.2 bits (151), Expect = 2e-12
Identities = 25/75 (33%), Positives = 39/75 (52%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L+ T++ + FS P++ VV D +TG SRG+ FV F +DA A
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 242 TGMEIDGRQIRVDFS 256
++ GR +R+D +
Sbjct: 62 KNKKLHGRILRLDIA 76
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 61.5 bits (150), Expect = 2e-12
Identities = 22/67 (32%), Positives = 34/67 (50%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
L TTE+++ +F +G + V + +D +T RS+GF FV F + A A G
Sbjct: 7 LPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIF 66
Query: 247 DGRQIRV 253
GR + V
Sbjct: 67 QGRLLHV 73
>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 = 61.8 bits (151), Expect = 3e-12
Identities = 20/63 (31%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
++++ +F KYG + +V+ D + G+S+GF FV FE+ + A A + G E++G++
Sbjct: 13 MDDEKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKAVEELNGKEVNGKK 71
Query: 251 IRV 253
+ V
Sbjct: 72 LYV 74
>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 = 61.1 bits (149), Expect = 4e-12
Identities = 24/65 (36%), Positives = 40/65 (61%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T++Q + S +G VER +V TG S+G+ FV + S+ A AK+ G +I GR++
Sbjct: 12 TDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKL 71
Query: 252 RVDFS 256
+VD++
Sbjct: 72 QVDWA 76
>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 = 66.8 bits (163), Expect = 4e-12
Identities = 67/264 (25%), Positives = 100/264 (37%), Gaps = 44/264 (16%)
Query: 28 RSHVSGRLLPKEPAQTSSDQCYYRLSPARSGSAGSIDDKKYRKSITRSRSGSPHRRSKRP 87
R GRL + R S +R S D YR RSRS SP+R +
Sbjct: 3 RDRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPR 62
Query: 88 QVACGRDNGLGNRSRSRSYSP-----RGRRGGY------RSRSR---------SPGYRKR 127
R + RS + P R R + ++R R +
Sbjct: 63 GDRSYRRDD--RRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQ 120
Query: 128 SSSYRSGGGSRGDSY----------------GGR--GKIIIAVVTEVEEEAEATAMVEEF 169
R+ S+G +Y G G+ II ++ E+ A A +
Sbjct: 121 CIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQP 180
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
D P + L V L TEQ++ IF +G +E V++ D +TGRS+GF F+ F
Sbjct: 181 GDI---PNFLK-LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFH 236
Query: 230 SRDDAAAAKDACTGMEIDGRQIRV 253
++A A + G E+ GR I+V
Sbjct: 237 DAEEAKEALEVMNGFELAGRPIKV 260
Score = 62.2 bits (151), Expect = 2e-10
Identities = 64/209 (30%), Positives = 79/209 (37%), Gaps = 45/209 (21%)
Query: 64 DDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPG 123
D ++ K RSR S R R R R R Y RGRRG RSRSRSP
Sbjct: 13 DTRRSDKGRERSRRRSRSRDRSR-------------RRRDRDY-YRGRRG--RSRSRSPN 56
Query: 124 YRKRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSRCLG 183
R RS R D GR E EAE R +
Sbjct: 57 RYYRPRGDRSY--RRDDRRSGRNTK------EPLTEAERDD---------------RTVF 93
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L++ E+ + FSK G V V+ + D + RS+G +V F + A A TG
Sbjct: 94 VLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTG 152
Query: 244 MEIDGRQIRVDFS-----VTQRAHTPTPG 267
+ GR I V S +A T PG
Sbjct: 153 QMLLGRPIIVQSSQAEKNRAAKAATHQPG 181
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is 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 = 77
Score = 58.8 bits (143), Expect = 2e-11
Identities = 31/80 (38%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
P+ C+ + GL TEQ + FS+YGPV VVID R RG V+F+ + A
Sbjct: 4 SMPTNCVWLDGLDESVTEQYLTRHFSRYGPVVH--VVID----RQRGQALVFFDKVEAAQ 57
Query: 236 AAKDACTGMEIDGRQIRVDF 255
AA + G ++ GR+++VDF
Sbjct: 58 AAVNEMKGRKLGGRKLQVDF 77
>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 = 58.9 bits (143), Expect = 3e-11
Identities = 20/64 (31%), Positives = 38/64 (59%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T++++ +F GP+E ++V D TG+S G+ FV + +DA A + G EI +++
Sbjct: 13 TQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRL 72
Query: 252 RVDF 255
+V +
Sbjct: 73 KVSY 76
>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 = 58.5 bits (142), Expect = 3e-11
Identities = 26/68 (38%), Positives = 38/68 (55%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS E I F +YG + V + D +GR +GF +V F S++ A AA DA G ++
Sbjct: 6 LSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDL 65
Query: 247 DGRQIRVD 254
GR +R+D
Sbjct: 66 LGRPVRLD 73
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 57.5 bits (140), Expect = 4e-11
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 196 INHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
+ +FS +G VE+++++ GF FV F + + A A G+ GR +RVD+
Sbjct: 1 LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
Query: 256 S 256
S
Sbjct: 56 S 56
>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 = 58.0 bits (141), Expect = 4e-11
Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE+ + +F + G V++V++ D ++GRS G V FE R+DA A G+ +DG+ +
Sbjct: 13 TEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPM 71
Query: 252 RVDF 255
+V+
Sbjct: 72 QVEL 75
>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 = 57.4 bits (139), Expect = 6e-11
Identities = 25/59 (42%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACT 242
V GLS TTE + FS++G VE ++ D +T R RGF FV FES D C
Sbjct: 4 VGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESED---VVDKVCE 59
>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 = 57.5 bits (140), Expect = 7e-11
Identities = 27/70 (38%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
TE + IFS GPV + V D T RS G+ +V F++ DA A D I G+
Sbjct: 11 VTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGKP 70
Query: 251 IRVDFSVTQR 260
IR+ +S QR
Sbjct: 71 IRIMWS--QR 78
>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 = 57.0 bits (138), Expect = 1e-10
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
V GLS TTE++I F K+G + +E+ +D KT + RGFCF+ F+S + K
Sbjct: 4 VGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE---PVKKIL 58
>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 = 56.7 bits (137), Expect = 1e-10
Identities = 25/65 (38%), Positives = 42/65 (64%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE+Q+ IFS+ GPV +V D +TG+ +G+ F ++ ++ A +A G E++GRQ+
Sbjct: 11 TEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQL 70
Query: 252 RVDFS 256
RVD +
Sbjct: 71 RVDNA 75
>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 = 56.9 bits (138), Expect = 1e-10
Identities = 24/49 (48%), Positives = 31/49 (63%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V GL TE+ + FS+YG VE VE+V D +TG+ RGF FV F+ D
Sbjct: 4 VGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYD 52
>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 = 56.6 bits (137), Expect = 1e-10
Identities = 29/73 (39%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL TTEQ + FS +G + V+V D KTG+S+GF FV F D
Sbjct: 2 LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFA---DYEDQVKVL 58
Query: 242 TGME-IDGRQIRV 253
+ IDGR V
Sbjct: 59 SQRHMIDGRWCDV 71
>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 = 56.4 bits (137), Expect = 2e-10
Identities = 28/66 (42%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GLS TTE+ + FSKYG V ++ D TGRSRGF FV F A
Sbjct: 5 GLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA-KPHV 63
Query: 246 IDGRQI 251
+DGR+I
Sbjct: 64 LDGREI 69
>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 = 56.1 bits (135), Expect = 2e-10
Identities = 31/80 (38%), Positives = 46/80 (57%), Gaps = 3/80 (3%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL E + FS++GPVE+ EV+ D +TG+ RGF FVYF++ D +A K A
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHD--SADKAAV 59
Query: 242 TGME-IDGRQIRVDFSVTQR 260
I+G ++ V +V +
Sbjct: 60 VKFHPINGHRVEVKKAVPKE 79
>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 = 55.5 bits (134), Expect = 3e-10
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T E+ I +F +GP+ R ++ + F FV FE +DA A +A G IDG
Sbjct: 12 TREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEALHGSRIDGSV 63
Query: 251 IRVDF 255
+ V+F
Sbjct: 64 LTVEF 68
>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 = 55.9 bits (135), Expect = 3e-10
Identities = 24/67 (35%), Positives = 34/67 (50%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
L E + +FSK+G + V V ID K+G+S+GF +V F +DA A G
Sbjct: 10 LPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVF 69
Query: 247 DGRQIRV 253
GR I +
Sbjct: 70 QGRLIHI 76
>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 = 55.8 bits (135), Expect = 3e-10
Identities = 23/62 (37%), Positives = 35/62 (56%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T ++ IFSKYG V +V +V D +T +S+G F+ F R+DA A E+ GR +
Sbjct: 14 TNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTL 73
Query: 252 RV 253
+
Sbjct: 74 KC 75
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 57.4 bits (138), Expect = 4e-10
Identities = 32/83 (38%), Positives = 45/83 (54%), Gaps = 1/83 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GLS T + + F+ +G V +V++D +TGRSRGF FV F A AA
Sbjct: 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96
Query: 242 TGMEIDGRQIRVDFSVTQRAHTP 264
G E++GR IRV+ + R P
Sbjct: 97 DGKELNGRHIRVNPA-NDRPSAP 118
>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 = 55.0 bits (133), Expect = 6e-10
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
FS++G V+ V D +TG S+G+ FV F SRD A + ++G +++V
Sbjct: 20 FSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQKHI-LEGNKLQV 72
>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 = 54.2 bits (131), Expect = 8e-10
Identities = 20/62 (32%), Positives = 39/62 (62%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+Q + +F+ +G V +V +D TG+S+ F FV +++ + A AA A G ++ G+++
Sbjct: 11 TDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRL 70
Query: 252 RV 253
+V
Sbjct: 71 KV 72
>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 = 53.7 bits (130), Expect = 1e-09
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 8/77 (10%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL +T+ ++ F ++G + R++ R + ++ +ES + A AAK+A
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYD------PGRNYAYIEYESIEAAQAAKEAL 54
Query: 242 TGMEI--DGRQIRVDFS 256
G + GR++RVDF+
Sbjct: 55 RGFPLGGPGRRLRVDFA 71
>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 = 53.9 bits (130), Expect = 1e-09
Identities = 22/66 (33%), Positives = 35/66 (53%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS + + F+ +G + VV D +TG+S+G+ FV F ++DA A + G +
Sbjct: 7 LSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWL 66
Query: 247 DGRQIR 252
GR IR
Sbjct: 67 GGRAIR 72
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 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 = 78
Score = 53.8 bits (129), Expect = 2e-09
Identities = 33/77 (42%), Positives = 45/77 (58%), Gaps = 3/77 (3%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ L V GLS TTE+ + F G + +V D TG S+GF FV F S +DA AAK+
Sbjct: 1 KTLFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57
Query: 240 ACTGMEIDGRQIRVDFS 256
A EIDG ++ +DF+
Sbjct: 58 AMEDGEIDGNKVTLDFA 74
>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 = 53.4 bits (128), Expect = 2e-09
Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
S+ L V LS +E + +F K + I GR +G+ FV FES +DA A
Sbjct: 1 SKVLVVNNLSYSASEDSLQEVFEK-----ATSIRIPQNNGRPKGYAFVEFESAEDAKEAL 55
Query: 239 DACTGMEIDGRQIRVDF 255
++C EI+GR IR++F
Sbjct: 56 NSCNNTEIEGRSIRLEF 72
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other EJC
components (such as Magoh, Aly/REF, RNPS1, Srm160, and
Upf3), plays critical roles in postsplicing processing,
including nuclear export and cytoplasmic localization of
the mRNA, and the nonsense-mediated mRNA decay (NMD)
surveillance process. RBM8 binds to mRNA 20-24
nucleotides upstream of a spliced exon-exon junction. It
is also involved in spliced mRNA nuclear export, and the
process of nonsense-mediated decay of mRNAs with
premature stop codons. RBM8 forms a specific heterodimer
complex with the EJC protein Magoh which then associates
with Aly/REF, RNPS1, DEK, and SRm160 on the spliced
mRNA, and inhibits ATP turnover by eIF4AIII, thereby
trapping the EJC core onto RNA. RBM8 contains an
N-terminal putative bipartite nuclear localization
signal, one RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
in the central region, and a C-terminal serine-arginine
rich region (SR domain) and glycine-arginine rich region
(RG domain). .
Length = 88
Score = 53.8 bits (130), Expect = 2e-09
Identities = 17/65 (26%), Positives = 40/65 (61%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
E+ ++ F+++G ++ + + +D +TG +G+ + +E++ +A AA + G E+ G+
Sbjct: 18 AQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQT 77
Query: 251 IRVDF 255
I VD+
Sbjct: 78 ISVDW 82
>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 = 53.7 bits (129), Expect = 2e-09
Identities = 24/69 (34%), Positives = 35/69 (50%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS T+ + FS + V+ D K+GRSRG+ FV F S+ DA A + G +
Sbjct: 7 LSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWL 66
Query: 247 DGRQIRVDF 255
R IR ++
Sbjct: 67 GSRPIRCNW 75
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 83
Score = 53.3 bits (128), Expect = 2e-09
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
++ IF +YG V + + G+ GF FV + R +A A + G+EIDGR + V
Sbjct: 16 VKLKKIFGRYGKVREATIPRK-RGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAV 74
Query: 254 DFSVTQRA 261
D++V +
Sbjct: 75 DWAVQKNR 82
>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 = 53.3 bits (128), Expect = 3e-09
Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL++ T++ + F++YG + V++D T RSRGF F+ F S D+A A +A
Sbjct: 5 LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA- 63
Query: 242 TGMEIDGRQIRVDFSV 257
IDG QI + +
Sbjct: 64 QPHSIDGNQIELKRAK 79
>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 = 53.1 bits (128), Expect = 3e-09
Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GL TE++ FS++G V +++ D TGRSRGF FV F+S + A +
Sbjct: 4 VGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSAGM 62
Query: 244 MEIDGRQIRV 253
+E+ G+Q+ V
Sbjct: 63 LELGGKQVEV 72
>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 = 52.7 bits (127), Expect = 4e-09
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 192 TEQQINHIFSKYGPVERVEVVI---DAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDG 248
TE + +FSKYG +++ + + G+ RG+CFV FE++++A A + G G
Sbjct: 12 TEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALG 71
Query: 249 RQIRVD 254
+++ V
Sbjct: 72 KKLVVR 77
>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 = 51.9 bits (125), Expect = 7e-09
Identities = 18/65 (27%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM---EIDG 248
+E I +F +G ++ + D +TG+ +G+ F+ +E+ +A+DA M ++ G
Sbjct: 13 SEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQ---SAQDAIASMNLFDLGG 69
Query: 249 RQIRV 253
+Q+RV
Sbjct: 70 QQLRV 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 = 51.9 bits (125), Expect = 8e-09
Identities = 24/76 (31%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
P+R V G+ TTE+++ FS++G V+ V+++ D + G S+G+ FV FE+++DA
Sbjct: 2 PNRIF-VGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKI 59
Query: 238 KDACTGMEIDGRQIRV 253
A + G+++ +
Sbjct: 60 L-AMGNLNFRGKKLNI 74
>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 = 51.6 bits (124), Expect = 9e-09
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL T++++ +F K+G V+ V +V + ++G+ +G +V +E+ A+ A
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQAVLKM 63
Query: 242 TGMEIDGRQIRVDFS 256
G EI + I V S
Sbjct: 64 DGTEIKEKTISVAIS 78
>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 = 51.0 bits (123), Expect = 1e-08
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
E+++ F G VE V +V D KTG +GF +V F+++D A A G+++ GR+
Sbjct: 11 IEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLNGIKLKGRK 69
Query: 251 IRV 253
IRV
Sbjct: 70 IRV 72
>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 = 50.7 bits (122), Expect = 2e-08
Identities = 29/77 (37%), Positives = 42/77 (54%), Gaps = 7/77 (9%)
Query: 180 RC-LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
RC L V L TE++ +FSKYG V EV ++ + +GF F+ ++R +A AK
Sbjct: 1 RCRLFVGNLPNDITEEEFKELFSKYGEV--SEVFLN----KEKGFGFIRLDTRTNAEKAK 54
Query: 239 DACTGMEIDGRQIRVDF 255
G+ GRQ+RV F
Sbjct: 55 AELDGIMRKGRQLRVRF 71
>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins
family. This subfamily corresponds to the RRM3 of the
Hu proteins family which represent a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. Hu
proteins perform their cytoplasmic and nuclear molecular
functions by coordinately regulating functionally
related mRNAs. In the cytoplasm, Hu proteins recognize
and bind to AU-rich RNA elements (AREs) in the 3'
untranslated regions (UTRs) of certain target mRNAs,
such as GAP-43, vascular epithelial growth factor
(VEGF), the glucose transporter GLUT1, eotaxin and
c-fos, and stabilize those ARE-containing mRNAs. They
also bind and regulate the translation of some target
mRNAs, such as neurofilament M, GLUT1, and p27. In the
nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 50.8 bits (122), Expect = 2e-08
Identities = 22/75 (29%), Positives = 40/75 (53%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
C+ V+ L E + +FS +G V V+V+ D T + +G+ FV + ++A +A +
Sbjct: 3 CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62
Query: 241 CTGMEIDGRQIRVDF 255
G + GR ++V F
Sbjct: 63 LNGYRLGGRVLQVSF 77
>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA
binding protein fox-1 homologs and similar proteins.
This subfamily corresponds to the RRM of several
tissue-specific alternative splicing isoforms of
vertebrate RNA binding protein Fox-1 homologs, which
show high sequence similarity to the Caenorhabditis
elegans feminizing locus on X (Fox-1) gene encoding
Fox-1 protein. RNA binding protein Fox-1 homolog 1
(RBFOX1), also termed ataxin-2-binding protein 1
(A2BP1), or Fox-1 homolog A, or
hexaribonucleotide-binding protein 1 (HRNBP1), is
predominantly expressed in neurons, skeletal muscle and
heart. It regulates alternative splicing of
tissue-specific exons by binding to UGCAUG elements.
Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and
forms an ataxin-2/A2BP1 complex involved in RNA
processing. RNA binding protein fox-1 homolog 2
(RBFOX2), also termed Fox-1 homolog B, or
hexaribonucleotide-binding protein 2 (HRNBP2), or
RNA-binding motif protein 9 (RBM9), or repressor of
tamoxifen transcriptional activity, is expressed in
ovary, whole embryo, and human embryonic cell lines in
addition to neurons and muscle. RBFOX2 activates
splicing of neuron-specific exons through binding to
downstream UGCAUG elements. RBFOX2 also functions as a
repressor of tamoxifen activation of the estrogen
receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or
NeuN or HRNBP3), also termed Fox-1 homolog C, is a
nuclear RNA-binding protein that regulates alternative
splicing of the RBFOX2 pre-mRNA, producing a message
encoding a dominant negative form of the RBFOX2 protein.
Its message is detected exclusively in post-mitotic
regions of embryonic brain. Like RBFOX1, both RBFOX2 and
RBFOX3 bind to the hexanucleotide UGCAUG elements and
modulate brain and muscle-specific splicing of exon
EIIIB of fibronectin, exon N1 of c-src, and
calcitonin/CGRP. Members in this family also harbor one
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 50.9 bits (122), Expect = 2e-08
Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
+ + +F ++GP+ VE++ + + S+GF FV F + DA A++ G ++GR+I
Sbjct: 14 DPDLRQMFGQFGPILDVEIIFNERG--SKGFGFVTFANSADADRAREKLHGTVVEGRKIE 71
Query: 253 VD 254
V+
Sbjct: 72 VN 73
>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 = 50.4 bits (121), Expect = 2e-08
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L T + ++ IF V+ V +V D +T + +GFC+V FE + A + G
Sbjct: 6 VGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YDG 63
Query: 244 MEIDGRQIRVD 254
D R +RVD
Sbjct: 64 ALFDDRSLRVD 74
>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 = 50.3 bits (121), Expect = 3e-08
Identities = 27/73 (36%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L T++++ F KYGP+ V V A+ GF FV FE DA A A G
Sbjct: 4 VGNLGPRATKRELEDEFEKYGPLRSVWV---AR--NPPGFAFVEFEDPRDAEDAVRALDG 58
Query: 244 MEIDGRQIRVDFS 256
I G ++RV+ S
Sbjct: 59 RRICGNRVRVELS 71
>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 = 50.1 bits (120), Expect = 3e-08
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GL TE + FS++G V V V+ D + R RGF F+ FES D + D
Sbjct: 7 VGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESED----SVDQVVN 62
Query: 244 M---EIDGRQIRV 253
+I+G+++ V
Sbjct: 63 EHFHDINGKKVEV 75
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of RBM23
remains unclear, it shows high sequence homology to
RBM39 and contains two RRMs. It may possibly function as
a pre-mRNA splicing factor. .
Length = 73
Score = 49.5 bits (119), Expect = 4e-08
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS+ E+ + FSK G V V ++ D + RS+G +V F + A TG +
Sbjct: 7 LSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLTGQRL 65
Query: 247 DGRQIRV 253
G+ I V
Sbjct: 66 LGQPIMV 72
>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 = 49.7 bits (119), Expect = 4e-08
Identities = 24/70 (34%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V G+ Y+TE +I FS G +E ++++ TGR RG F+ F++ ++AA A G
Sbjct: 3 VGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKT-EEAAKRALALDG 61
Query: 244 MEIDGRQIRV 253
++ GR ++V
Sbjct: 62 EDMGGRFLKV 71
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 77
Score = 49.5 bits (119), Expect = 5e-08
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 11/79 (13%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC---T 242
GL Y +E Q+ + +G ++ +V D+ TG S+G+ F + D + A
Sbjct: 7 GLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYL---DPSVTDQAIAGLN 63
Query: 243 GMEIDGRQIRVDFSVTQRA 261
GM++ +++ V QRA
Sbjct: 64 GMQLGDKKLTV-----QRA 77
>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 = 49.6 bits (119), Expect = 5e-08
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
E I F++ G V V+++ + +TG+S G+ FV F + + A A + G I Q
Sbjct: 12 DEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNTQQ 71
Query: 252 R 252
R
Sbjct: 72 R 72
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
or Set1 complex component, is encoded by SET1 from the
fission yeast S. pombe. It is essential for the H3
lysine-4 methylation. in vivo, and plays an important
role in telomere maintenance and DNA repair in an ATM
kinase Rad3-dependent pathway. spSet1p is the homology
counterpart of Saccharomyces cerevisiae Set1p (scSet1p).
However, it is more closely related to Set1 found in
mammalian. Moreover, unlike scSet1p, spSet1p is not
required for heterochromatin assembly in fission yeast.
spSet1p contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 86
Score = 49.7 bits (119), Expect = 6e-08
Identities = 28/78 (35%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD--------AAAA 237
GLS TT +QI F +G +E E+ +D +TG+S G C V F A AA
Sbjct: 5 GLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGDPLRPSAAHEAAKAA 64
Query: 238 KDACTGMEIDGRQIRVDF 255
D G I G+++RV+
Sbjct: 65 VDGLNGRRIGGKRVRVEL 82
>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 = 49.2 bits (118), Expect = 6e-08
Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSR---GFCFVYFESRDDAAAAKDA 240
V L E + IFSK+G VE + + + R GF FV F+ DA++A++A
Sbjct: 5 VRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFK---DASSAENA 61
Query: 241 CT--GMEIDGRQIRV 253
G E+ GR+I V
Sbjct: 62 LQLNGTELGGRKISV 76
>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 = 49.2 bits (117), Expect = 7e-08
Identities = 22/45 (48%), Positives = 29/45 (64%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
V GLS TTE+QI F +G +E +E+ +D KT RGFCFV +
Sbjct: 4 VGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTY 48
>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 = 49.2 bits (117), Expect = 7e-08
Identities = 21/49 (42%), Positives = 29/49 (59%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V GLS+ TT + + F ++G V+ ++ D T R RGF FV FES D
Sbjct: 4 VGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
>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 = 49.3 bits (118), Expect = 7e-08
Identities = 21/65 (32%), Positives = 40/65 (61%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+++ +F GPV+ ++V D +TG S GF FV ++S +DA A G+++ ++I
Sbjct: 13 TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72
Query: 252 RVDFS 256
+V ++
Sbjct: 73 KVAYA 77
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 48.9 bits (116), Expect = 7e-08
Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGP--VERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
+ L V L I T+E I F ++ P VERV+ + R + FV+F SR+DA A
Sbjct: 2 KILYVRNLMIETSEDTIKKTFGQFNPGCVERVKKI--------RDYAFVHFTSREDAVHA 53
Query: 238 KDACTGMEIDGRQIRV 253
+ G E++G I V
Sbjct: 54 MNNLNGTELEGSCIEV 69
>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 = 48.8 bits (117), Expect = 7e-08
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD--DAAAAKDACTGMEIDG 248
E ++ +FSK G + V +V + K G+S+G+ +V FE+ + A D I G
Sbjct: 11 VPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLDR---ELIKG 66
Query: 249 RQIRVD 254
R + V
Sbjct: 67 RPMFVS 72
>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 = 48.8 bits (117), Expect = 7e-08
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVI--DAKTGRSRGFCFVYFESRDDAAAAKDAC 241
V L+ +TT++ + ++ G V+ + G+S+GF +V F S AAA K+
Sbjct: 3 VGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKL 62
Query: 242 TGMEIDGRQIRV 253
G E +G++ V
Sbjct: 63 EGREFNGKKCVV 74
>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 = 49.0 bits (117), Expect = 8e-08
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTG-RSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
E+++ +F KYGP+ V ID K R G+ F+ FE DA A G + DG+++
Sbjct: 13 EREVEDLFYKYGPI----VDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDGYDFDGQRL 68
Query: 252 RVD 254
RV+
Sbjct: 69 RVE 71
>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 = 48.7 bits (117), Expect = 8e-08
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
E ++ FS++G V R+ + KTG+S+G+ FV FES + A +
Sbjct: 13 EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAET 60
>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM3 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 it also
regulates the neurite elongation and morphological
differentiation. HuD specifically bound 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 = 86
Score = 48.9 bits (116), Expect = 9e-08
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
C+ V+ LS + E + +F +G V V+V+ D T + +GF FV + D+AA A +
Sbjct: 5 CIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64
Query: 241 CTGMEIDGRQIRVDFSVTQRAH 262
G + R ++V F T + H
Sbjct: 65 LNGYRLGDRVLQVSFK-TNKTH 85
>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 = 48.8 bits (117), Expect = 9e-08
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 192 TEQQINHIF-SKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T+ + F ++Y V +VV+D TGRS+G+ FV F D+ A G+ R
Sbjct: 14 TDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRP 73
Query: 251 IRV 253
+RV
Sbjct: 74 MRV 76
>gnl|CDD|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast
Saccharomyces cerevisiae SET domain-containing protein 1
(scSet1p) and similar proteins. This subfamily
corresponds to the RRM of scSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase, or
COMPASS component SET1, or lysine N-methyltransferase 2,
which is encoded by SET1 from the yeast S. cerevisiae.
It is a nuclear protein that may play a role in both
silencing and activating transcription. scSet1p is
closely related to the SET domain proteins of
multicellular organisms, which are implicated in diverse
aspects of cell morphology, growth control, and
chromatin-mediated transcriptional silencing. scSet1p
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a conserved SET
domain that may play a role in DNA repair and telomere
function. .
Length = 110
Score = 49.7 bits (119), Expect = 1e-07
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 8/80 (10%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF---ESRDDAAA---- 236
V+G T+E I + FS +G + + D T G + + + D AA
Sbjct: 7 VWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAKAAL 66
Query: 237 -AKDACTGMEIDGRQIRVDF 255
A I G + +V+
Sbjct: 67 KAVRKAQDCRIGGAEFKVEL 86
>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 = 48.6 bits (116), Expect = 1e-07
Identities = 23/57 (40%), Positives = 36/57 (63%), Gaps = 2/57 (3%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
P+R V G+ T E + FS+YG V+ V++V D + G S+G+ FV FE+++DA
Sbjct: 2 PNRIF-VGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDA 56
>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 = 48.1 bits (114), Expect = 1e-07
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V GLS T E++I F +G VE +E+ +D KT + RGFCF+ F+ +
Sbjct: 4 VGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>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 = 47.8 bits (114), Expect = 2e-07
Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GLS TT+ + + FS++G + V+ D T RSRGF FV F S + AA +A +
Sbjct: 6 GLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA-RPHK 64
Query: 246 IDGRQI 251
+DGR++
Sbjct: 65 VDGREV 70
>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 = 47.3 bits (112), Expect = 2e-07
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ L V L+ TE+ + FS++G +ERV+ + D + FV+FE RD A A D
Sbjct: 2 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAMD 53
Query: 240 ACTGMEIDGRQIRV 253
G EI+G +I +
Sbjct: 54 EMNGKEIEGEEIEI 67
>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding
protein 19 (RBM19), yeast multiple RNA-binding
domain-containing protein 1 (MRD1) and similar proteins.
This subfamily corresponds to the RRM1 of RBM19 and
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 77
Score = 47.6 bits (114), Expect = 3e-07
Identities = 20/73 (27%), Positives = 37/73 (50%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L TE ++ FSK+G ++ + G+SR F+ +++ ++A AKD
Sbjct: 5 VKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNN 64
Query: 244 MEIDGRQIRVDFS 256
I+ +I V+F+
Sbjct: 65 TYINTSKISVEFA 77
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP R)
and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 47.3 bits (112), Expect = 3e-07
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 10/79 (12%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGP--VERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
+ L V L I TTE+ I F+K+ P VERV+ + R + FV+F +R+DA AA
Sbjct: 2 KVLYVRNLMISTTEETIKAEFNKFKPGVVERVK--------KLRDYAFVHFFNREDAVAA 53
Query: 238 KDACTGMEIDGRQIRVDFS 256
G IDG I V +
Sbjct: 54 MSVMNGKCIDGASIEVTLA 72
>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 = 47.8 bits (114), Expect = 3e-07
Identities = 23/61 (37%), Positives = 30/61 (49%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQ 259
F KYGP+ V + +D T R RGF +V FE DA A GR+I + F+
Sbjct: 21 FGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFAQGD 80
Query: 260 R 260
R
Sbjct: 81 R 81
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 46.7 bits (111), Expect = 3e-07
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V T+E I IFS YG V+ V+++ F FV FES + A AKD+
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDSV 53
Query: 242 TGMEIDGRQIRV 253
G ++ + V
Sbjct: 54 HGKVLNNNPLYV 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 = 47.3 bits (112), Expect = 4e-07
Identities = 20/49 (40%), Positives = 29/49 (59%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V G+ T E + F KYG +E +EV+ D ++G+ RGF FV F+ D
Sbjct: 5 VGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHD 53
>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 = 47.1 bits (112), Expect = 4e-07
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L+ TE+++ +FS YG VE + ++ D +SRG FV + S++ A AA A
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60
Query: 242 TGMEI 246
G+
Sbjct: 61 NGVYT 65
>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 = 46.9 bits (112), Expect = 4e-07
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS T++++N FS++G + +EV + + + F F+ FE AA A ++ +
Sbjct: 11 LSPDVTKEELNERFSRHGKI--LEVNLIKRANHTNAFAFIKFEREQAAARAVESENHSML 68
Query: 247 DGRQIRVDF 255
+ + V +
Sbjct: 69 KNKTMHVQY 77
>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 = 46.8 bits (111), Expect = 4e-07
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEV-VIDAKTGRSRGFCFVYFESRDDAAAA 237
+R L V L T ++ +F + V++ + K G S+G ++ F++ +A A
Sbjct: 3 ARTLFVKNLPYNITVDELKEVFE-----DAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKA 57
Query: 238 KDACTGMEIDGRQIRVDFS 256
+ G E+DGR I VD++
Sbjct: 58 LEEKQGAEVDGRSIVVDYT 76
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 46.7 bits (111), Expect = 5e-07
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L +F L + + + IF YG V+ + + R FV F DAA A A
Sbjct: 4 LVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQR-----FVEFFDVRDAAKALRAM 58
Query: 242 TGMEIDGRQIRVD 254
G EI G+ + ++
Sbjct: 59 NGKEISGKPVVIE 71
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 46.9 bits (112), Expect = 5e-07
Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVV---IDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
L+ TE+ + F ++GP+ V+++ + + R+R FV F +R DA A D G
Sbjct: 9 LNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERALDELDG 68
Query: 244 MEIDGRQIRVDFS 256
++ G ++++ +
Sbjct: 69 KDVMGYELKLGWG 81
>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 = 46.4 bits (110), Expect = 5e-07
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 8/71 (11%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V +S T ++ +F ++G V + V D + FV+ E ++A AA +A G
Sbjct: 5 VGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEALNG 56
Query: 244 MEIDGRQIRVD 254
E+ GR+I V+
Sbjct: 57 KEVKGRRINVE 67
>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 = 46.8 bits (112), Expect = 5e-07
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGF-CFVYFESRDDAAAAKDACTGMEI--DG 248
T ++ +FS YG VE++ + ++ G V F+S + A AK A G I
Sbjct: 14 TVDVLHQVFSPYGAVEKILIFE-----KNTGVQALVQFDSVESAENAKKALNGRNIYDGC 68
Query: 249 RQIRVDFS 256
+ + FS
Sbjct: 69 CTLDIQFS 76
>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 = 46.7 bits (111), Expect = 5e-07
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E I FS +GP++ +++ D T + +GF FV +E + A A + G+ + GR I+
Sbjct: 14 EDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIK 73
Query: 253 V 253
V
Sbjct: 74 V 74
>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 = 46.6 bits (111), Expect = 5e-07
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 190 YTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI--D 247
TE + F+ +G ++ + VV D +T S+G +V F AA A + G + D
Sbjct: 13 SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72
Query: 248 GRQIRV 253
+ ++V
Sbjct: 73 TKPLKV 78
>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 = 46.6 bits (111), Expect = 5e-07
Identities = 25/64 (39%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSR-GFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
E+ I +F KYGP++ ID K R F FV FE DA A G + DG ++
Sbjct: 13 ERDIEDLFYKYGPIKA----IDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDGYDFDGYRL 68
Query: 252 RVDF 255
RV+F
Sbjct: 69 RVEF 72
>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 = 46.5 bits (111), Expect = 5e-07
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 188 SIY-------TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
SI+ TT +++ F G + R+ ++ D TG+ +GF ++ F + A
Sbjct: 1 SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-L 59
Query: 241 CTGMEIDGRQIRV 253
E GRQI+V
Sbjct: 60 LNESEFRGRQIKV 72
>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 = 46.4 bits (110), Expect = 6e-07
Identities = 31/70 (44%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GLS TT++ + FSK+G V + ID TGRSRGF FV F+ DAA+ +
Sbjct: 3 VGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFK---DAASVEKVLDQ 59
Query: 244 ME--IDGRQI 251
E +DGR I
Sbjct: 60 KEHKLDGRVI 69
>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 = 46.5 bits (111), Expect = 6e-07
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T++++ +FS +G V+ V + G RGF FV F ++ +A A +A + GR +
Sbjct: 13 TKKELRELFSPFGQVKSVRLPKKF-DGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHL 71
Query: 252 RVDFS 256
++++
Sbjct: 72 VLEYA 76
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 46.3 bits (110), Expect = 6e-07
Identities = 19/65 (29%), Positives = 37/65 (56%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+ +I +FS G +E +++ D TG+S G+ FV + +DA A + G+ + + I
Sbjct: 14 TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTI 73
Query: 252 RVDFS 256
+V ++
Sbjct: 74 KVSYA 78
>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 = 46.5 bits (110), Expect = 7e-07
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V G+ T E + F +YG +E +E++ D +G+ RGF FV F+ D
Sbjct: 5 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 53
>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 = 46.2 bits (110), Expect = 7e-07
Identities = 22/67 (32%), Positives = 34/67 (50%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
L+ TE+ + +FSKYGP+ V + ID T + +GF FV + + A A G
Sbjct: 10 LAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAELDGTVF 69
Query: 247 DGRQIRV 253
GR + +
Sbjct: 70 QGRLLHL 76
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 46.4 bits (111), Expect = 7e-07
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 199 IFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
FS +G + +V D G S+G+ FV+FE+ + A A + GM ++ +++ V
Sbjct: 22 TFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75
>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM3 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 85
Score = 46.6 bits (110), Expect = 7e-07
Identities = 24/80 (30%), Positives = 42/80 (52%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
C+ V+ LS E + +F +G V V+V+ D T + +GF FV + D+AA A +
Sbjct: 3 CIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIAS 62
Query: 241 CTGMEIDGRQIRVDFSVTQR 260
G + R ++V F +++
Sbjct: 63 LNGYRLGDRVLQVSFKTSKQ 82
>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 = 45.8 bits (109), Expect = 8e-07
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
L TE + +FS+ GP++ +++ + + + FV + AAAA G I
Sbjct: 6 LDRTVTEDLLAELFSQIGPIKSCKLIREHG---NDPYAFVEYYDHRSAAAALQTMNGRLI 62
Query: 247 DGRQIRVDFS 256
G++I+V+++
Sbjct: 63 LGQEIKVNWA 72
>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 = 45.9 bits (109), Expect = 8e-07
Identities = 18/61 (29%), Positives = 34/61 (55%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E+++ FS++G V+ V V KTG S+ + F+ F + + AA A + + G+ ++
Sbjct: 13 EKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72
Query: 253 V 253
V
Sbjct: 73 V 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 = 45.9 bits (109), Expect = 9e-07
Identities = 28/67 (41%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG-M 244
GLS TT + + FSK+G ++ V+ D T RSRGF FV F D A+ K G
Sbjct: 5 GLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTF--SDPASVDKVLAQGPH 62
Query: 245 EIDGRQI 251
E+DG++I
Sbjct: 63 ELDGKKI 69
>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 = 45.7 bits (109), Expect = 1e-06
Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T Q + +F + G V R +V D GRS+GF V FES +DA A + G +++GR+
Sbjct: 10 VTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRE 68
Query: 251 IRV 253
+ V
Sbjct: 69 LEV 71
>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 = 45.7 bits (108), Expect = 1e-06
Identities = 23/75 (30%), Positives = 38/75 (50%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + L T+QQ + +G +ER +V TG S+G+ FV + +D AA AK
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDL 61
Query: 242 TGMEIDGRQIRVDFS 256
G ++ R + V ++
Sbjct: 62 LGKQLGSRTLYVHWT 76
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 45.3 bits (108), Expect = 1e-06
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGP-VERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
R +G+F +S E+QI F K GP V ++E+ D + V FES DA A
Sbjct: 1 RTIGLFNVSDTVNEEQIKAFFEKIGPDVRKIELFPDHEG------ALVEFESPSDAGKAS 54
Query: 239 DACTGMEIDGRQIRVD 254
+ G + G+ I++
Sbjct: 55 LSLNGSQFGGKTIKIG 70
>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 = 46.1 bits (110), Expect = 1e-06
Identities = 28/83 (33%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 179 SRCLGVFGL-SIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
SRCL V L + + +FS+ G ++ I A G+ RGF FV + + +DA A
Sbjct: 2 SRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAI-APNGQPRGFAFVEYATAEDAEEA 60
Query: 238 KDACTGMEIDGRQIRVDFSVTQR 260
+ A G + G IRV F R
Sbjct: 61 QQALNGHSLQGSPIRVSFGNPGR 83
>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 = 45.3 bits (107), Expect = 2e-06
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL T++++ +FS+YG + ++ D TG SRG F+ F+ R +A A
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 242 TGMEIDG 248
G + +G
Sbjct: 63 NGQKPEG 69
>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 = 44.9 bits (107), Expect = 2e-06
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE+++ FS +G +E V V D +G+ FV F++ + AA A A G I+G+ +
Sbjct: 13 TEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAVNGTSINGQTV 66
Query: 252 RV 253
+
Sbjct: 67 KC 68
>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 = 45.0 bits (106), Expect = 2e-06
Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
P + + V GL+ TE++I F ++G +E +E+ +D KT + RGF F+ F+ D
Sbjct: 2 DPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEED 57
>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 = 44.6 bits (106), Expect = 3e-06
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V L TE+ + +F + GP+E V++ D G+ + F FV F+ A
Sbjct: 2 RTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKD-PNGKPKSFAFVTFKHEVSVPYAIQ 60
Query: 240 ACTGMEIDGRQIRVD 254
G+ + GR++R+
Sbjct: 61 LLNGIRLFGRELRIK 75
>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM3 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 = 86
Score = 44.7 bits (105), Expect = 3e-06
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
C+ V+ L+ E + +F +G V V+V+ D T + +GF FV + D+AA A +
Sbjct: 5 CIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS 64
Query: 241 CTGMEIDGRQIRVDFSVTQRAH 262
G + R ++V F T + H
Sbjct: 65 LNGYRLGDRVLQVSFK-TNKTH 85
>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 = 49.0 bits (117), Expect = 3e-06
Identities = 22/66 (33%), Positives = 36/66 (54%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE ++ +F +GPV V V D+ T RS G+ +V F++ DA A + + G+ I
Sbjct: 13 TEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPI 72
Query: 252 RVDFSV 257
R+ +S
Sbjct: 73 RIMWSQ 78
Score = 47.1 bits (112), Expect = 1e-05
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 199 IFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSV- 257
FSK+G + +V D + G+SRG+ FV+FE + A AA GM ++ +++ V +
Sbjct: 108 TFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIK 166
Query: 258 -TQRAHTPTP 266
+R P
Sbjct: 167 KHEREAAPLK 176
Score = 46.7 bits (111), Expect = 1e-05
Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDG 248
E ++ +F+K+G + V+ D +GRSRGF FV FE +DAA A + G +I
Sbjct: 191 NEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
Score = 40.2 bits (94), Expect = 0.002
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T++++ +FS+ G + +V++D K G SRGF FV F + ++A A G + G+ +
Sbjct: 298 TDEKLRELFSECGEITSAKVMLDEK-GVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPL 356
Query: 252 RV 253
V
Sbjct: 357 YV 358
>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 = 44.7 bits (105), Expect = 3e-06
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
L V G+ T E + F +YG ++ +E++ D ++G+ RGF FV F+ D
Sbjct: 3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHD 53
>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 = 44.2 bits (105), Expect = 3e-06
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
L V LS + + + + FS++G VER V++D + GRS G V F + A AA
Sbjct: 1 ALRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEFSRKPGAQAAIKR 59
Query: 241 CT 242
C+
Sbjct: 60 CS 61
>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-1, CELF-2, Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM1 of CELF-1, CELF-2 and
Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1,
or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3,
or CUG-BP2, or NAPOR) belong to the CUGBP1 and
ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family
of RNA-binding proteins that have been implicated in
regulation of pre-mRNA splicing, and control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. The
human CELF-1 is a nuclear and cytoplasmic RNA-binding
protein that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for onset
of type 1 myotonic dystrophy (DM1), a neuromuscular
disease associated with an unstable CUG triplet
expansion in the 3'-UTR (3'-untranslated region) of the
DMPK (myotonic dystrophy protein kinase) gene; it
preferentially targets UGU-rich mRNA elements. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contain three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains): two consecutive RRMs (RRM1
and RRM2) situated in the N-terminal region followed by
a linker region and the third RRM (RRM3) close to the
C-terminus of the protein. The two N-terminal RRMs of
EDEN-BP are necessary for the interaction with EDEN as
well as a part of the linker region (between RRM2 and
RRM3). Oligomerization of EDEN-BP is required for
specific mRNA deadenylation and binding. CELF-2 is
expressed in all tissues at some level, but highest in
brain, heart, and thymus. It has been implicated in the
regulation of nuclear and cytoplasmic RNA processing
events, including alternative splicing, RNA editing,
stability and translation. CELF-2 shares high sequence
identity with CELF-1, but shows different binding
specificity; it binds preferentially to sequences with
UG repeats and UGUU motifs. It has been shown to bind to
a Bruno response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to the
3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2
of CELF-2, can activate cardiac troponin T (cTNT) exon 5
inclusion. In addition, CELF-2 possesses a typical
arginine and lysine-rich nuclear localization signal
(NLS) in the C-terminus, within RRM3. This subgroup also
includes Drosophila melanogaster Bruno protein, which
plays a central role in regulation of Oskar (Osk)
expression in flies. It mediates repression by binding
to regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 84
Score = 44.4 bits (105), Expect = 4e-06
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGR--SRGFCFVYFESRDDAAAAKDACTGMEI 246
E+ + +F +YG V ++ V+ D S+G CFV F +R A A++A M+
Sbjct: 15 EKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKT 70
>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 = 44.2 bits (105), Expect = 4e-06
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGP-VERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
L + L E+ + FS +G ++ +++ D TG S+GF F+ ++S + + AA +
Sbjct: 3 NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62
Query: 240 ACTGMEIDGRQIRVDFS 256
A G + R I V ++
Sbjct: 63 AMNGQYLCNRPITVSYA 79
>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 = 44.2 bits (104), Expect = 5e-06
Identities = 24/70 (34%), Positives = 34/70 (48%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T + + F +YGP+ V V +D T R RGF ++ FE DA A + GRQ
Sbjct: 12 TRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQ 71
Query: 251 IRVDFSVTQR 260
I + F+ R
Sbjct: 72 IEIQFAQGDR 81
>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 = 43.8 bits (104), Expect = 5e-06
Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
++ I +F+++G +++ V D ++GRS G V FE R DA A G+ +DGR +
Sbjct: 13 SDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMKQYNGVPLDGRPM 71
Query: 252 RVDF 255
++
Sbjct: 72 KIQL 75
>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 = 47.6 bits (113), Expect = 5e-06
Identities = 29/105 (27%), Positives = 52/105 (49%), Gaps = 5/105 (4%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+++I +F+ G +E ++V D TG+S G+ FV + +DA A ++ G+ + + I
Sbjct: 16 TQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTI 75
Query: 252 RVDFSVTQRAHTPTPGIYM-GRPTYEQLNNTQSELGSLLSEKHAI 295
+V ++ +Y+ G P TQ EL S+ S I
Sbjct: 76 KVSYARPSSDSIKGANLYVSGLPK----TMTQHELESIFSPFGQI 116
Score = 46.9 bits (111), Expect = 1e-05
Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 1/87 (1%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
C+ V+ LS T E + +F +G V+ V+++ D T + +G+ FV + D+AA
Sbjct: 266 DGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAA 325
Query: 236 AAKDACTGMEIDGRQIRVDFSVTQRAH 262
A + G + R ++V F T +A+
Sbjct: 326 MAILSLNGYTLGNRVLQVSFK-TNKAY 351
Score = 43.0 bits (101), Expect = 2e-04
Identities = 38/187 (20%), Positives = 64/187 (34%), Gaps = 11/187 (5%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL T+ ++ IFS +G + ++ D TG S+G F+ F+ RD+A A
Sbjct: 92 LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151
Query: 242 TGMEIDG--RQIRVDFSVTQRAHTPTPGIYMGRPTYEQLNNTQSELGSLLSEKHAIKGGK 299
G G I V F+ + G+ E + N Q+ L + A G
Sbjct: 152 NGTTPSGCTEPITVKFANNPSSSNSK-GL---LSQLEAVQNPQTTRVPLSTILTAAGIGP 207
Query: 300 FEEVFGEIATVVGVGAVTMTEMSGNGRISPLQFSGGMENTDPICTQEKAKKMKKSIGMNL 359
G + ++ + P T + + + G +
Sbjct: 208 MHHAAARFRPSAGDFTAVLAHQQQQHAVAQ---QHAAQRASPPATDGQTAGL--AAGAQI 262
Query: 360 SALPQWG 366
+A G
Sbjct: 263 AASDGAG 269
>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 = 43.8 bits (103), Expect = 5e-06
Identities = 26/70 (37%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GLS T+++ + F+K+G V + +D TGRSRGF F+ F+ DA++ +
Sbjct: 4 VGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFK---DASSVEKVLEQ 60
Query: 244 ME--IDGRQI 251
E +DGR I
Sbjct: 61 KEHRLDGRLI 70
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 44.1 bits (105), Expect = 5e-06
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 14/87 (16%)
Query: 179 SRCL---GVFGLSIYTTEQQINHI-------FSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
SRC+ +F + T ++ + I SK+GPVE ++V D + G +V F
Sbjct: 1 SRCVILKNMFDPAEETEDEWDDEIKEDVLEECSKFGPVEHIKV--DKNS--PEGVVYVKF 56
Query: 229 ESRDDAAAAKDACTGMEIDGRQIRVDF 255
++ + A A G DGRQI ++
Sbjct: 57 KTVEAAQKCIQALNGRWFDGRQITAEY 83
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 43.5 bits (102), Expect = 6e-06
Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V LS TE I +FS+ GP + ++++D T + +CFV F AAA+ A
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59
Query: 242 TGMEIDGRQIRVDFS 256
G +I G++++V+++
Sbjct: 60 NGRKIMGKEVKVNWA 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 = 43.7 bits (103), Expect = 6e-06
Identities = 18/44 (40%), Positives = 27/44 (61%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
GL+ TT+ + F ++G V V+ D+ TGRSRGF F+ F+
Sbjct: 5 GLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFK 48
>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 = 43.7 bits (103), Expect = 6e-06
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGR 249
TE ++ IF YG + + ++ D TG RG FV ++ R++A AA + G G
Sbjct: 13 TEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGS 70
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy suppressor
of sporulation protein Msa1. It is a putative
RNA-binding protein encoded by a novel gene, msa1, from
the fission yeast Schizosaccharomyces pombe. Msa1 may be
involved in the inhibition of sexual differentiation by
controlling the expression of Ste11-regulated genes,
possibly through the pheromone-signaling pathway. Like
RIM4, Msa1 also contains two RRMs, both of which are
essential for the function of Msa1. .
Length = 86
Score = 43.9 bits (104), Expect = 6e-06
Identities = 29/82 (35%), Positives = 41/82 (50%), Gaps = 9/82 (10%)
Query: 178 PSRCLGVFGLSIYTTEQQI-----NHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
PS C+ V L ++ ++ H FSKYG + V+V+ D R R + FV F + D
Sbjct: 1 PSACVFVASLPASKSDDELEAAVTEH-FSKYGTLVFVKVLRDW---RQRPYAFVQFTNDD 56
Query: 233 DAAAAKDACTGMEIDGRQIRVD 254
DA A G +DGR IR +
Sbjct: 57 DAKNALAKGQGTILDGRHIRCE 78
>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 = 43.4 bits (102), Expect = 7e-06
Identities = 18/46 (39%), Positives = 30/46 (65%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
TEQ++ +F ++G V V ++ D +TG +G CFV + +RD+A A
Sbjct: 12 TEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRA 57
>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 = 43.5 bits (102), Expect = 7e-06
Identities = 25/70 (35%), Positives = 38/70 (54%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS T + I F+ +G + VV D TG+S+G+ FV F ++ DA A G +
Sbjct: 9 LSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWL 68
Query: 247 DGRQIRVDFS 256
GRQIR +++
Sbjct: 69 GGRQIRTNWA 78
>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 = 43.5 bits (103), Expect = 8e-06
Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS + + F + G V V + D GRS+GF V F + + A A +G E+
Sbjct: 7 LSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKAL-EKSGEEL 64
Query: 247 DGRQIRVD 254
GR+IRVD
Sbjct: 65 LGREIRVD 72
>gnl|CDD|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein C (hnRNP C)-related proteins.
This subfamily corresponds to the RRM in the hnRNP
C-related protein family, including hnRNP C proteins,
Raly, and Raly-like protein (RALYL). hnRNP C proteins,
C1 and C2, are produced by a single coding sequence.
They are the major constituents of the heterogeneous
nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in
vertebrates. They bind hnRNA tightly, suggesting a
central role in the formation of the ubiquitous hnRNP
complex; they are involved in the packaging of the hnRNA
in the nucleus and in processing of pre-mRNA such as
splicing and 3'-end formation. Raly, also termed
autoantigen p542, is an RNA-binding protein that may
play a critical role in embryonic development. The
biological role of RALYL remains unclear. It shows high
sequence homology with hnRNP C proteins and Raly.
Members of this family are characterized by an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal auxiliary domain. The Raly proteins
contain a glycine/serine-rich stretch within the
C-terminal regions, which is absent in the hnRNP C
proteins. Thus, the Raly proteins represent a newly
identified class of evolutionarily conserved
autoepitopes. .
Length = 68
Score = 43.0 bits (102), Expect = 8e-06
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 190 YTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGR 249
+++ + IFSKYG + + + +G+ FV F++ +DA AA G EI G+
Sbjct: 12 KVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAGENGREIAGQ 63
Query: 250 QI 251
++
Sbjct: 64 KL 65
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup corresponds
to the RRM3 of ACF, also termed APOBEC-1-stimulating
protein, an RNA-binding subunit of a core complex that
interacts with apoB mRNA to facilitate C to U RNA
editing. It may also act as an apoB mRNA recognition
factor and chaperone and play a key role in cell growth
and differentiation. ACF shuttles between the cytoplasm
and nucleus. ACF contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high affinity
for an 11 nucleotide AU-rich mooring sequence 3' of the
edited cytidine in apoB mRNA. All three RRMs may be
required for complementation of editing activity in
living cells. RRM2/3 are implicated in ACF interaction
with APOBEC-1. .
Length = 83
Score = 43.5 bits (102), Expect = 8e-06
Identities = 29/76 (38%), Positives = 40/76 (52%), Gaps = 10/76 (13%)
Query: 180 RCLGVFGLSIYTTEQQINHIFS--KYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
+ L V L + TTE+ I F+ K G VERV+ + R + FV+F +R+DA A
Sbjct: 9 KILYVRNLMLSTTEETIEKEFNSIKPGAVERVKKI--------RDYAFVHFSNREDAVDA 60
Query: 238 KDACTGMEIDGRQIRV 253
+A G IDG I V
Sbjct: 61 MNALNGKVIDGSPIEV 76
>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 = 43.1 bits (102), Expect = 8e-06
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
V L T + + +FSKYG V V + TG +GF F+ FE+ ++A A
Sbjct: 4 VECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57
>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 = 43.0 bits (102), Expect = 8e-06
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 7/80 (8%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFV-YFESRDDAAAA 237
SR L V ++ ++++ +F ++G + + + RGF V Y++ R A A
Sbjct: 1 SRTLFVRNINSNVEDEELRALFEQFGDIRTLYTAC-----KHRGFIMVSYYDIRA-ARRA 54
Query: 238 KDACTGMEIDGRQIRVDFSV 257
K A G E+ GR++ + FS+
Sbjct: 55 KRALQGTELGGRKLDIHFSI 74
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 43.6 bits (102), Expect = 8e-06
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V LS TE I +FS+ GP + +++ + + +CFV F DAAAA A
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59
Query: 242 TGMEIDGRQIRVDFSVT 258
G +I G++++V+++ T
Sbjct: 60 NGRKILGKEVKVNWATT 76
>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 = 43.1 bits (101), Expect = 1e-05
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L + GLS TT++ + F ++G + V+ D T RSRGF FV + S ++ AA +
Sbjct: 3 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62
Query: 240 ACTGMEIDGRQIRVDFSVTQ 259
A ++DGR + +V++
Sbjct: 63 A-RPHKVDGRVVEPKRAVSR 81
>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 = 43.1 bits (101), Expect = 1e-05
Identities = 25/70 (35%), Positives = 37/70 (52%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS T I F+ +G + VV D TG+S+G+ FV F ++ DA A G +
Sbjct: 9 LSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL 68
Query: 247 DGRQIRVDFS 256
GRQIR +++
Sbjct: 69 GGRQIRTNWA 78
>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 = 43.1 bits (101), Expect = 1e-05
Identities = 20/49 (40%), Positives = 27/49 (55%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
V GLS T + + F ++G VE ++ D T R RGF FV FE+ D
Sbjct: 8 VGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENED 56
>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 = 42.8 bits (101), Expect = 1e-05
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
TE+ + F ++G +E V +V D TG S+GF +V F AA A + C
Sbjct: 13 TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENC 62
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
TT +++ +F KYG V +VV + + FV+ E +DA A A G E G++
Sbjct: 11 TTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKALNGYEFMGKR 62
Query: 251 IRV 253
I V
Sbjct: 63 INV 65
>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 = 43.1 bits (102), Expect = 1e-05
Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL T+Q++ +FS YG + ++ D TG SRG F+ F+ R +A A A
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 242 TGMEIDG--RQIRVDFS 256
G G I V F+
Sbjct: 63 NGTIPPGATEPITVKFA 79
>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 = 42.7 bits (101), Expect = 1e-05
Identities = 26/73 (35%), Positives = 38/73 (52%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GLS T + +FSKYG V ++V +A++ +R F FV S ++AA
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61
Query: 242 TGMEIDGRQIRVD 254
E+ GR I V+
Sbjct: 62 HRTELHGRVISVE 74
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM1
of U1A/U2B"/SNF protein family which contains Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs), connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. Moreover,
U2B" does not require an auxiliary protein for binding
to RNA, and its nuclear transport is independent of U2
snRNA binding. .
Length = 78
Score = 42.9 bits (102), Expect = 1e-05
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+ + +FS++GPV +++V +KT + RG FV F+ + A A A G + +R+
Sbjct: 18 RSLYALFSQFGPV--LDIVA-SKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRI 74
Query: 254 DFS 256
++
Sbjct: 75 QYA 77
>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 = 43.0 bits (102), Expect = 1e-05
Identities = 24/84 (28%), Positives = 34/84 (40%), Gaps = 9/84 (10%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSR-------GFCFVYFESRD 232
L V L+ TTE+ + F K G V V I K G+ FV F+S++
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGV--RSVTIAKKKDPKGPGKLLSMGYGFVEFKSKE 58
Query: 233 DAAAAKDACTGMEIDGRQIRVDFS 256
A A G +DG + + S
Sbjct: 59 AAQKALKRLQGTVLDGHALELKLS 82
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 42.6 bits (101), Expect = 1e-05
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 11/71 (15%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDA-----KTGRSRGFCFVYFESRDDAAAAKDACTGME 245
+ I +F +YG + + + ++R FC+V F S + AAAA G
Sbjct: 12 FDQSDIRDLFEQYGEI------LSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLNGKL 65
Query: 246 IDGRQIRVDFS 256
+G ++ V S
Sbjct: 66 GEGYKLVVKIS 76
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 46.9 bits (111), Expect = 1e-05
Identities = 31/93 (33%), Positives = 46/93 (49%), Gaps = 15/93 (16%)
Query: 168 EFADGRENPQPS-----RCLGVFGLSIYTTEQQINHIFSKYGP--VERVEVVIDAKTGRS 220
++A+ E + L V L TTE+ I FS++ P VERV+ +
Sbjct: 217 DWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------- 268
Query: 221 RGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
R + FV+FE R+DA A D G E++G +I V
Sbjct: 269 RDYAFVHFEDREDAVKAMDELNGKELEGSEIEV 301
Score = 31.9 bits (72), Expect = 0.72
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 4/89 (4%)
Query: 172 GRENPQPSRCLGVFGLSIYTT--EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFE 229
G QP R VF I E ++ +F K GP+ + +++D +G++RG+ FV F
Sbjct: 49 GWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF-SGQNRGYAFVTFC 107
Query: 230 SRDDAAAAKDACTGMEI-DGRQIRVDFSV 257
+++A A EI GR + V SV
Sbjct: 108 GKEEAKEAVKLLNNYEIRPGRLLGVCISV 136
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 199 IFSKYGPVERVEVVI-DAKTGRSRGFCFVYFESRDDAAAAKDACTGMEID 247
IFSK+G + V + + +TG+++G+ FV F + ++A A A G ++D
Sbjct: 27 IFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLD 76
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
+R L V L + +++ +F KYG + ++ + +T RG FV +E DA A
Sbjct: 2 NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNAC 58
Query: 239 DACTGMEIDGRQIRV 253
D +G + R + V
Sbjct: 59 DHLSGFNVANRYLVV 73
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 42.3 bits (99), Expect = 2e-05
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ L V L+ TE+ + F ++G +ERV+ + D + F++F+ RD A A +
Sbjct: 2 KVLFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 53
Query: 240 ACTGMEIDGRQIRVDFS 256
G E++G I + F+
Sbjct: 54 EMNGKELEGENIEIVFA 70
>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM2 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. It promotes the formation of
D-loops in superhelical duplex DNA, and is involved in
cell proliferation. PSF can also interact with multiple
factors. It is an RNA-binding component of spliceosomes
and binds to insulin-like growth factor response element
(IGFRE). Moreover, PSF functions as a transcriptional
repressor interacting with Sin3A and mediating silencing
through the recruitment of histone deacetylases (HDACs)
to the DNA binding domain (DBD) of nuclear hormone
receptors. PSF is an essential pre-mRNA splicing factor
and is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. PSF
forms a heterodimer with the nuclear protein p54nrb,
also known as non-POU domain-containing octamer-binding
protein (NonO). The PSF/p54nrb complex displays a
variety of functions, such as DNA recombination and RNA
synthesis, processing, and transport. PSF contains two
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which are responsible for interactions with
RNA and for the localization of the protein in speckles.
It also contains an N-terminal region rich in proline,
glycine, and glutamine residues, which may play a role
in interactions recruiting other molecules. .
Length = 80
Score = 42.4 bits (99), Expect = 2e-05
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V LS Y + + + FS++GPVER V++D + GRS G V F S+ A A + C
Sbjct: 2 LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVDDR-GRSTGKGIVEFASKPAARKAFERC 60
Query: 242 T 242
T
Sbjct: 61 T 61
>gnl|CDD|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM4 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in theThe CD
corresponds to the RRM. regulation of poly(A) tail
length during the polyadenylation reaction, translation
initiation, mRNA stabilization by influencing the rate
of deadenylation and inhibition of mRNA decapping. The
family represents type I polyadenylate-binding proteins
(PABPs), including polyadenylate-binding protein 1
(PABP-1 or PABPC1), polyadenylate-binding protein 3
(PABP-3 or PABPC3), polyadenylate-binding protein 4
(PABP-4 or APP-1 or iPABP), polyadenylate-binding
protein 5 (PABP-5 or PABPC5), polyadenylate-binding
protein 1-like (PABP-1-like or PABPC1L),
polyadenylate-binding protein 1-like 2 (PABPC1L2 or
RBM32), polyadenylate-binding protein 4-like
(PABP-4-like or PABPC4L), yeast polyadenylate-binding
protein, cytoplasmic and nuclear (PABP or ACBP-67), and
similar proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found in
the nucleus. PABP-1 may be involved in nucleocytoplasmic
trafficking and utilization of mRNP particles. PABP-1
contains four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a less well conserved
linker region, and a proline-rich C-terminal conserved
domain (CTD). PABP-3 is a testis-specific
poly(A)-binding protein specifically expressed in round
spermatids. It is mainly found in mammalian and may play
an important role in the testis-specific regulation of
mRNA homeostasis. PABP-3 shows significant sequence
similarity to PABP-1. However, it binds to poly(A) with
a lower affinity than PABP-1. Moreover, PABP-1 possesses
an A-rich sequence in its 5'-UTR and allows binding of
PABP and blockage of translation of its own mRNA. In
contrast, PABP-3 lacks the A-rich sequence in its
5'-UTR. PABP-4 is an inducible poly(A)-binding protein
(iPABP) that is primarily localized to the cytoplasm. It
shows significant sequence similarity to PABP-1 as well.
The RNA binding properties of PABP-1 and PABP-4 appear
to be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal brain
and in a range of adult tissues in mammalian, such as
ovary and testis. It may play an important role in germ
cell development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 79
Score = 42.2 bits (100), Expect = 2e-05
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
++++ FS +G + +V+ D K GRS+GF FV F S ++A A G I G+ +
Sbjct: 14 DDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPL 72
Query: 252 RV 253
V
Sbjct: 73 YV 74
>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 = 42.3 bits (99), Expect = 2e-05
Identities = 25/61 (40%), Positives = 31/61 (50%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFSVTQ 259
F +YGP+ V V +D T R RGF +V FE DA A I GRQI + F+
Sbjct: 21 FGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFAQGD 80
Query: 260 R 260
R
Sbjct: 81 R 81
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 41.9 bits (99), Expect = 2e-05
Identities = 16/63 (25%), Positives = 32/63 (50%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GL TT++ + + +G + + ++D KT + +G+ FV F+S + A A + G
Sbjct: 7 GLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGRG 66
Query: 246 IDG 248
+
Sbjct: 67 VQA 69
>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 = 3e-05
Identities = 18/47 (38%), Positives = 25/47 (53%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
TE+ + FSK+G V VID TGR++G FV F+ + A
Sbjct: 13 ATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59
>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 = 41.3 bits (97), Expect = 4e-05
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
LS TTE ++ F + G + RV ++ +G+ +GF FV FE + A +A G +
Sbjct: 6 LSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE---FATNALKGKHL 62
Query: 247 DGRQIRVDF 255
+GR +RV++
Sbjct: 63 NGRALRVEY 71
>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 = 41.0 bits (97), Expect = 4e-05
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYG-PVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
+ + GL TE+ I FS P + + +V D GR G +V F S +DA A
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRAL- 58
Query: 240 ACTGMEIDGRQIRV 253
++ GR I V
Sbjct: 59 RKHNNKMGGRYIEV 72
>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 = 41.1 bits (96), Expect = 4e-05
Identities = 21/49 (42%), Positives = 30/49 (61%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD 232
+ GLS TT++ + FSK+G V + +D TGRSRGF FV F+ +
Sbjct: 3 IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESE 51
>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 = 41.2 bits (96), Expect = 4e-05
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L + GLS TTE+ + + + ++G + V+ D + RSRGF FV F ++ AA
Sbjct: 3 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM- 61
Query: 240 ACTGMEIDGRQI 251
A IDGR +
Sbjct: 62 AARPHTIDGRVV 73
>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM1 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10,
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 = 81
Score = 41.2 bits (97), Expect = 4e-05
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVER-VEVVIDAKTGRSRGFCFVYFESRDDAAA 236
P+ + + GL + TE+ I + +G + V ++ TG SRGF FV F S ++A
Sbjct: 1 PNNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60
Query: 237 AKDACTG-MEIDGRQIRVDFS 256
+ G +++ +I + +S
Sbjct: 61 WMELNQGKLQLQDYKITLHYS 81
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 76
Score = 41.0 bits (97), Expect = 5e-05
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L Y TE ++ F G V V+V + + G+SR F FV F+S +DA A
Sbjct: 5 VKNLPKYVTEDRLREHFESKGEVTDVKV-MRTRDGKSRRFGFVGFKSEEDAQQAVKYFNK 63
Query: 244 MEIDGRQIRVDF 255
ID +I V+
Sbjct: 64 TFIDTSKISVEL 75
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 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 = 75
Score = 41.2 bits (97), Expect = 5e-05
Identities = 16/54 (29%), Positives = 30/54 (55%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
T++Q++ +F +E ++ D TG+S+GF +V + + A AK+ G E
Sbjct: 12 TQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNGFE 65
>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 = 41.0 bits (96), Expect = 5e-05
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
TE+++ +F KYG E+ I + +GF F+ E+R A AK M + G+Q
Sbjct: 13 ITEEEMRKLFEKYGKAG--EIFIH----KDKGFGFIRLETRTLAEIAKAELDNMPLRGKQ 66
Query: 251 IRVDF 255
+RV F
Sbjct: 67 LRVRF 71
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 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. Its cellular function remains
unknown currently, however, 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 = 71
Score = 40.7 bits (95), Expect = 6e-05
Identities = 30/77 (38%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 180 RC-LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
RC L V L TE+ +F KYG E EV I+ R RGF F+ ESR A AK
Sbjct: 1 RCRLFVGNLPTDITEEDFKKLFEKYG--EPSEVFIN----RDRGFGFIRLESRTLAEIAK 54
Query: 239 DACTGMEIDGRQIRVDF 255
G + R +R+ F
Sbjct: 55 AELDGTILKNRPLRIRF 71
>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 = 41.2 bits (97), Expect = 6e-05
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
E+ + +F ++G + + V+ D TG +G F+ + +R+ A A+ A
Sbjct: 18 EEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66
>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 = 41.0 bits (96), Expect = 6e-05
Identities = 25/68 (36%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GLS TT++ + FS+YG V ++ D T RSRGF FV F+ +
Sbjct: 4 VGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG-GP 62
Query: 244 MEIDGRQI 251
+DGR I
Sbjct: 63 HTLDGRTI 70
>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 = 40.8 bits (96), Expect = 7e-05
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
FS G + RV + D +TG S+GF ++ F+S D A + G ++ G + VD
Sbjct: 24 FSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALE-LDGSDLGGGNLVVD 77
>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 = 40.5 bits (95), Expect = 7e-05
Identities = 23/63 (36%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
+ I +F KYG + ID K R F FV FE DA A G + DG ++R
Sbjct: 13 TKDIEDLFYKYGAIRD----IDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR 68
Query: 253 VDF 255
V+F
Sbjct: 69 VEF 71
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. 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.
Length = 76
Score = 40.5 bits (94), Expect = 9e-05
Identities = 25/76 (32%), Positives = 40/76 (52%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
R L V GLS T + ++FSKYG V +VV +A++ +R + FV + ++A
Sbjct: 1 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60
Query: 239 DACTGMEIDGRQIRVD 254
+ E+ GR I V+
Sbjct: 61 NHLHRTELHGRMISVE 76
>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 = 40.5 bits (94), Expect = 9e-05
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL T++++ +FS+YG + +++D TG SRG F+ F+ R +A A
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64
Query: 242 TGMEIDG 248
G + G
Sbjct: 65 NGQKPSG 71
>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 = 40.2 bits (95), Expect = 9e-05
Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 199 IFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEID-GRQIRVDFS 256
+F K GP+ + +++D +G +RG+ FV + +++ A A EI G+++ V S
Sbjct: 21 LFEKAGPIYELRLMMDF-SGLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGVCIS 78
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2, Smad3
and Smad4, and stimulates Smad-mediated transactivation.
Cpo may play an important role in regulating normal
function of the nervous system, whereas mutations in
Mec-8 affect mechanosensory and chemosensory neuronal
function. All members contain a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Some
uncharacterized family members contain two RRMs; this
subfamily includes their RRM1. Their RRM2 shows high
sequence homology to the RRM of yeast proteins scw1,
Whi3, and Whi4.
Length = 79
Score = 40.3 bits (95), Expect = 9e-05
Identities = 24/69 (34%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRG-FCFVYFESRDDAAAAK 238
R L V GL E+++ H+F + E +V K G + FV F S AAAA
Sbjct: 1 RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60
Query: 239 DACTGMEID 247
DA G D
Sbjct: 61 DALQGYRFD 69
>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding
protein 7 (RBM7). This subfamily corresponds to the RRM
of RBM7, a ubiquitously expressed pre-mRNA splicing
factor that enhances messenger RNA (mRNA) splicing in a
cell-specific manner or in a certain developmental
process, such as spermatogenesis. RBM7 interacts with
splicing factors SAP145 (the spliceosomal splicing
factor 3b subunit 2) and SRp20. It may play a more
specific role in meiosis entry and progression. Together
with additional testis-specific RNA-binding proteins,
RBM7 may regulate the splicing of specific pre-mRNA
species that are important in the meiotic cell cycle.
RBM7 contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. .
Length = 75
Score = 40.3 bits (94), Expect = 1e-04
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V L TE+ I +F + GPV +V++ D K G+ + F FV F+ A +
Sbjct: 2 RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSVPYAMN 60
Query: 240 ACTGMEIDGRQIRV 253
G+++ GR + +
Sbjct: 61 LLNGIKLYGRPLNI 74
>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 = 40.3 bits (95), Expect = 1e-04
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
T++ + FSKY ++ +VV D +TG+S+G+ FV F +D A
Sbjct: 18 VTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKA 64
>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM3 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 40.4 bits (94), Expect = 1e-04
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 1/82 (1%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
C+ ++ L E + +F +G V V+V+ D T + +GF FV + ++AA A +
Sbjct: 3 CIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIAS 62
Query: 241 CTGMEIDGRQIRVDFSVTQRAH 262
G + + ++V F T ++H
Sbjct: 63 LNGYRLGDKILQVSFK-TSKSH 83
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM2 of HuR,
also termed ELAV-like protein 1 (ELAV-1), the
ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs and
enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 84
Score = 40.0 bits (93), Expect = 1e-04
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GL T++ + +FS++G + V++D TG SRG F+ F+ R +A A +
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62
Query: 242 TGMEIDG--RQIRVDFS 256
G + G I V F+
Sbjct: 63 NGHKPPGSSEPITVKFA 79
>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 = 40.0 bits (93), Expect = 1e-04
Identities = 26/67 (38%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD-ACTGM 244
GLS TT++ + F ++G V+ V+ D T RSRGF FV F D A K A +
Sbjct: 7 GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF--MDQAGVDKVLAQSRH 64
Query: 245 EIDGRQI 251
E+D + I
Sbjct: 65 ELDSKTI 71
>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 = 39.9 bits (94), Expect = 1e-04
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
GL + +++ +F KYG VE + + G+ +CFV + S +DAAAA DA G E
Sbjct: 10 GLGNGVSREELLRVFEKYGTVEDLVMP----PGKP--YCFVSYSSIEDAAAAYDALNGKE 63
Query: 246 IDGRQIRVDF 255
++ Q
Sbjct: 64 LELPQQNKPL 73
>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate
paraspeckle protein 1 (PSP1 or PSPC1). This subgroup
corresponds to the RRM2 of PSPC1, also termed
paraspeckle component 1 (PSPC1), a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. It is ubiquitously
expressed and highly conserved in vertebrates. Although
its cellular function remains unknown currently, PSPC1
forms a novel heterodimer with the nuclear protein
p54nrb, also known as non-POU domain-containing
octamer-binding protein (NonO), which localizes to
paraspeckles in an RNA-dependent manner. PSPC1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), at the N-terminus. .
Length = 80
Score = 40.0 bits (93), Expect = 1e-04
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V LS + + + FS++GPVER V++D + GR G FV F ++ A A + C
Sbjct: 2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDR-GRPTGKGFVEFAAKPAARKALERC 60
Query: 242 T 242
Sbjct: 61 A 61
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 39.5 bits (92), Expect = 1e-04
Identities = 30/77 (38%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 180 RC-LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
RC L V L TE + +F+KYG E EV I+ + +GF F+ ESR A AK
Sbjct: 1 RCRLFVGNLPADITEDEFKKLFAKYG--EPGEVFIN----KGKGFGFIKLESRALAEIAK 54
Query: 239 DACTGMEIDGRQIRVDF 255
+ GRQ+RV F
Sbjct: 55 AELDDTPMRGRQLRVRF 71
>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 = 39.8 bits (94), Expect = 1e-04
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 3/57 (5%)
Query: 200 FSKYGPVERVEV---VIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
KYG V V + + G FV F +DA A+ A G + DGR +
Sbjct: 32 CGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVVA 88
>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 = 39.7 bits (92), Expect = 2e-04
Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L + GLS TT+ + F K+G + V+ D +T RSRGF FV + ++ AA
Sbjct: 3 RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62
Query: 240 ACTGMEIDGRQIRVDFSVTQ 259
A ++DGR + +V++
Sbjct: 63 A-RPHKVDGRVVEPKRAVSR 81
>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM1 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 39.7 bits (92), Expect = 2e-04
Identities = 18/65 (27%), Positives = 37/65 (56%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+++ +F G +E ++V D TG+S G+ FV + +DA A + G+++ + I
Sbjct: 16 TQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTI 75
Query: 252 RVDFS 256
+V ++
Sbjct: 76 KVSYA 80
>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 = 39.8 bits (93), Expect = 2e-04
Identities = 19/45 (42%), Positives = 29/45 (64%), Gaps = 1/45 (2%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
V G+ I E +I F+KYG V+ V+++ D +TG S+G+ FV F
Sbjct: 10 VGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSF 53
>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 = 39.8 bits (92), Expect = 2e-04
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL T++++ +FS+YG + +++D TG SRG F+ F+ R +A A
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67
Query: 242 TGMEIDG 248
G + G
Sbjct: 68 NGQKPPG 74
>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 = 39.5 bits (92), Expect = 2e-04
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L I T ++ + YG +ER +V TG S+G+ FV + +D A+ A+
Sbjct: 2 LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKAR--- 58
Query: 242 TGMEIDGRQI 251
+E+ G+Q+
Sbjct: 59 --LELLGKQL 66
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 39.7 bits (92), Expect = 2e-04
Identities = 18/65 (27%), Positives = 36/65 (55%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T++++ +F G +E ++V D TG+S G+ FV + DA A + G+ + + I
Sbjct: 17 TQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 76
Query: 252 RVDFS 256
+V ++
Sbjct: 77 KVSYA 81
>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 = 43.0 bits (101), Expect = 2e-04
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 1/81 (1%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L +Y E QI + +G ++ ++ D TG S+G+ F ++ A A G +
Sbjct: 302 NLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD 361
Query: 246 IDGRQIRVDFSVTQRAHTPTP 266
++ V + A+ T
Sbjct: 362 TGDNKLHVQRA-CVGANQATI 381
Score = 38.7 bits (90), Expect = 0.005
Identities = 27/71 (38%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 65 DKKYRKSITRSRSGSPHRRSK-RPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPG 123
++ R+S RSR HRRS+ R R +R R S SPR R RSR
Sbjct: 22 ERPRRRSRDRSRFRDRHRRSRERSYREDSRPR---DRRRYDSRSPRSLRYSSVRRSRDRP 78
Query: 124 YRKRSSSYRSG 134
R+RS S RS
Sbjct: 79 -RRRSRSVRSI 88
Score = 29.5 bits (66), Expect = 3.3
Identities = 19/72 (26%), Positives = 25/72 (34%), Gaps = 12/72 (16%)
Query: 64 DDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPG 123
D ++Y RS S RRS+ R RSRS + R R RSP
Sbjct: 54 DRRRYDSRSPRSLRYSSVRRSRDR-----------PRRRSRSVR-SIEQHRRRLRDRSPS 101
Query: 124 YRKRSSSYRSGG 135
+ R +
Sbjct: 102 NQWRKDDKKRSL 113
>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 = 39.3 bits (92), Expect = 2e-04
Identities = 23/79 (29%), Positives = 33/79 (41%), Gaps = 3/79 (3%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R + V G+ +E + FS G V RV + S F FV F + A +A
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLC--GDRQHSARFAFVEFADAESALSAL- 57
Query: 240 ACTGMEIDGRQIRVDFSVT 258
+G + G +RV S T
Sbjct: 58 NLSGTLLGGHPLRVSPSKT 76
>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 = 39.2 bits (91), Expect = 2e-04
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI-DGRQI 251
E ++ +F K GP+ + +++D +G++RG+ F+ F ++ A A C EI G+ +
Sbjct: 15 EDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLCDNYEIRPGKHL 74
Query: 252 RVDFS 256
V S
Sbjct: 75 GVCIS 79
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 39.6 bits (93), Expect = 3e-04
Identities = 20/78 (25%), Positives = 32/78 (41%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
P R + L+ E + + KYG VE V++ KT + G V F+S A
Sbjct: 1 PPREVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRC 60
Query: 238 KDACTGMEIDGRQIRVDF 255
+ + G+ I+V
Sbjct: 61 VEKLNQTSVMGKIIKVFL 78
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains). The
RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 38.8 bits (91), Expect = 3e-04
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVV---IDAKTGRSRGFCFVYFESRDDAAAA 237
+ V +S TE+Q+ +F G +E + + D S+ CFV +E +D A
Sbjct: 2 VQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSK-VCFVKYEDPEDVGVA 59
>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 = 3e-04
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
S L + LS TE+ + ++F +YG ++ ++++ RG +V E+R DA A
Sbjct: 2 STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRAL 55
Query: 239 DACTGMEIDGRQIRVD 254
+++ G++I+V
Sbjct: 56 QKLRNVKLAGKKIKVA 71
>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 = 38.9 bits (91), Expect = 3e-04
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 4/70 (5%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSR--GFCFVYFESRDDAAAAKDACTGM 244
L TE ++ F ++G V +EV I++K G R F FV F+ +
Sbjct: 11 LPHDITEDELKEFFKEFGNV--LEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANKPIY 68
Query: 245 EIDGRQIRVD 254
++ V+
Sbjct: 69 FRGDHRLNVE 78
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 38.8 bits (90), Expect = 3e-04
Identities = 20/62 (32%), Positives = 34/62 (54%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+ + F +G V +V ID +T S+ F FV +++ D A AA A G +I +++
Sbjct: 17 TDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAMNGFQIGTKRL 76
Query: 252 RV 253
+V
Sbjct: 77 KV 78
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 38.5 bits (90), Expect = 3e-04
Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
+ + + ++ + S YG V+ E V + V +ES + A A + G E
Sbjct: 7 NIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETAT---VNVTYESPEQAQQAVNKLNGHE 63
Query: 246 IDGRQIRVDFS 256
+G +++V +
Sbjct: 64 YEGSKLKVSYI 74
>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 = 38.5 bits (89), Expect = 4e-04
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+ ++ +FS G VE +++ D G S G+ FV + + DA A + G+ + + I
Sbjct: 14 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTI 73
Query: 252 RVDFS 256
+V ++
Sbjct: 74 KVSYA 78
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 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. 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 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 = 38.2 bits (89), Expect = 4e-04
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 6/66 (9%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
+ YTT+ + +F +G +++ + RGF FV ++ + AA A G +
Sbjct: 8 IPPYTTQADLIPLFQNFG------YILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFPV 61
Query: 247 DGRQIR 252
GR +R
Sbjct: 62 HGRPLR 67
>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 = 38.3 bits (89), Expect = 5e-04
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 10/68 (14%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI--DG 248
+ +I +F KYG V+RV D K+ GF FVY E DA A E
Sbjct: 12 ARQSEIERLFGKYGRVDRV----DMKS----GFAFVYMEDERDAEDAIRGLDNFEFGRQR 63
Query: 249 RQIRVDFS 256
R++RV+++
Sbjct: 64 RRLRVEWA 71
>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 = 38.1 bits (89), Expect = 5e-04
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
E ++ +F +G + V++ K G+ R F FV +++ ++A A ID +I
Sbjct: 13 KEDKLRKLFEAFGTITDVQLKYT-KDGKFRKFGFVGYKTEEEAQKALKHFNNSFIDTSKI 71
Query: 252 RVDF 255
V+
Sbjct: 72 TVEI 75
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and similar
proteins. This subfamily corresponds to the RRM of
Acinus, a caspase-3-activated nuclear factor that
induces apoptotic chromatin condensation after cleavage
by caspase-3 without inducing DNA fragmentation. It is
essential for apoptotic chromatin condensation and may
also participate in nuclear structural changes occurring
in normal cells. Acinus contains a P-loop motif and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), which
indicates Acinus might have ATPase and DNA/RNA-binding
activity. .
Length = 90
Score = 38.4 bits (90), Expect = 6e-04
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM---EIDG 248
T Q+ + S+ G +D +S C+V + + ++A A ++A G+ +
Sbjct: 14 TLNQLKELLSETGTGVIEGFWMD--KIKSH--CYVTYSTVEEAVATREALHGLQWPSSNP 69
Query: 249 RQIRVDFSVTQ 259
++++VDF +
Sbjct: 70 KRLKVDFVPQE 80
>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 = 41.2 bits (96), Expect = 6e-04
Identities = 39/193 (20%), Positives = 75/193 (38%), Gaps = 23/193 (11%)
Query: 119 SRSPGYRKRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQP 178
S +R+ + + GGS G G + T ++ +D +
Sbjct: 52 STGRQHRQGYNDFYGNGGSSACGLGSMGNMANMASTN-----SLNSLGSGGSDDNDTNNS 106
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
L V L T++++ +F GP+ ++ D KTG S G+ FV F S D+ A
Sbjct: 107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI 166
Query: 239 DACTGMEIDGRQIRVDFSVTQRAHTPTPGIYMGRPTYEQLNNTQSELGSLLSEKHAIKGG 298
G+ + ++++V ++ RP E + +T + +L I
Sbjct: 167 KNLNGITVRNKRLKVSYA---------------RPGGESIKDTNLYVTNL---PRTITDD 208
Query: 299 KFEEVFGEIATVV 311
+ + +FG+ +V
Sbjct: 209 QLDTIFGKYGQIV 221
Score = 40.8 bits (95), Expect = 0.001
Identities = 22/59 (37%), Positives = 31/59 (52%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
L V L T+ Q++ IF KYG + + ++ D TG RG FV F R++A A A
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISA 254
>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM1 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence CT(A/T)(A/T)T, and stimulates DNA replication
in the system using SV40 DNA. MSSP-1 is identical with
Scr2, a human protein which complements the defect of
cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has
been implied in regulating DNA replication,
transcription, apoptosis induction, and cell-cycle
movement, via the interaction with C-MYC, the product of
protooncogene c-myc. MSSP-1 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 86
Score = 38.3 bits (88), Expect = 6e-04
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GL TT+Q + + YG + + ++D T + +G+ FV F D AAA+ A
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF---DSPAAAQKAV 66
Query: 242 TGMEIDGRQIRV 253
+ ++ G Q ++
Sbjct: 67 SALKASGVQAQM 78
>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM1 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells, as well as the
neurite elongation and morphological differentiation.
HuD specifically binds poly(A) RNA. Like other Hu
proteins, HuD contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 83
Score = 38.2 bits (88), Expect = 6e-04
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T+++ +F G +E ++V D TG+S G+ FV + DA A + G+ + + I
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 252 RVDFS 256
+V ++
Sbjct: 75 KVSYA 79
>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 = 38.2 bits (89), Expect = 6e-04
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
+R L V L I TE+++ F +YG VE V++ + G+ + FV F + D A AK
Sbjct: 2 TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPR-GQGNAYAFVKFLNLDMAHRAK 60
Query: 239 DACTGMEIDGRQIRV 253
A +G I QI++
Sbjct: 61 VAMSGQYIGRNQIKI 75
>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 = 38.3 bits (89), Expect = 6e-04
Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYG--PVERVEVVIDAKT-GR--SRGFCFVYFESRDDAAA 236
L V L+ TT Q + F RV+ D K G+ S GF FV F++++ A A
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 237 AKDACTGMEIDGRQIRVDFS 256
A A G +DG + V FS
Sbjct: 63 ALKAMDGFVLDGHTLVVKFS 82
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 37.6 bits (88), Expect = 7e-04
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 9/65 (13%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFC-FV-YFESRDDAAAAKDACTGMEIDGR 249
++Q++ +FS++G V+ + + R FV +++ R A AA DA G G
Sbjct: 14 SDQELRSLFSQFGEVKDI------RETPLRPSQKFVEFYDIR-AAEAALDALNGRPFLGG 66
Query: 250 QIRVD 254
+++V
Sbjct: 67 RLKVK 71
>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 = 37.4 bits (87), Expect = 8e-04
Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
+++ +F G V R ++ D K G+SRG V FE +A A G + R +
Sbjct: 11 GWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPM 69
Query: 252 RV 253
RV
Sbjct: 70 RV 71
>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 = 37.4 bits (87), Expect = 8e-04
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
L+ TE + F K + V + D +TG +GF V F +++ A G +
Sbjct: 7 LAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFAD-EESLDAALKLDGTVL 64
Query: 247 DGRQIRVD 254
GR IR+
Sbjct: 65 CGRPIRIA 72
>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 = 37.7 bits (87), Expect = 9e-04
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI-DGRQI 251
E ++ +F K GP+ + +++D TG +RG+ FV F +++ A A EI G+ I
Sbjct: 15 EDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLYNNHEIRPGKHI 74
Query: 252 RVDFS 256
V S
Sbjct: 75 GVCIS 79
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen
C (HuC). This subgroup corresponds to the RRM2 of HuC,
also termed ELAV-like protein 3 (ELAV-3), or
paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles in
neuronal differentiation, plasticity and memory. Like
other Hu proteins, HuC contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
The AU-rich element binding of HuC can be inhibited by
flavonoids. RRM3 may help to maintain the stability of
the RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 81
Score = 37.7 bits (87), Expect = 9e-04
Identities = 20/64 (31%), Positives = 35/64 (54%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GL +++++ +FS+YG + +++D TG SRG F+ F+ R +A A
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63
Query: 242 TGME 245
G +
Sbjct: 64 NGQK 67
>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 = 37.5 bits (87), Expect = 9e-04
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRD--DAAAAKDACTGMEIDGR 249
T +++ FS GP+ RV ++ D +G +G+ ++ F +RD +AA A D + GR
Sbjct: 12 TAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALDESS---FRGR 68
Query: 250 QIRV 253
I+V
Sbjct: 69 VIKV 72
>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 = 37.2 bits (87), Expect = 0.001
Identities = 23/70 (32%), Positives = 35/70 (50%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L TE+ + +F + GPV V + D T +G+ FV F S +DA A
Sbjct: 3 VGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNM 62
Query: 244 MEIDGRQIRV 253
+++ G+ IRV
Sbjct: 63 IKLYGKPIRV 72
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both, nuclear and
cytoplasmic, roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 37.3 bits (87), Expect = 0.001
Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 8/85 (9%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
PS + V GL TE + S++GP+ V ++ + V FE DA A
Sbjct: 1 PSPVVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQA------LVEFEDISDAKAC 54
Query: 238 KDACTGME--IDGRQIRVDFSVTQR 260
+ I GRQ ++S +Q
Sbjct: 55 VNHAQQNPVYIAGRQAYFNYSTSQE 79
>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM4 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 = 98
Score = 37.6 bits (88), Expect = 0.001
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 15/71 (21%)
Query: 182 LGVFGLSIYTTEQQINHIFSKY---------GPVERVEVVIDAK------TGRSRGFCFV 226
L + L E+++ +F K +++V+++ D K G+S+G+ FV
Sbjct: 3 LSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFV 62
Query: 227 YFESRDDAAAA 237
F + + A A
Sbjct: 63 EFTNHEHALKA 73
>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM2 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. It binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. p54nrb forms a heterodimer
with paraspeckle component 1 (PSPC1 or PSP1), localizing
to paraspeckles in an RNA-dependent manner. It also
forms a heterodimer with polypyrimidine tract-binding
protein-associated-splicing factor (PSF). p54nrb
contains two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at the N-terminus. .
Length = 80
Score = 37.3 bits (86), Expect = 0.001
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L + + + + FS +G VER V++D + GR G V F + A A D C
Sbjct: 2 LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDR-GRPTGKGIVEFAGKPSARKALDRC 60
>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 = 37.1 bits (86), Expect = 0.001
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L TE + IF GPV+ V+++ D K + + FV + DA A
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQTL 59
Query: 242 TGMEIDGRQIRVDFS 256
G +I+ +IRV+++
Sbjct: 60 NGRQIENNEIRVNWA 74
>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 = 36.9 bits (85), Expect = 0.001
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA--CTG 243
GLS T+++ + S++G V + D TGRSRGF FV F+ DAA+
Sbjct: 6 GLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFK---DAASVDKVLELKE 62
Query: 244 MEIDGRQI 251
++DG+ I
Sbjct: 63 HKLDGKLI 70
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM of
some eukaryotic DnaJ homolog subfamily C member 17 and
similar proteins. DnaJ/Hsp40 (heat shock protein 40)
proteins are highly conserved and play crucial roles in
protein translation, folding, unfolding, translocation,
and degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonine
family. Members in this family contains an N-terminal
DnaJ domain or J-domain, which mediates the interaction
with Hsp70. They also contains a RNA recognition motif
(RRM), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), at the C-terminus, which may
play an essential role in RNA binding. .
Length = 74
Score = 36.9 bits (86), Expect = 0.002
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+E ++ IFSKYG V +VV+ +K S V F S+ A AA + G
Sbjct: 17 SEDELRKIFSKYGDVS--DVVVSSKKKGSA---IVEFASKKAAEAAVENECG 63
>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 = 37.2 bits (87), Expect = 0.002
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
S++G +E + V D G +V FE+ +DA AA A G GR + + S
Sbjct: 46 LSRFGEIEDLVVC-DNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPELS 101
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. The proteins represented by this model contain
three RNA recognition motifs (rrm: pfam00076) and have
been characterized as poly-pyrimidine tract binding
proteins associated with RNA splicing factors. In the
case of PUF60 (GP|6176532), in complex with p54, and in
the presence of U2AF, facilitates association of U2
snRNP with pre-mRNA.
Length = 612
Score = 40.1 bits (93), Expect = 0.002
Identities = 20/61 (32%), Positives = 32/61 (52%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E I F +GP++ + + D TG+ +GF FV +E + A A + G + GR I+
Sbjct: 121 EDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIK 180
Query: 253 V 253
V
Sbjct: 181 V 181
Score = 34.7 bits (79), Expect = 0.085
Identities = 15/86 (17%), Positives = 33/86 (38%), Gaps = 6/86 (6%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM---EIDG 248
+E I +F +G + + ++ +G+ F+ + + + +A M ++ G
Sbjct: 217 SETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYN---NLQSQSEAIASMNLFDLGG 273
Query: 249 RQIRVDFSVTQRAHTPTPGIYMGRPT 274
+ +RV VT P P
Sbjct: 274 QYLRVGKCVTPPDALLQPATVSAIPA 299
>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 = 36.6 bits (84), Expect = 0.002
Identities = 19/43 (44%), Positives = 24/43 (55%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
GLS T+ + FSK+G + V+ D T RSRGF FV F
Sbjct: 6 GLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48
>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 = 36.9 bits (85), Expect = 0.002
Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 5/84 (5%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRG--FCFVYFESR 231
++ + +R L + L +E ++ F KYG +E EVVI + R +G + F+ F++
Sbjct: 3 DDQRATRNLFIGNLDHNVSEVELRRAFDKYGIIE--EVVIK-RPARGQGGAYAFLKFQNL 59
Query: 232 DDAAAAKDACTGMEIDGRQIRVDF 255
D A AK A +G I I++ +
Sbjct: 60 DMAHRAKVAMSGRVIGRNPIKIGY 83
>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 = 36.5 bits (84), Expect = 0.002
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V L E+ + +F + GP+ +V + D K G+ + F FV F+ + A
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYAIA 60
Query: 240 ACTGMEIDGRQIRV 253
G+ + GR I+V
Sbjct: 61 LLNGIRLYGRPIKV 74
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), 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
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are 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 = 92
Score = 37.0 bits (85), Expect = 0.002
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
+Q + +F +G V +V ID +T S+ F FV +++ A AA A G +I ++++
Sbjct: 21 DQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLK 80
Query: 253 VDFSVTQRAHTP 264
V ++ P
Sbjct: 81 VQLKRSKNDSKP 92
>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM1 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3), a double- and single-stranded DNA binding
protein that belongs to the c-myc single-strand binding
proteins (MSSP) family. It specifically recognizes the
sequence T(C/A)TT, and stimulates DNA replication in the
system using SV40 DNA. MSSP-2 is identical with Scr3, a
human protein which complements the defect of cdc2
kinase in Schizosaccharomyces pombe. MSSP-2 has been
implied in regulating DNA replication, transcription,
apoptosis induction, and cell-cycle movement, via the
interaction with C-MYC, the product of protooncogene
c-myc. MSSP-2 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity as
well as induction of apoptosis. .
Length = 75
Score = 36.7 bits (84), Expect = 0.002
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GL TT+Q + + YG + + ++D T + +G+ FV F D +AA+ A
Sbjct: 4 LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF---DSPSAAQKAV 60
Query: 242 TGMEIDGRQIRV 253
T ++ G Q ++
Sbjct: 61 TALKASGVQAQM 72
>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 = 36.3 bits (84), Expect = 0.002
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 187 LSIYTTEQQINHIF-SKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
LS E + +F S++ + +++ D TG SRG+ FV F +D A G+
Sbjct: 9 LSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEMQGVY 68
Query: 246 IDGRQIRV 253
GR +R+
Sbjct: 69 CGGRPMRI 76
>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM2 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 = 36.0 bits (83), Expect = 0.002
Identities = 17/60 (28%), Positives = 28/60 (46%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V G + TE+ + F + +E + + D +G+ +CF+ F A AA D TG
Sbjct: 3 VSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHITG 62
>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 = 36.2 bits (84), Expect = 0.002
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
L TT + + F G V ++ D KTG+S+G FV F++ + A +
Sbjct: 8 LPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL-HHTLL 66
Query: 247 DGRQIRVD 254
GR+I V+
Sbjct: 67 KGRKINVE 74
>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 = 35.9 bits (83), Expect = 0.003
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+ +F GPV +V ++ + + F+ FE+ + A A + G +DG I+V
Sbjct: 14 SDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETLNGASVDGNCIKV 69
>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 = 35.6 bits (83), Expect = 0.003
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 191 TTEQQINHIFSKY-GPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
TT++ + +F+++ G E V +V RG FV FE+ + A A A G +I
Sbjct: 14 TTKEMLEMLFNQFPGFKE-VRLV------PRRGIAFVEFETEEQATVALQALQGFKI 63
>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 = 35.9 bits (83), Expect = 0.003
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 192 TEQQINHIF-SKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGR 249
TE QI F S+ GP++RV + + + G+S G + F+ DA A D G DG
Sbjct: 12 TEAQIREYFVSQIGPIKRVLLSYN-EGGKSTGIANITFKRAGDATKAYDKFNGRIDDGN 69
>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 = 35.6 bits (82), Expect = 0.004
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRS-RGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T++ + +FS YG ++ V V K +S RGF FV F + +A A +A + GR+
Sbjct: 13 TKKDVRTLFSSYGQLKSVRV--PKKFDQSARGFAFVEFSTAKEALNAMNALKDTHLLGRR 70
Query: 251 IRVDFS 256
+ + ++
Sbjct: 71 LVLQYA 76
>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subgroup corresponds
to the RRM2 in 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 = 70
Score = 35.6 bits (82), Expect = 0.004
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 8/69 (11%)
Query: 189 IYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDG 248
I T + + F YG + V + R F FV +E+++DA A ++ ++
Sbjct: 10 INTRTRDLERHFEPYGKLVNVRI--------RRNFAFVQYETQEDATKALESTNMSKVLD 61
Query: 249 RQIRVDFSV 257
R I V+++
Sbjct: 62 RVISVEYAA 70
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 and RRM4 of MRN1, also termed
multicopy suppressor of RSC-NHP6 synthetic lethality
protein 1, or post-transcriptional regulator of 69 kDa,
and is an RNA-binding protein found in yeast. Although
its specific biological role remains unclear, MRN1 might
be involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 82
Score = 35.6 bits (82), Expect = 0.004
Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
E+++ KYG +E + ++ R + F+ F + +A AA G + +
Sbjct: 20 PEKELRKECEKYGEIESIRIL------REKACAFINFMNIPNAIAALQTLNGKKPYDTIV 73
Query: 252 RVDF 255
R+++
Sbjct: 74 RINY 77
>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM2 of Bruno, a Drosophila
RNA recognition motif (RRM)-containing protein that
plays a central role in regulation of Oskar (Osk)
expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 81
Score = 35.9 bits (83), Expect = 0.004
Identities = 22/58 (37%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
R L V LS E + +F+ +G +E V+ D G+SRG FV F SR A A
Sbjct: 2 RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQCALNA 58
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 36.2 bits (84), Expect = 0.004
Identities = 23/56 (41%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 201 SKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
SK+G VE + V D G +V F + AAAA A G DGR I V+FS
Sbjct: 48 SKFGEVEALNVC-DNLGDHMVGNVYVKFRDEEHAAAALKALQGRFYDGRPIIVEFS 102
>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 = 35.3 bits (82), Expect = 0.004
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 13/68 (19%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCF--VYFESRDDAAAA--KDACTGMEI 246
TTE +I F G + V++V S G + FE+ D+A AA KD +
Sbjct: 12 TTENKIRQFFKDCGEIREVKIV------ESEGGLVAVIEFETEDEALAALTKD---HKRL 62
Query: 247 DGRQIRVD 254
G +I V
Sbjct: 63 GGNEISVS 70
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. SKAR is
widely expressed and localizes to the nucleus. It may be
a critical player in the function of S6K1 in cell and
organism growth control by binding the activated,
hyperphosphorylated form of S6K1 but not S6K2.
Furthermore, SKAR functions as a protein partner of the
p50 subunit of DNA polymerase delta. In addition, SKAR
may have particular importance in pancreatic beta cell
size determination and insulin secretion. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 34.9 bits (81), Expect = 0.006
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 7/62 (11%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
TE I +FS G ++R +V G V + +DDA A D E+DG+ +
Sbjct: 13 TEDDIVELFSAIGALKRARLV-------RPGVAEVVYVRKDDALTAIDKYNNRELDGQPM 65
Query: 252 RV 253
+
Sbjct: 66 KC 67
>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM2 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity. Both,
MSSP-1 and -2, have been identified as protein factors
binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with C-MYC, the product of protooncogene c-myc.
Moreover, they family includes a new member termed
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3), which is not a transcriptional regulator. RBMS3
binds with high affinity to A/U-rich stretches of RNA,
and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 79
Score = 35.0 bits (81), Expect = 0.006
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
L ++ EQ + + YG V ++ D+K G+SRG F ESR+
Sbjct: 7 NLPLHMDEQDLETMLKPYGQVISTRILRDSK-GQSRGVGFARMESREKC 54
>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM1 of
RBMS3, a new member of the c-myc gene single-strand
binding proteins (MSSP) family of DNA regulators. Unlike
other MSSP proteins, RBMS3 is not a transcriptional
regulator. It binds with high affinity to A/U-rich
stretches of RNA, and to A/T-rich DNA sequences, and
functions as a regulator of cytoplasmic activity. RBMS3
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and its C-terminal region
is acidic and enriched in prolines, glutamines and
threonines. .
Length = 80
Score = 35.2 bits (80), Expect = 0.007
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L + GL TT+Q + + YG + + ++D T + +G+ FV F D AAA+ A
Sbjct: 7 LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDF---DSPAAAQKAV 63
Query: 242 TGMEIDGRQIRV 253
++ +G Q ++
Sbjct: 64 ASLKANGVQAQM 75
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 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 = 75
Score = 34.7 bits (80), Expect = 0.008
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V L E++I+ F +YG VE V+++ + FV F A A +A
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA-AFVDFVDIKSAQKAHNAV 60
Query: 242 TGMEIDGRQIRVDFS 256
M R +R D++
Sbjct: 61 NKM--GDRDLRTDYN 73
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains 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. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a specific
inhibitory effect on oestrogen action, SLTM is shown to
exert a generalized inhibitory effect on gene expression
associated with induction of apoptosis in a wide range
of cell lines. .
Length = 74
Score = 34.7 bits (79), Expect = 0.009
Identities = 22/73 (30%), Positives = 36/73 (49%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V GLS T + ++F KYG V +VV +A++ ++ + V S + A
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61
Query: 242 TGMEIDGRQIRVD 254
E+ G+QI V+
Sbjct: 62 HRTELHGQQISVE 74
>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 = 34.9 bits (81), Expect = 0.011
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 18/85 (21%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVE---VVIDAKTGRSRGFC--------------FVYFE 229
L + T ++ + +F ++GP+E V V + K + +V F+
Sbjct: 8 LPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYVVFK 67
Query: 230 SRDDAAAAKDACTGMEIDGRQIRVD 254
+ A A G E +G IRVD
Sbjct: 68 EEESAEKALKL-NGTEFEGHHIRVD 91
>gnl|CDD|241199 cd12755, RRM2_RBM5, RNA recognition motif 2 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM2 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 86
Score = 34.5 bits (79), Expect = 0.011
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 206 VERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG----MEIDGRQIRVDFS 256
V + ++ D +T ++RGF FV S +A+ ++IDG+ I VDF+
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIGVDFA 85
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 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 = 34.3 bits (79), Expect = 0.012
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 192 TEQQINHIFSKYGPVERVEVVID-AKTGRSRGFCFVYFESRDDAAAAKDA-CTGMEIDGR 249
T +++ +FS +G ++ V + TG RGF FV F ++ DA A A C + GR
Sbjct: 13 TVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAFKALCHSTHLYGR 72
Query: 250 QI 251
++
Sbjct: 73 RL 74
>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 = 34.4 bits (79), Expect = 0.012
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQ 250
T +++ F G V RV ++ D +G +GF ++ F ++ A A GRQ
Sbjct: 11 ATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-ALDESLFRGRQ 69
Query: 251 IRV 253
I+V
Sbjct: 70 IKV 72
>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 = 34.3 bits (79), Expect = 0.013
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R + V G T+E+Q+ FS +GPV V++D G + V F+S++
Sbjct: 3 RSVFVSGFKRGTSEEQLMDYFSAFGPVM--NVIMDKDKGV---YAIVEFDSKEGVDKVLS 57
Query: 240 ACTGMEIDGRQIRV 253
++G ++RV
Sbjct: 58 EP-QHTLNGHRLRV 70
>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 = 34.5 bits (80), Expect = 0.013
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 201 SKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
K+G V++V VV D G V F+ ++A +A G GRQ+ +
Sbjct: 34 EKFGQVKKV-VVFD---RHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEAER 84
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 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 = 74
Score = 33.9 bits (77), Expect = 0.014
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
G++ TEQ + FS +G + V V D +G+ FV F S + AA A + G
Sbjct: 7 GVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSVNGTT 60
Query: 246 IDGRQIR 252
I+G ++
Sbjct: 61 IEGHVVK 67
>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 = 34.3 bits (79), Expect = 0.014
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 11/79 (13%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSR--------GFCFVYFESRDDAAAAK 238
LS ++E+ + + PV V+I ++T R G + F S + A
Sbjct: 7 LSYSSSEEDLEEFLKDFEPVS---VLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKVV 63
Query: 239 DACTGMEIDGRQIRVDFSV 257
G R++ V V
Sbjct: 64 KDLNGKVFKNRKLFVKLHV 82
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding
protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or modifier
of damage tolerance Mdt1, a novel phosphothreonine
(pThr)-containing protein that specifically interacts
with the pThr-binding site of the Rad53 FHA1 domain. It
is encoded by gene MDT1 (YBL051C) from yeast
Saccharomyces cerevisiae. PIN4 is involved in normal
G2/M cell cycle progression in the absence of DNA damage
and functions as a novel target of checkpoint-dependent
cell cycle arrest pathways. It contains an N-terminal
RRM, a nuclear localization signal, a coiled coil, and a
total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein
1) and cip2 (Csx1-interacting protein 2) are novel
cytoplasmic RRM-containing proteins that counteract Csx1
function during oxidative stress. They are not essential
for viability in fission yeast Schizosaccharomyces
pombe. Both cip1 and cip2 contain one RRM. Like PIN4,
Cip2 also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 34.0 bits (78), Expect = 0.016
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 221 RGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
RG F F S ++A +A G EI GR++RV++
Sbjct: 43 RGLAFANFRSPEEAQTVVEALNGYEISGRRLRVEY 77
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT motif
responsible for docking many substrates to calcineurin,
and an unrecognized C-terminal TxxP motif of unknown
function. .
Length = 75
Score = 33.7 bits (78), Expect = 0.017
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 6/57 (10%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
FS YG V R+R V F S ++AA A+ G +G +RV F
Sbjct: 24 FSSYGE--IATFVYLPSFRRAR----VVFSSPEEAALARIELHGTVFEGSVLRVYFG 74
>gnl|CDD|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding
protein 5 (RBM5) and similar proteins. This subgroup
corresponds to the RRM2 of RNA-binding protein 5 (RBM5
or LUCA15 or H37), RNA-binding protein 10 (RBM10 or
S1-1) and similar proteins. RBM5 is a known modulator of
apoptosis. It may also act as a tumor suppressor or an
RNA splicing factor; it specifically binds poly(G) RNA.
RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10,
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 = 86
Score = 34.1 bits (78), Expect = 0.018
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 206 VERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME----IDGRQIRVDFS 256
V + ++ D +T ++RGF FV S +A+ + IDG+ I VDF+
Sbjct: 31 VSNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTIGVDFA 85
>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 = 34.2 bits (78), Expect = 0.019
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 8/80 (10%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVE--------RVEVVIDAKTGRSRGFCFVYFESRDDAA 235
V GL T + + F + G ++ + + D +TG+ +G V F+ A
Sbjct: 7 VQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAK 66
Query: 236 AAKDACTGMEIDGRQIRVDF 255
AA D G E G I+V F
Sbjct: 67 AAIDWFDGKEFSGNPIKVSF 86
>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 = 33.3 bits (77), Expect = 0.019
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 187 LSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
L TTE+++ +F K+G + R+ ++ ++T V F DA A
Sbjct: 8 LPFGTTEEELRELFEKFGSLGRL-LLPPSRT-----IALVEFLEPSDARKA 52
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an N-terminal
C4C4 type RING finger motif, followed by a RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). The RING
fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 34.1 bits (79), Expect = 0.020
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCF-VY--FESRDDAAAAKDACTGMEIDGRQIRVDFS 256
F +YG ++++ + + S+G Y + ++DA A G +DGR ++ F
Sbjct: 29 FGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDGFYLDGRLLKASFG 88
Query: 257 VT 258
T
Sbjct: 89 TT 90
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing
protein 1 (RDM1) and similar proteins. This subfamily
corresponds to the RRM of RDM1, also termed RAD52
homolog B, a novel factor involved in the cellular
response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 33.9 bits (78), Expect = 0.020
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 182 LGVFGLSIYTTEQQINH----IFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
L V+G+S TE++I FS++G + V+V +A + FV F S A+ A
Sbjct: 3 LYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASRA 62
Query: 238 KDACTGME-IDGRQIRVDF 255
+ AC G G ++V F
Sbjct: 63 QKACNGKWLFQGSPLKVRF 81
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 33.7 bits (78), Expect = 0.020
Identities = 20/66 (30%), Positives = 25/66 (37%), Gaps = 5/66 (7%)
Query: 193 EQQINHIFSKYGPVERVEVVIDA---KTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGR 249
+ +I KYG V V V A R FV F D+A A A G GR
Sbjct: 20 KDEIEEECEKYGKVLNVIVHEVASSEADDAVR--IFVEFSDADEAIKAVRALNGRFFGGR 77
Query: 250 QIRVDF 255
++ F
Sbjct: 78 KVTARF 83
>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 = 33.5 bits (77), Expect = 0.021
Identities = 22/59 (37%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA--KDACT 242
GL TE I FS PV V + +A GR+ G V F + +DA AA KD
Sbjct: 7 GLPYRATENDIFEFFSPLNPV-NVRIEYNAD-GRATGEADVEFATHEDAVAAMSKDREH 63
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but 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. Some
family members also contain another RRM domain.
Length = 78
Score = 33.6 bits (77), Expect = 0.022
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
F +YG + R ++ +T +SR F FV +ES DA A
Sbjct: 20 FERYGRLVRCDIPP-PRTFQSRPFAFVEYESHRDAEDA 56
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split end)
protein family. This subfamily corresponds to the RRM1
domain in the Spen (split end) family which includes RNA
binding motif protein 15 (RBM15), putative RNA binding
motif protein 15B (RBM15B), and similar proteins found
in Metazoa. RBM15, also termed one-twenty two protein 1
(OTT1), conserved in eukaryotes, is a novel mRNA export
factor and component of the NXF1 pathway. It binds to
NXF1 and serves as receptor for the RNA export element
RTE. It also possesses mRNA export activity and can
facilitate the access of DEAD-box protein DBP5 to mRNA
at the nuclear pore complex (NPC). RNA-binding protein
15B (RBM15B), also known as one twenty-two 3 (OTT3), is
a paralog of RBM15 and therefore has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong- to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 33.4 bits (77), Expect = 0.023
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E + H F K+G V V V+ D + R +V F +DA AK A + + R +
Sbjct: 19 EDVLYHEFKKFGDV-SVRVLHDGEDER---VAYVNFRHPEDAREAKHAKGRLVLFDRPLN 74
Query: 253 VDFS 256
V+
Sbjct: 75 VEPV 78
>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis
thaliana zinc finger CCCH domain-containing protein 46
(AtC3H46) and similar proteins. This subfamily
corresponds to the RRM domain in AtC3H46, a putative
RNA-binding protein that contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCCH class of zinc
finger, typically C-X8-C-X5-C-X3-H. It may possess
ribonuclease activity. .
Length = 70
Score = 32.8 bits (75), Expect = 0.031
Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 4/71 (5%)
Query: 183 GVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACT 242
F TE+ ++ F ++GPV V + K R F FV FE+ +
Sbjct: 3 LTFPADSRFTEEDVSEYFGQFGPVLDVRIPYQQK----RMFGFVTFENAETVKRILSKGN 58
Query: 243 GMEIDGRQIRV 253
I G ++RV
Sbjct: 59 PHFICGSRVRV 69
>gnl|CDD|241179 cd12735, RRM3_hnRNPH3, RNA recognition motif 3 in heterogeneous
nuclear ribonucleoprotein H3 (hnRNP H3) and similar
proteins. This subgroup corresponds to the RRM3 of
hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding
protein that belongs to the hnRNP H protein family that
also includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), and hnRNP F. This
family is involved in mRNA processing and exhibit
extensive sequence homology. Currently, little is known
about the functions of hnRNP H3 except for its role in
the splicing arrest induced by heat shock. In addition,
the typical hnRNP H proteins contain contain three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), except for
hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. Members in this family can regulate the
alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts, and function as
silencers of FGFR2 exon IIIc through an interaction with
the exonic GGG motifs. The lack of RRM1 could account
for the reduced silencing activity within hnRNP H3. In
addition, like other hnRNP H protein family members,
hnRNP H3 has an extensive glycine-rich region near the
C-terminus, which may allow it to homo- or
heterodimerize. .
Length = 75
Score = 33.1 bits (75), Expect = 0.034
Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
GL TE I + FS P+ RV + I A GR+ G V F + +DA AA
Sbjct: 7 GLPFRATESDIANFFSPLTPI-RVHIDIGAD-GRATGEADVEFVTHEDAVAA 56
>gnl|CDD|241196 cd12752, RRM1_RBM5, RNA recognition motif 1 in vertebrate
RNA-binding protein 5 (RBM5). This subgroup corresponds
to the RRM1 of RBM5, also termed protein G15, or
putative tumor suppressor LUCA15, or renal carcinoma
antigen NY-REN-9, a known modulator of apoptosis. It may
also act as a tumor suppressor or an RNA splicing
factor. RBM5 shows high sequence similarity to
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). Both, RBM5 and RBM6, specifically bind poly(G)
RNA. They contain two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
a nuclear localization signal, and a G-patch/D111
domain. .
Length = 87
Score = 33.0 bits (75), Expect = 0.036
Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 2/80 (2%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKY-GPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
S+ + + GL I TE I + + GP ++ KTG SRGF FV F DA +
Sbjct: 5 SKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVSRGFAFVEFYHLQDATSW 64
Query: 238 KDACTG-MEIDGRQIRVDFS 256
+A + I G+ I + +S
Sbjct: 65 MEANQKKLVIQGKTIAMHYS 84
>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 = 32.7 bits (74), Expect = 0.045
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V L T Q++ FS+ G V E I + G+S+G V F+S + A A G
Sbjct: 4 VRNLPFDLTWQKLKEKFSQCGHVMFAE--IKMENGKSKGCGTVRFDSPESAEKACRLMNG 61
Query: 244 MEIDGRQIRV 253
++I+GR+I V
Sbjct: 62 IKINGREIDV 71
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 32.7 bits (75), Expect = 0.046
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 198 HIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
H F K+G V V+V TG R + V+F +DA A + G G +I V
Sbjct: 22 HEFKKHGKVTSVKVH---GTGSER-YAIVFFRKPEDAEKALEVSKGKLFFGAEIEV 73
>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 = 32.6 bits (75), Expect = 0.050
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 199 IFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+ K G V + V D TG+ + F F FE + A A G+E+ G+++ V
Sbjct: 20 LLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLV 74
>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 = 32.7 bits (75), Expect = 0.053
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 3/60 (5%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVE---VVIDAKTGRSRGFCFVYFESRDDAAAA 237
+ + GL T I F PV + + GR G FV FE+ +DA A
Sbjct: 3 IIRMRGLPYSATAADILAFFGGLCPVVGGPDGILFVTGPDGRPTGDAFVLFETEEDAQRA 62
>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 = 32.4 bits (74), Expect = 0.053
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 214 DAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
GR RGF + FE RD A + + R+IRVD +
Sbjct: 36 PGDPGRLRGFGYAEFEDRDSLLQAL-SLNDESLKNRRIRVDIA 77
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM2 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 bind 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),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two RRMs.
.
Length = 82
Score = 32.6 bits (75), Expect = 0.055
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVI----DAKTGRSRGFCFVYFESRDDAAAA 237
L V G+ T+++I FSK V+V++ D K ++RGF FV +ES AA A
Sbjct: 4 LFVGGIPKTKTKEEILEEFSKVTE-GVVDVIVYRSPDDKN-KNRGFAFVEYESHRAAAMA 61
Query: 238 KDACT 242
+
Sbjct: 62 RRKLV 66
>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777). This is
a family of eukaryotic proteins of unknown function.
Some of the proteins in this family are putative nucleic
acid binding proteins.
Length = 158
Score = 34.1 bits (78), Expect = 0.055
Identities = 33/72 (45%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 74 RSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRS 133
RSRS SP RRS+R + RD R RSRS R R RSRSRSP +R R S
Sbjct: 3 RSRSRSP-RRSRRRGRSRSRDRRERRRERSRS---RERDRRRRSRSRSP-HRSRRSRSPR 57
Query: 134 GGGSRGDSYGGR 145
SR S R
Sbjct: 58 RHRSRSRSPSRR 69
Score = 32.9 bits (75), Expect = 0.15
Identities = 26/74 (35%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 61 GSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRS-YSPRGRRGGYRSRS 119
G + R+S R RS S RR +R + + R+ RSRSRS + R R R RS
Sbjct: 2 GRSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRS 61
Query: 120 RSPGYRKRSSSYRS 133
RS +R R
Sbjct: 62 RSRSPSRRRDRKRE 75
>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 = 32.3 bits (73), Expect = 0.057
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 8/72 (11%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L V +S T Q++ F +YGPV ++V D + FV+ E +DA A
Sbjct: 3 LHVGNISSSCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 54
Query: 242 TGMEIDGRQIRV 253
E G+++ V
Sbjct: 55 DNTEFQGKRMHV 66
>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 = 32.9 bits (75), Expect = 0.058
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 179 SRCLGVFGL-SIYTTEQQINHIFSK-YGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA 236
S+CL V L Y +++ IFS+ Y PV ++ D + GF V +E+ + A
Sbjct: 2 SKCLCVDKLPKDYEDSEELLQIFSESYKPV-FCQLAQD-EGSCVGGFAVVEYETAEQAEE 59
Query: 237 AKDACTGMEIDGRQIRVDF 255
+ A G I G +I++ F
Sbjct: 60 VQLAMDGTTIKGSRIQLSF 78
>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 = 32.1 bits (73), Expect = 0.066
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 12/68 (17%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAA--AKDACTGMEIDG 248
T+++++ +F YG V V+ R F FV+ R +AAA A + G E+ G
Sbjct: 12 TSQEELRALFEAYGAVLSCAVM--------RQFAFVHL--RGEAAADRAIEELNGRELHG 61
Query: 249 RQIRVDFS 256
R++ V+ S
Sbjct: 62 RKLVVEHS 69
>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 = 32.3 bits (74), Expect = 0.067
Identities = 19/64 (29%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 186 GLSIYTTEQQINHIFSKYG-PVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM 244
L Y E I F+ G V V+++ + TG G+CFV F A G
Sbjct: 6 DLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGK 65
Query: 245 EIDG 248
I G
Sbjct: 66 PIPG 69
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily corresponds
to the RRM2 of La and LARP7. La is a highly abundant
nuclear phosphoprotein and well conserved in eukaryotes.
It specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. LARP7
is an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3' -UUU-OH)
of 7SK RNA. It is a stable component of the 7SK small
nuclear ribonucleoprotein (7SK snRNP), intimately
associates with all the nuclear 7SK and is required for
7SK stability. LARP7 also acts as a negative
transcriptional regulator of cellular and viral
polymerase II genes, acting by means of the 7SK snRNP
system. LARP7 plays an essential role in the inhibition
of positive transcription elongation factor b
(P-TEFb)-dependent transcription, which has been linked
to the global control of cell growth and tumorigenesis.
Both La and LARP7 contain an N-terminal La motif (LAM),
followed by two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 31.9 bits (73), Expect = 0.075
Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
+ T + I +F+++G V+ V+ A TG ++ F++ + A A++A
Sbjct: 8 SIGPGVTREDIKAVFAQFGEVKYVDFTEGADTG------YIRFKTPEAAQKAREAFVEKG 61
Query: 246 IDGRQIRVDFSV 257
+ S
Sbjct: 62 EGLLGKEIKLSA 73
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM2 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both nuclear and
cytoplasmic roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 86
Score = 31.9 bits (73), Expect = 0.085
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 196 INHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGR--QIRV 253
I I + +G V R+ VI K G V F+S D A AK A G +I +++
Sbjct: 20 IYTICNPHGKVLRI--VIFRKNGVQ---AMVEFDSVDSAQRAKAALNGADIYAGCCTLKI 74
Query: 254 DFSVTQR 260
+++ R
Sbjct: 75 EYAKPDR 81
>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 = 32.0 bits (73), Expect = 0.085
Identities = 13/58 (22%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 177 QPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
SR + + L +E+++ K+GP++++++V + + FV+F S +A
Sbjct: 1 GASRNVYIGNLPESYSEEELREDLEKFGPIDQIKIV------KEKNIAFVHFLSIANA 52
>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 = 31.7 bits (73), Expect = 0.090
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
++N FSK+G + ++V S V F + ++A A
Sbjct: 15 NITKLNEHFSKFGTIVNIQV---NYNPES---ALVQFSTSEEAKKA 54
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing
factor Cwc2 and similar proteins. This subfamily
corresponds to the RRM of yeast protein Cwc2, also
termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and an intervening loop, also termed
RNA-binding loop or RB loop, between ZnF and RRM, all of
which are necessary and sufficient for RNA binding. The
ZnF is also responsible for mediating protein-protein
interaction. The C-terminal flexible region of Cwc2
interacts with the WD40 domain of Prp19.
Length = 78
Score = 31.9 bits (73), Expect = 0.098
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
E+ + F ++G +E + V+ S+G FV ++ R A AK+A +DG ++
Sbjct: 18 IEEILRRHFGEWGDIEDIRVL------PSKGIAFVRYKYRASAEFAKEAMADQSLDGGEV 71
>gnl|CDD|241178 cd12734, RRM3_hnRNPH_hnRNPH2_hnRNPF, RNA recognition motif 3 in
heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP
H2, hnRNP F and similar proteins. This subgroup
corresponds to the RRM3 of hnRNP H (also termed
mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and
hnRNP F, which represent a group of nuclear RNA binding
proteins that play important roles in the regulation of
alternative splicing decisions. hnRNP H and hnRNP F are
two closely related proteins, both of which bind to the
RNA sequence DGGGD. They are present in a complex with
the tissue-specific splicing factor Fox2, and regulate
the alternative splicing of the fibroblast growth factor
receptor 2 (FGFR2) transcripts. The presence of Fox 2
can allows hnRNP H and hnRNP F to better compete with
the SR protein ASF/SF2 for binding to FGFR2 exon IIIc.
Thus, hnRNP H and hnRNP F can function as potent
silencers of FGFR2 exon IIIc inclusion through an
interaction with the exonic GGG motifs. Furthermore,
hnRNP H and hnRNP H2 are almost identical; bothe have
been found to bind nuclear-matrix proteins. hnRNP H
activates exon inclusion by binding G-rich intronic
elements downstream of the 5' splice site in the
transcripts of c-src, human immunodeficiency virus type
1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons
when bound to exonic elements in the transcripts of
beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2
has been implicated in pre-mRNA 3' end formation.
Members in this family contain three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). RRM1 and RRM2 are
responsible for the binding to the RNA at DGGGD motifs,
and they play an important role in efficiently silencing
the exon. In addition, the family members have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. .
Length = 76
Score = 31.6 bits (71), Expect = 0.11
Identities = 22/57 (38%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
C+ + GL TE I + FS PV RV + I GR G V F + +DA AA
Sbjct: 2 CVHMRGLPYRATENDIYNFFSPLNPV-RVHIEIGPD-GRVTGEADVEFATHEDAVAA 56
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM2 of RBM40 and the RRM of RBM41.
RBM40, also known as RNA-binding region-containing
protein 3 (RNPC3) or U11/U12 small nuclear
ribonucleoprotein 65 kDa protein (U11/U12-65K protein).
It serves as a bridging factor between the U11 and U12
snRNPs. It contains two RNA recognition motifs (RRMs),
also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), connected by a linker that
includes a proline-rich region. It binds to the
U11-associated 59K protein via its RRM1 and employs the
RRM2 to bind hairpin III of the U12 small nuclear RNA
(snRNA). The proline-rich region might be involved in
protein-protein interactions. RBM41 contains only one
RRM. Its biological function remains unclear. .
Length = 82
Score = 31.4 bits (72), Expect = 0.13
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 187 LSIYTTEQQINHIFSKYGP---VERVEVVID-AKTGRSRGFCFVYFESRDDAAAAKDACT 242
LS TE+ + +IF ++ E+ I GR +G FV F S + A A +
Sbjct: 9 LSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATKALNLVN 68
Query: 243 GMEIDGRQIRVDFS 256
G + G+ + + F
Sbjct: 69 GYVLKGKPMVIQFG 82
>gnl|CDD|241177 cd12733, RRM3_GRSF1, RNA recognition motif 3 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subgroup
corresponds to the RRM3 of G-rich sequence factor 1
(GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein
which interacts with RNA in a G-rich element-dependent
manner. It may function in RNA packaging, stabilization
of RNA secondary structure, or other macromolecular
interactions. GRSF-1 contains three potential RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which are
responsible for the RNA binding. In addition, GRSF-1 has
two auxiliary domains, an acidic alpha-helical domain
and an N-terminal alanine-rich region, that may play a
role in protein-protein interactions and provide binding
specificity. .
Length = 75
Score = 31.3 bits (71), Expect = 0.14
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 6/59 (10%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVID-AKTGRSRGFCFVYFESRDDAAAA--KDAC 241
GL + Q I + F+ P++ ++I+ + GR+ G V+FES DDA AA KD
Sbjct: 7 GLPFQASGQDIVNFFA---PLKPTRILIEYSSDGRATGEADVHFESHDDAVAAMAKDRA 62
>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) 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), 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 = 96
Score = 31.6 bits (72), Expect = 0.14
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 16/68 (23%)
Query: 196 INHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI---- 251
++ IFSK+G V + ++ K + + + F A AAK + +DG+ I
Sbjct: 20 LHQIFSKFGTVLK--IITFTKNNQFQA--LIQFADAVSAQAAK-----LSLDGQNIYNGC 70
Query: 252 ---RVDFS 256
R+D+S
Sbjct: 71 CTLRIDYS 78
>gnl|CDD|221526 pfam12316, Dsh_C, Segment polarity protein dishevelled (Dsh) C
terminal. This domain family is found in eukaryotes,
and is typically between 177 and 207 amino acids in
length. The family is found in association with
pfam00778, pfam02377, pfam00610, pfam00595. The segment
polarity gene dishevelled (dsh) is required for pattern
formation of the embryonic segments. It is involved in
the determination of body organisation through the
Wingless pathway (analogous to the Wnt-1 pathway).
Length = 202
Score = 33.0 bits (75), Expect = 0.15
Identities = 29/92 (31%), Positives = 36/92 (39%), Gaps = 3/92 (3%)
Query: 57 SGSAGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYR 116
SGSAGS + R S +RS R+ + + G G+ S S S R GG R
Sbjct: 63 SGSAGSQHSEGSRSS-GSNRSDGERSRAADGREGGRKSGGSGSESEHTSRSGSRRSGGRR 121
Query: 117 SRSRSPGYRKRSSSYRSGGGSRGD--SYGGRG 146
+ S G S RS SYG G
Sbjct: 122 APSERSGPPPSEGSVRSSLSHPSSHSSYGAPG 153
>gnl|CDD|241128 cd12684, RRM_cpo, RNA recognition motif in Drosophila couch potato
(cpo) coding RNA-binding protein and similar proteins.
This subfamily corresponds to the RRM of Cpo, an
RNA-binding protein encoded by Drosophila couch potato
(cpo) gene. Cpo contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It may
control the processing of RNA molecules required for the
proper functioning of the peripheral nervous system
(PNS). .
Length = 83
Score = 31.2 bits (70), Expect = 0.15
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 4/81 (4%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRG-FCFVYFESRDDAAAAK 238
R L V GL + +++ +F Y E + + +K G++ FV FE+R A AAK
Sbjct: 2 RTLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSPVGFVTFETRAGAEAAK 61
Query: 239 DACTGMEID---GRQIRVDFS 256
G+ D + IR++F+
Sbjct: 62 QDLQGVRFDPDIPQTIRLEFA 82
>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1
small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or
U1A). This subgroup corresponds to the RRM2 of U1A
(also termed U1 snRNP A or U1-A), an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins,
including polypyrimidine tract binding protein (PTB),
polypyrimidine-tract binding protein-associated factor
(PSF), and non-POU-domain-containing, octamer-binding
(NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5).
U1A also binds to a flavivirus NS5 protein and plays an
important role in virus replication. It contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and it
may be free for binding other proteins. U1A also
contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 80
Score = 31.2 bits (70), Expect = 0.16
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
ENP P+ L + L T E ++ +F+++ + V +V GR FV F++
Sbjct: 1 ENP-PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV----PGR-HDIAFVEFDNEVQ 54
Query: 234 AAAAKDACTGMEI-DGRQIRVDFS 256
A AA++A G +I +++ F+
Sbjct: 55 AGAAREALQGFKITQSNAMKISFA 78
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and similar
proteins. This subfamily corresponds to the RRM of
Nab3p, an acidic nuclear polyadenylated RNA-binding
protein encoded by Saccharomyces cerevisiae NAB3 gene
that is essential for cell viability. Nab3p is
predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA processing.
Nab3p contains an N-terminal aspartic/glutamic acid-rich
region, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal region rich
in glutamine and proline residues. .
Length = 71
Score = 30.9 bits (70), Expect = 0.16
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
+++ + IFS YG + ++V+ G FV F+S + A A + G I GR++
Sbjct: 13 SKEDLFRIFSTYGEL--AQIVLKNAYG------FVQFDSPESCANAINCEQGKMIRGRKL 64
Query: 252 RVDFS 256
++ S
Sbjct: 65 HLEVS 69
>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 = 31.0 bits (70), Expect = 0.16
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYF 228
C+ V L E+ + +F K G +E V +V D KT +GF +V F
Sbjct: 1 CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQF 48
>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds to
the RRM1 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), 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 carboxyl terminus which
also harbors a methionine-rich region. The subgroup also
includes NAM8, 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 = 81
Score = 31.2 bits (71), Expect = 0.17
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 192 TEQQINHIFSKYG--PVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
E I +++ G PV V+V+ +G + G+CFV F S A A
Sbjct: 12 DENFIKQVWASLGLEPVN-VKVIRSRNSGLNAGYCFVEFPSPHAAQNA 58
>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 = 30.8 bits (70), Expect = 0.18
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
G E+ I FS PV + +V + GR GF FV +S +D A
Sbjct: 7 GAPFNVKEKHIREFFSPLKPVA-IRIVKNDH-GRKTGFAFVDLKSEEDLKKAL-KRNKDY 63
Query: 246 IDGRQIRV 253
+ GR I +
Sbjct: 64 MGGRYIEL 71
>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 = 0.18
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V LS TE + +F +G +E ++ G S+G FV F S +A AA +
Sbjct: 2 RKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSSHAEAQAAIN 60
Query: 240 ACTG 243
A G
Sbjct: 61 ALHG 64
>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 = 30.7 bits (70), Expect = 0.19
Identities = 22/69 (31%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
V GL TE ++ +F +G + V K +G FV F R A AA G
Sbjct: 6 VGGLDPAVTEDELRSLFGPFGEIVYV------KIPPGKGCGFVQFVHRAAAEAAIQQLQG 59
Query: 244 MEIDGRQIR 252
I G +IR
Sbjct: 60 TIIGGSRIR 68
>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 = 30.8 bits (70), Expect = 0.20
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 8/71 (11%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
L E+ + F YG + + + GF FV FE DA A G E
Sbjct: 6 RLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYELNGKE 57
Query: 246 IDGRQIRVDFS 256
+ G ++ V+ +
Sbjct: 58 LCGERVIVEHA 68
>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 = 31.0 bits (71), Expect = 0.20
Identities = 15/49 (30%), Positives = 24/49 (48%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA 234
GLS TE + FS++G V VE++ G RGF ++ + +
Sbjct: 6 GLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQ 54
>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 = 30.8 bits (69), Expect = 0.20
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
+ ++ F YGP+ V V + GF FV FE DAA A G + G ++R
Sbjct: 18 KTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRELDGRTLCGCRVR 72
Query: 253 VDFS 256
V+ S
Sbjct: 73 VELS 76
>gnl|CDD|218233 pfam04732, Filament_head, Intermediate filament head (DNA binding)
region. This family represents the N-terminal head
region of intermediate filaments. Intermediate filament
heads bind DNA. Vimentin heads are able to alter nuclear
architecture and chromatin distribution, and the
liberation of heads by HIV-1 protease liberates may play
an important role in HIV-1 associated cytopathogenesis
and carcinogenesis. Phosphorylation of the head region
can affect filament stability. The head has been shown
to interaction with the rod domain of the same protein.
Length = 89
Score = 31.0 bits (70), Expect = 0.20
Identities = 16/65 (24%), Positives = 22/65 (33%), Gaps = 2/65 (3%)
Query: 76 RSGSPHRRS--KRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRS 133
S S +RR+ + + R +G + S S R R S S K S RS
Sbjct: 1 YSTSSYRRTFGDPTRSSSSRSSGGSSGRSSSSSGFRSRSVSRSSSSSPSPSLKSSYRKRS 60
Query: 134 GGGSR 138
Sbjct: 61 SSAPP 65
>gnl|CDD|240721 cd12275, RRM1_MEI2_EAR1_like, RNA recognition motif 1 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM1 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding protein
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 30.6 bits (69), Expect = 0.21
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 179 SRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFV-YFESRDDAAAA 237
SR L V + TE + +F YG V V+ S G V +++ RD A
Sbjct: 1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQT-----ERISEGIVTVHFYDIRDAKRAV 55
Query: 238 KDAC 241
++ C
Sbjct: 56 RELC 59
>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 = 30.8 bits (69), Expect = 0.22
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+++ +FS G V+R ++ D K G+SRG V FE +A A G + R + V
Sbjct: 15 KKLKEVFSIAGTVKRADIKED-KDGKSRGMGTVTFEQPIEAVQAISMFNGQFLFDRPMHV 73
>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 = 30.6 bits (69), Expect = 0.23
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 11/59 (18%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
L V L TEQ+I +F +YG V +++ + + FV+ DD AA +A
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHM---DDKTAADEA 50
>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 = 30.5 bits (69), Expect = 0.23
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 194 QQINHIF-SKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
Q + +F K G V VE+ D + G+SRG V F+ ++ A + E+ GR++
Sbjct: 14 QDLKDLFREKVGEVTYVELFKDEE-GKSRGCGVVEFKDKESVQKALETMNRYELKGRKLV 72
Query: 253 V 253
V
Sbjct: 73 V 73
>gnl|CDD|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2
small nuclear ribonucleoprotein B" (U2B"). This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B"), a unique protein that comprises the U2 snRNP.
It was initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA and its nuclear
transport is independent of U2 snRNA binding. U2B"
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). It also contains a nuclear localization signal
(NLS) in the central domain. However, nuclear import of
U2B'' does not depend on this NLS. The N-terminal RRM is
sufficient to direct U2B" to the nucleus. .
Length = 80
Score = 30.8 bits (69), Expect = 0.26
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 174 ENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDD 233
+NP P+ L + L T E ++ +F+++ + V +V GR FV FE+
Sbjct: 1 DNP-PNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLV----PGR-HDIAFVEFENEAQ 54
Query: 234 AAAAKDACTGMEI 246
A AA+DA G +I
Sbjct: 55 AGAARDALQGFKI 67
>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509). This
family consists of several uncharacterized viral
proteins from the Marek's disease-like viruses. Members
of this family are typically around 400 residues in
length. The function of this family is unknown.
Length = 377
Score = 33.1 bits (75), Expect = 0.28
Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 11/83 (13%)
Query: 59 SAGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSR 118
AG+ DD +I+ +G H +RP + + R+RS S S RSR
Sbjct: 292 RAGTPDDGS---AISEDSAGGSHHTMRRPPHSTSGERRGRRRNRSESRS--------RSR 340
Query: 119 SRSPGYRKRSSSYRSGGGSRGDS 141
SRS R R R G R +S
Sbjct: 341 SRSGSRRYRRRRGRGVPGRRSES 363
>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 = 30.7 bits (69), Expect = 0.28
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 171 DGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFES 230
D R N R L + L I TE + F ++G + V++ G++ + F+ FE+
Sbjct: 3 DQRAN----RTLFLGNLDITVTETDLRRAFDRFGVITEVDIK-RPGRGQTSTYGFLKFEN 57
Query: 231 RDDAAAAKDACTGMEIDGRQIRVDF 255
D A AK A +G + I++ +
Sbjct: 58 LDMAHRAKLAMSGKVLRRNPIKIGY 82
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 32.7 bits (75), Expect = 0.29
Identities = 15/37 (40%), Positives = 16/37 (43%)
Query: 110 GRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRG 146
GR GG R+ S SS GGG G GG G
Sbjct: 6 GRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFG 42
>gnl|CDD|240993 cd12549, RRM_Set1B, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1B (Set1B). This
subgroup corresponds to the RRM of Setd1B, also termed
SET domain-containing protein 1B (Set1B), or lysine
N-methyltransferase 2G, a ubiquitously expressed
vertebrates histone methyltransferase that exhibits high
homology to yeast Set1. Set1B is localized to
euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1B complex is a histone
methyltransferase that produces trimethylated histone H3
at Lys4. Set1B contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), an N- SET domain, and a
C-terminal catalytic SET domain followed by a post-SET
domain. .
Length = 93
Score = 30.8 bits (69), Expect = 0.29
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 202 KYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
KYG VE VE++ + K + G V F + AKDA
Sbjct: 25 KYGEVEEVEILYNPKNKKHLGIAKVVFAT---VKGAKDA 60
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM3
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 = 73
Score = 30.4 bits (68), Expect = 0.30
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME 245
G++ TEQ + FS +G + + V + +G+ F+ F + + AA A + G
Sbjct: 7 GIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSVNGTT 60
Query: 246 IDGRQIR 252
I+G ++
Sbjct: 61 IEGHVVK 67
>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM2 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 = 82
Score = 30.4 bits (69), Expect = 0.30
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 9/64 (14%)
Query: 195 QINHIFS-KYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGME----IDGR 249
Q+ FS +Y + +VV+D G SRG+ FV F + K A T M+ + G+
Sbjct: 17 QLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESE---QKRALTEMQGASGLGGK 72
Query: 250 QIRV 253
IRV
Sbjct: 73 PIRV 76
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of 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 is 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 = 72
Score = 30.0 bits (68), Expect = 0.31
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 218 GRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+ V F + D A + G E++GR+I++
Sbjct: 34 KQRPNEGVVEFATYSDMKRAIEKLDGTELNGRKIKL 69
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 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 is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 30.2 bits (68), Expect = 0.32
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC 241
L VF L + ++ IF YG ++ + +T R F+ F A AA A
Sbjct: 4 LVVFNLDPSVSNDDLHQIFGAYGEIKEIR-----ETPNKRHHKFIEFYDVRSAEAALKAL 58
Query: 242 TGMEIDGRQIRVD 254
EI G++I+++
Sbjct: 59 NRSEIAGKRIKLE 71
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 30.4 bits (69), Expect = 0.34
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTG 243
+FG+ E +I F ++G + V V AK G FV FE+R+ A A +
Sbjct: 7 LFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAKCG------FVRFETREAAEKFAAAISE 60
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 30.8 bits (70), Expect = 0.34
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 8/70 (11%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
L GL+ T+ + I FS++G V+ V+ + K G R F++ + A A +
Sbjct: 3 ILKFSGLNKPTSREDIKEAFSQHGEVKYVDFLEGDKEGYVR------FKTPEAAKKALEK 56
Query: 241 --CTGMEIDG 248
++I
Sbjct: 57 ATEAKLKIKE 66
>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 = 30.3 bits (68), Expect = 0.39
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVE--------RVEVVIDAKTGRSRGFCFVYFESRDDAA 235
V GL+ T +++ F G V+ V + D +TG+ +G V +E A
Sbjct: 5 VQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPSAK 64
Query: 236 AAKDACTGMEIDGRQIRV 253
AA + G + G +++V
Sbjct: 65 AAVEWFDGKDFQGSKLKV 82
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome
proliferator-activated receptor gamma coactivator 1A
(PGC-1alpha) family of regulated coactivators. This
subfamily corresponds to the RRM of PGC-1alpha,
PGC-1beta, and PGC-1-related coactivator (PRC), which
serve as mediators between environmental or endogenous
signals and the transcriptional machinery governing
mitochondrial biogenesis. They play an important
integrative role in the control of respiratory gene
expression through interacting with a number of
transcription factors, such as NRF-1, NRF-2, ERR, CREB
and YY1. All family members are multi-domain proteins
containing the N-terminal activation domain, an LXXLL
coactivator signature, a tetrapeptide motif (DHDY)
responsible for HCF binding, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). In contrast to PGC-1alpha
and PRC, PGC-1beta possesses two glutamic/aspartic
acid-rich acidic domains, but lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 89
Score = 30.4 bits (69), Expect = 0.41
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 7/62 (11%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRG--FCFVYFESRDDAAAA 237
R + V + I TT ++ F +G +E + + R G + FV + DA A
Sbjct: 3 RVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHF-----RDDGDNYGFVTYRYACDAFRA 57
Query: 238 KD 239
+
Sbjct: 58 IE 59
>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 = 29.8 bits (67), Expect = 0.41
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 6/59 (10%)
Query: 196 INHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
I+ FSK + + V D + G S+ F +V FES +D A + TG ++ G +I+++
Sbjct: 21 ISEFFSK----KNLAVQ-DVRIGSSKKFGYVDFESAEDLEKALE-LTGKKLLGNEIKLE 73
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element (TAR)
RNA which is synthesized by cellular RNA polymerase II
at the viral long terminal repeat. NELF is a
heterotetrameric protein consisting of NELF A, B, C or
the splice variant D, and E. NELF-E contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It plays a
role in the control of HIV transcription by binding to
TAR RNA. In addition, NELF-E is associated with the
NELF-B subunit, probably via a leucine zipper motif. .
Length = 75
Score = 29.9 bits (68), Expect = 0.42
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 176 PQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAA 235
P+ L V G + TE+ + FS +G + + + + ++ GF V FE + A
Sbjct: 1 PRKGNTLYVHGYGL--TEEILKKAFSPFGNIINISMEKE----KNCGF--VTFEKMESAD 52
Query: 236 AAKDACTGMEIDGRQIRVDFS 256
A G + G Q++V +
Sbjct: 53 RAIAELNGTTVQGVQLKVSLA 73
>gnl|CDD|240710 cd12264, RRM_AKAP17A, RNA recognition motif found in A-kinase
anchor protein 17A (AKAP-17A) and similar proteins.
This subfamily corresponds to the RRM domain of
AKAP-17A, also termed 721P, or splicing factor,
arginine/serine-rich 17A (SFRS17A). It was originally
reported as the pseudoautosomal or X inactivation escape
gene 7 (XE7) and as B-lymphocyte antigen precursor. It
has been suggested that AKAP-17A is an alternative
splicing factor and an SR-related splicing protein that
interacts with the classical SR protein ASF/SF2 and the
SR-related factor ZNF265. Additional studies have
indicated that AKAP-17A is a dual-specific protein
kinase A anchoring protein (AKAP) that can bind both
type I and type II protein kinase A (PKA) with high
affinity and co-localizes with the catalytic subunit of
PKA in nuclear speckles as well as the splicing factor
SC35 in splicing factor compartments. It is involved in
regulation of pre-mRNA splicing possibly by docking a
pool of PKA in splicing factor compartments. AKAP-17A
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 121
Score = 30.7 bits (70), Expect = 0.46
Identities = 28/110 (25%), Positives = 43/110 (39%), Gaps = 36/110 (32%)
Query: 169 FADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVID---AKTGRSRGF-- 223
FA+ R + +PS E + +FSK+G + V++ + K RG
Sbjct: 17 FAEPRVSDKPS-------------ELVLRTVFSKFGEIRNVDIPMLDPYRKEMDDRGSDT 63
Query: 224 ----------CFVYFESRDDAAAAKDACTGM----EIDGR----QIRVDF 255
+V +E D A DA GM + DG+ I+VDF
Sbjct: 64 FSFGSHLHFEVYVQYEEYDGFVKAMDALRGMKLQYKGDGKALAANIKVDF 113
>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 = 29.7 bits (67), Expect = 0.48
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
TE+++ + FS+YG +E V R + FV F + +A A D
Sbjct: 16 TEEKLRNDFSQYGEIESV------NYLREKNCAFVNFTNISNAIKAIDG 58
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 32.5 bits (74), Expect = 0.56
Identities = 17/111 (15%), Positives = 29/111 (26%)
Query: 37 PKEPAQTSSDQCYYRLSPARSGSAGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNG 96
+ P+ + S + S+ S ++ S T S S S + P + R
Sbjct: 293 ERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPS 352
Query: 97 LGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRGK 147
S +R SP + R + R
Sbjct: 353 PSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDA 403
Score = 29.8 bits (67), Expect = 3.1
Identities = 22/110 (20%), Positives = 32/110 (29%), Gaps = 4/110 (3%)
Query: 37 PKEPAQTSSDQCYYRLSPARSGSAGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNG 96
P SS + S +R S+ S G RS P R
Sbjct: 303 PGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSP----SRPPP 358
Query: 97 LGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRG 146
+ S R R + S R+R+ + +G R D+ G
Sbjct: 359 PADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDATGRFP 408
>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 = 30.4 bits (68), Expect = 0.57
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T Q + +F YG V+RV+++ + K + + + A G ++ G+ I
Sbjct: 27 TPQSLFTLFGVYGDVQRVKILYNKKDS-----ALIQMADGNQSQLAMSHLNGQKMYGKII 81
Query: 252 RVDFSVTQRAHTPTPGI 268
RV S Q P G+
Sbjct: 82 RVTLSKHQTVQLPREGL 98
>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 = 29.3 bits (66), Expect = 0.65
Identities = 15/53 (28%), Positives = 23/53 (43%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAK 238
GL ++++I FS V + GRS G +V F S++ A A
Sbjct: 7 GLPFGCSKEEIAQFFSGLEIVPNGITLPMDYRGRSTGEAYVQFASQESAERAL 59
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 31.6 bits (72), Expect = 0.74
Identities = 20/58 (34%), Positives = 22/58 (37%), Gaps = 8/58 (13%)
Query: 75 SRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYR 132
RS RRS+R GR G RSR RS RR S R+ YR
Sbjct: 14 RRSRRAARRSRRD----GRVGSRG-RSRYRSRRRSSRR---SSTRRAELADTERDRYR 63
>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 = 29.2 bits (65), Expect = 0.84
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 195 QINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVD 254
++ FS YGP+ V + + GF FV FE DA A G I G ++RV+
Sbjct: 15 ELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE 69
Query: 255 FS 256
S
Sbjct: 70 LS 71
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 28.7 bits (65), Expect = 0.92
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 200 FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
F K+G V + + D + +G FV F++ +DA +
Sbjct: 20 FEKFGKVNNIRMRRD-LDKKFKGSVFVEFKTEEDAKKFLEK 59
>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 = 28.8 bits (65), Expect = 1.0
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 181 CLGVFGLSIYTTEQQINHIFSKYGPVER-VEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
C+ + + T+ ++ F+ E+ + ++ D KTG++ G +V F S +DA A
Sbjct: 1 CIKIKNIPFDVTKGEVLAFFAGIAIAEQGIHILYD-KTGKTLGEAYVEFVSEEDAMRA 57
>gnl|CDD|241159 cd12715, RRM2_MATR3, RNA recognition motif 2 in vertebrate
matrin-3. This subgroup corresponds to the RRM2 of
Matrin 3 (MATR3 or P130), a highly conserved inner
nuclear matrix protein with a bipartite nuclear
localization signal (NLS), two zinc finger domains
predicted to bind DNA, and two RNA recognition motifs
(RRM), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that are known to interact
with RNA. MATR3 has been implicated in various
biological processes. It is involved in RNA processing
by interacting with other nuclear proteins to anchor
hyperedited RNAs to the nuclear matrix. It plays a role
in mRNA stabilization through maintaining the stability
of certain mRNA species. Besides, it modulates the
activity of proximal promoters by binding to highly
repetitive sequences of matrix/scaffold attachment
region (MAR/SAR). The phosphorylation of MATR3 is
assumed to cause neuronal death. It is phosphorylated by
the protein kinase ATM, which activates the cellular
response to double strand breaks in the DNA. Its
phosphorylation by protein kinase A (PKA) is responsible
for the activation of the N-methyl-d-aspartic acid
(NMDA) receptor. Furthermore, MATR3 has been identified
as both a Ca2+-dependent CaM-binding protein and a
downstream substrate of caspases. Additional research
indicates that matrin 3 also binds Rev/Rev responsive
element (RRE)-containing viral RNA and functions as a
cofactor that mediates the post-transcriptional
regulation of HIV-1. .
Length = 80
Score = 28.7 bits (64), Expect = 1.0
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 219 RSRGFCFVYFESRDDAAAAKDAC--TGMEIDGRQIRVDFS 256
R + F+ E+R+DA A D C + G+ ++VD S
Sbjct: 35 RMKNQAFIEMETREDAEAMVDHCKKNALWFQGKCLKVDLS 74
>gnl|CDD|240953 cd12509, RRM3_ESRPs_Fusilli, RNA recognition motif 3 in epithelial
splicing regulatory protein ESRP1, ESRP2, Drosophila
RNA-binding protein Fusilli and similar proteins. This
subfamily corresponds to the RRM3 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. Fusilli 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 = 81
Score = 29.0 bits (65), Expect = 1.1
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 4/76 (5%)
Query: 181 CLGVFGLSIYTTEQQINHI---FSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
C+ + GL T + I + ++ + V +V++A+ GR G F+ S + A A
Sbjct: 3 CIRLRGLPYEATVEDILNFLGELARSIAPQGVHMVLNAQ-GRPSGDAFIQMLSAEFATRA 61
Query: 238 KDACTGMEIDGRQIRV 253
+ + R I V
Sbjct: 62 ANELHKHHMGERYIEV 77
>gnl|CDD|240911 cd12465, RRM_UHMK1, RNA recognition motif found in U2AF homology
motif kinase 1 (UHMK1) and similar proteins. This
subgroup corresponds to the RRM of UHMK1. UHMK1, also
termed kinase interacting with stathmin (KIS) or P-CIP2,
is a serine/threonine protein kinase functionally
related to RNA metabolism and neurite outgrowth. It
contains an N-terminal kinase domain and a C-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), with
high homology to the corresponding motif of the
mammalian U2 small nuclear ribonucleoprotein auxiliary
factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1
targets two key regulators of cell proliferation and
migration, the cyclin-dependent kinase (CDK) inhibitor
p27Kip1 and the microtubule-destabilizing protein
stathmin. It plays a critical role during vascular wound
repair by preventing excessive vascular smooth muscle
cell (VSMC) migration into the vascular lesion.
Moreover, UHMK1 may control cell migration and neurite
outgrowth by interacting with and phosphorylating the
splicing factor SF1, thereby probably contributing to
the control of protein expression. Furthermore, UHMK1
may be functionally related to microtubule dynamics and
axon development. It localizes to RNA granules,
interacts with three proteins found in RNA granules
(KIF3A, NonO, and eEF1A), and further enhances the local
translation. UHMK1 is highly expressed in regions of the
brain implicated in schizophrenia and may play a role in
susceptibility to schizophrenia.
Length = 88
Score = 29.2 bits (65), Expect = 1.1
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 202 KYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDF 255
KYGPV V ++I K +G FV + + D+ AA+ TG DG+ + F
Sbjct: 36 KYGPV--VSLLI-PKENPGKGQVFVEYANAGDSKAAQKLLTGRIFDGKFVVATF 86
>gnl|CDD|109943 pfam00906, Hepatitis_core, Hepatitis core antigen. The core
antigen of hepatitis viruses possesses a carboxyl
terminus rich in arginine. On this basis it was
predicted that the core antigen would bind DNA. There is
some experimental evidence to support this.
Length = 182
Score = 30.2 bits (68), Expect = 1.2
Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 17/54 (31%)
Query: 69 RKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSP 122
+ R R SP RR+ P+ R RS SPR R RS+S S
Sbjct: 144 ETIVVRRRGRSPRRRTPSPR-------------RRRSQSPRRR----RSQSPSS 180
>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 = 28.9 bits (64), Expect = 1.3
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDA 240
E I +FS +G +E + + G SRG FV F +R A A A
Sbjct: 14 NENDIRVMFSPFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKA 61
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living cells.
RRM2/3 are implicated in ACF interaction with APOBEC-1.
.
Length = 78
Score = 28.8 bits (64), Expect = 1.3
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI-DGRQI 251
E ++ + K G + + +++D G +RG+ FV F ++ +A A EI +GR +
Sbjct: 15 EDELIPLCEKIGKIYEMRMMMDF-NGNNRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLL 73
Query: 252 RV 253
V
Sbjct: 74 GV 75
>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 = 28.2 bits (63), Expect = 1.3
Identities = 25/77 (32%), Positives = 34/77 (44%), Gaps = 14/77 (18%)
Query: 184 VFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDAC-- 241
V LS TE+ I FS G +E VE+ ++G +V F+ D A + A
Sbjct: 3 VTNLSPKATERDIYDFFSFSGDIEYVEI---QRSGEQSQTAYVTFK---DPQAQETALLL 56
Query: 242 TGMEIDGRQIRVDFSVT 258
+G I VD SVT
Sbjct: 57 SGATI------VDQSVT 67
>gnl|CDD|235494 PRK05482, PRK05482, potassium-transporting ATPase subunit A;
Provisional.
Length = 559
Score = 30.9 bits (71), Expect = 1.3
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 310 VVGVGAVTMTEMSGNGRISPLQFSGGME 337
+ G+ E+ GN ++ L G ME
Sbjct: 293 LAGLAVTMWAELQGNPALAALGIDGNME 320
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of nuclear
proteins consisting of Matrin 3 (MATR3), nuclear protein
220 (NP220) and similar proteins. MATR3 is a highly
conserved inner nuclear matrix protein that has been
implicated in various biological processes. NP220 is a
large nucleoplasmic DNA-binding protein that binds to
cytidine-rich sequences, such as CCCCC (G/C), in
double-stranded DNA (dsDNA). Both, Matrin 3 and NP220,
contain two RNA recognition motif (RRM), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a Cys2-His2 zinc finger-like motif at the
C-terminal region. .
Length = 76
Score = 28.4 bits (64), Expect = 1.5
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 8/68 (11%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACT--GMEIDG 248
TE ++ + +G V+ + +R F+ ES +DA A + I G
Sbjct: 13 YTEAELLKLAEPFGKVDHYIFL------PNRNKAFIEMESPEDAQALVSFYKTYPLTIGG 66
Query: 249 RQIRVDFS 256
+ I+V S
Sbjct: 67 KSIKVALS 74
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 30.7 bits (69), Expect = 1.5
Identities = 31/106 (29%), Positives = 39/106 (36%), Gaps = 18/106 (16%)
Query: 82 RRSKRPQVACGRDNGLGN-------RSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSG 134
R + P D+ G+ +R + + RRGG RS G S S G
Sbjct: 395 RPPRVPVEGEEADDEAGDSVGTIFREAREQRAAEEQRRGGGRS-----GPGGGSRSGSVG 449
Query: 135 GGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEEFADGRENPQPSR 180
GG R D G GK VE EA+A A G E P +
Sbjct: 450 GGGRRDGAGADGKPRPRRKPRVEGEADAA------AAGAETPVVAA 489
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 28.0 bits (62), Expect = 1.5
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 188 SIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEID 247
++ + + IFSKYG + V +GF FV + + +A AA G I
Sbjct: 11 TLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIA 62
Query: 248 GRQIRVDFS 256
G+ + ++ +
Sbjct: 63 GQVLDINLA 71
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 28.1 bits (63), Expect = 1.7
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 202 KYGPVERV-EVVIDAKTGR--SRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
+G V ++ ++ ID RG ++ FE +DAA A G DGR ++
Sbjct: 15 YFGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVK 68
>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM1 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP
M is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs.
hnRNP M functions as the receptor of carcinoembryonic
antigen (CEA) that contains the penta-peptide sequence
PELPK signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 28.1 bits (62), Expect = 1.7
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 202 KYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
K G V VE+++DA+ G+SRG V F+ + A + ++GR ++V
Sbjct: 23 KVGEVTYVELLMDAE-GKSRGCAVVEFKMEESMKKAVEVLNKHVLNGRPLKV 73
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding
protein with multiple splicing (RBP-MS). This subfamily
corresponds to the RRM of RBP-MS, also termed heart and
RRM expressed sequence (hermes), an RNA-binding proteins
found in various vertebrate species. It contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). RBP-MS
physically interacts with Smad2, Smad3 and Smad4 and
plays a role in regulation of Smad-mediated
transcriptional activity. In addition, RBP-MS may be
involved in regulation of mRNA translation and
localization during Xenopus laevis development. .
Length = 76
Score = 28.1 bits (62), Expect = 1.8
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 7/79 (8%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKD 239
R L V GL + +++ +F + E + + +K + FV F+SR +A AAK+
Sbjct: 2 RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSK----QPVGFVSFDSRSEAEAAKN 57
Query: 240 ACTGMEID---GRQIRVDF 255
A G+ D + +R++F
Sbjct: 58 ALNGIRFDPEIPQTLRLEF 76
>gnl|CDD|240992 cd12548, RRM_Set1A, RNA recognition motif in vertebrate
histone-lysine N-methyltransferase Setd1A (Set1A). This
subgroup corresponds to the RRM of Setd1A, also termed
SET domain-containing protein 1A (Set1A), or lysine
N-methyltransferase 2F, or Set1/Ash2 histone
methyltransferase complex subunit Set1, a ubiquitously
expressed vertebrates histone methyltransferase that
exhibits high homology to yeast Set1. Set1A is localized
to euchromatic nuclear speckles and associates with a
complex containing six human homologs of the yeast
Set1/COMPASS complex, including CXXC finger protein 1
(CFP1; homologous to yeast Spp1), Rbbp5 (homologous to
yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5
(homologous to yeast Swd3), and Wdr82 (homologous to
yeast Swd2). Set1A contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), an N- SET
domain, and a C-terminal catalytic SET domain followed
by a post-SET domain. In contrast to Set1B, Set1A
additionally contains an HCF-1 binding motif that
interacts with HCF-1 in vivo. .
Length = 95
Score = 28.4 bits (63), Expect = 1.8
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 202 KYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGM 244
K+G VE VE+++ KT + G V F S AKD +
Sbjct: 25 KFGEVEEVEILLHPKTRKHLGLARVLFTS---TRGAKDTVKHL 64
>gnl|CDD|233436 TIGR01490, HAD-SF-IB-hyp1, HAD-superfamily subfamily IB hydrolase,
TIGR01490. This hypothetical equivalog is a member of
the IB subfamily (TIGR01488) of the haloacid
dehalogenase (HAD) superfamily of aspartate-nucleophile
hydrolases. The sequences modelled by This model are all
bacterial. The IB subfamily includes the enzyme
phosphoserine phosphatase (TIGR00338). Due to this
relationship, several of these sequences have been
annotated as "phosphoserine phosphatase related
proteins," or "Phosphoserine phosphatase-family
enzymes." There is presently no evidence that any of the
enzymes in This model possess PSPase activity.
OMNI|NTL01ML1250 is annotated as a "possible
transferase," however this is due to the C-terminal
domain found on this sequence which is homologous to a
group of glycerol-phosphate acyltransferases (between
trusted and noise to TIGR00530). A subset of these
sequences including OMNI|CC1962, the Caulobacter
crescentus CicA protein cluster together and may
represent a separate equivalog [Unknown function,
Enzymes of unknown specificity].
Length = 202
Score = 30.0 bits (68), Expect = 1.9
Identities = 12/71 (16%), Positives = 20/71 (28%), Gaps = 4/71 (5%)
Query: 106 YSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAM 165
+ R P R + + RG Y + E + A+
Sbjct: 20 LKFLASKNILFEELRLPKVLARFEFFLN----RGLDYMAYYRAFALDALAGLLEEDVRAI 75
Query: 166 VEEFADGRENP 176
VEEF + +
Sbjct: 76 VEEFVNQKIES 86
>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 = 28.0 bits (62), Expect = 1.9
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 213 IDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
I + G+S+G V FES + A A G +++GR+I V
Sbjct: 31 IKMENGKSKGCGVVRFESPEVAERACRMMNGYKLNGREIDV 71
>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 = 28.2 bits (63), Expect = 2.0
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 178 PSRCLGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
P++ + V L TE+ + + +++G + V+V G+ + V F + + A A
Sbjct: 6 PTKMIHVSNLPSDVTEEDVINHLAEHGVIVNVKVF--ESNGKKQA--LVEFATEEQATEA 61
Query: 238 KDACTGMEIDGRQIRVDF 255
++G IR+ F
Sbjct: 62 LACKHASSLNGSTIRLAF 79
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 28.0 bits (62), Expect = 2.0
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 194 QQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+++ +FS G V R +++ D K G+SRG V FE +A A G + R + V
Sbjct: 15 KKLKEVFSMAGMVVRADILED-KDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHV 73
>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 = 27.6 bits (62), Expect = 2.5
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 9/66 (13%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACT-GMEIDGR 249
TE+ + FS++G V V + R F FV F D A+ C I G
Sbjct: 12 MTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTF---ADPEVAQSLCGEDHIIKGV 63
Query: 250 QIRVDF 255
+ V
Sbjct: 64 SVHVSN 69
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 27.5 bits (61), Expect = 2.5
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 193 EQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIR 252
E+ + +F KYG + +E+ F FV FE DA A G + ++R
Sbjct: 13 EKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAVFGRNGYDFGQCRLR 69
Query: 253 VDF 255
V+F
Sbjct: 70 VEF 72
>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM3 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence show that the
RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 93
Score = 28.1 bits (62), Expect = 2.9
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 192 TEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQI 251
T Q + +F YG V+RV+++ + K V + A A G ++ G+ +
Sbjct: 13 TPQCLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSHLNGQKLHGKPL 67
Query: 252 RVDFSVTQRAHTPTPG 267
R+ S Q P G
Sbjct: 68 RITLSKHQTVQLPREG 83
>gnl|CDD|222011 pfam13257, DUF4048, Domain of unknown function (DUF4048). This
presumed domain is functionally uncharacterized. This
domain family is found in eukaryotes, and is typically
between 228 and 257 amino acids in length.
Length = 242
Score = 29.4 bits (66), Expect = 3.1
Identities = 16/46 (34%), Positives = 19/46 (41%), Gaps = 1/46 (2%)
Query: 99 NRSRSRSYSPR-GRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYG 143
N + SR+ P RR G RS SRS + S S S G
Sbjct: 115 NATESRTVPPPRSRRSGSRSTSRSRLRLQGGSLSSSRSSRSSTSKG 160
>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 = 27.2 bits (61), Expect = 3.2
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 182 LGVFGLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDA-AAAKDA 240
L V GL TE+ + F ++G + + VV + FV F +R+ A AA+
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREAAEKAAERL 57
Query: 241 CTGMEIDGRQIRV 253
+ I+GR++++
Sbjct: 58 FNKLIINGRRLKL 70
>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 = 28.0 bits (63), Expect = 3.3
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 180 RCLGVFGLSIYTTEQQINHIFSKYGPVERVEV 211
R L V + Y TE+ + +FS+ G VE VE+
Sbjct: 1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVEL 32
>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated
hydrophilic C-term. This domain is a hydrophilic region
found at the C-terminus of plant and metazoan
pre-mRNA-splicing factor 38 proteins. The function is
not known.
Length = 97
Score = 27.8 bits (62), Expect = 3.4
Identities = 17/66 (25%), Positives = 20/66 (30%), Gaps = 3/66 (4%)
Query: 74 RSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRS 133
R RRS R + R + + R R R R R R R RS
Sbjct: 29 AERDVDRGRRSPRRR---TRRRSRRRKRSRKRRRRRRDRDRARYRDRDDRDRDRYDRSRS 85
Query: 134 GGGSRG 139
SR
Sbjct: 86 RSRSRS 91
Score = 27.4 bits (61), Expect = 4.3
Identities = 14/50 (28%), Positives = 16/50 (32%), Gaps = 1/50 (2%)
Query: 98 GNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSS-YRSGGGSRGDSYGGRG 146
R R + R R RSR R R R + YR D Y
Sbjct: 35 RGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDRDDRDRDRYDRSR 84
>gnl|CDD|221931 pfam13136, DUF3984, Protein of unknown function (DUF3984). This
family of proteins is functionally uncharacterized. This
family of proteins is found in eukaryotes. Proteins in
this family are typically between 393 and 442 amino
acids in length.
Length = 301
Score = 29.3 bits (66), Expect = 3.5
Identities = 18/79 (22%), Positives = 25/79 (31%), Gaps = 11/79 (13%)
Query: 100 RSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGD----SYGGRGKIIIAVVTE 155
R R S RRG + S +R S S GSR D R +
Sbjct: 171 REREHSSRRASRRGRSGYSTPSAALSRRGSRSASRRGSRADLSMTPLEARR-------AD 223
Query: 156 VEEEAEATAMVEEFADGRE 174
E+ + + +F D
Sbjct: 224 AEDSRDTVLLGPDFVDEDI 242
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 29.3 bits (66), Expect = 3.5
Identities = 26/147 (17%), Positives = 30/147 (20%), Gaps = 14/147 (9%)
Query: 2 WTIFLKVLGLCGLSEPDGKVPVWYLCRS--HVSGRLLPKEPAQTSSDQCYYRLSPARSGS 59
FL VL ++ S V G P+
Sbjct: 162 TVFFLAVLAFI----------LYKFFLSCGGVRGGPRPERAGYGGGGGGGGGGGGGGGSG 211
Query: 60 AGSIDDKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRS 119
G KS G S R G + G GY S
Sbjct: 212 PG--PPPPGFKSSFPPPYGPGAGPSSGYGSGGTRSGQGGWGPGFWTGLGAGGALGYLFGS 269
Query: 120 RSPGYRKRSSSYRSGGGSRGDSYGGRG 146
R SY SG S S
Sbjct: 270 RRNNNSSYGRSYGSGSPSYSPSSSSNS 296
>gnl|CDD|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence
factor 1 (GRSF-1) and similar proteins. This subfamily
corresponds to the RRM2 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 = 75
Score = 27.4 bits (61), Expect = 3.6
Identities = 15/52 (28%), Positives = 22/52 (42%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
GL TE I F V+ V++ + GR G +V F + + A A
Sbjct: 8 GLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKA 59
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 29.4 bits (66), Expect = 3.9
Identities = 29/132 (21%), Positives = 47/132 (35%), Gaps = 34/132 (25%)
Query: 155 EVEEEAEATAMVEEFAD------GRE---NPQPSRCLGVFGLSIYTTEQQ---------- 195
E E+E A A V G+ N S+ + G S + +
Sbjct: 44 EFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVEN 103
Query: 196 ---------INHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEI 246
+ IF+ YG V R +V K + V FES + A AK A G +I
Sbjct: 104 PMYPITLDVLYQIFNPYGKVLR--IVTFTKNNVFQA--LVEFESVNSAQHAKAALNGADI 159
Query: 247 DGR--QIRVDFS 256
++++++
Sbjct: 160 YNGCCTLKIEYA 171
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 26.8 bits (60), Expect = 4.1
Identities = 13/44 (29%), Positives = 18/44 (40%)
Query: 210 EVVIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRV 253
+V G V F S++D A G E GR++RV
Sbjct: 26 DVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGTEFRGRRVRV 69
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 29.3 bits (65), Expect = 4.2
Identities = 24/109 (22%), Positives = 49/109 (44%), Gaps = 14/109 (12%)
Query: 200 FSKYGPVERVEV---VIDAKTGRSRGFCFVYFESRDDAAAAKDACTGMEIDGRQIRVDFS 256
F +YG ++++ V + S ++ + +++DAA G +DGR ++ +
Sbjct: 141 FGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYG 200
Query: 257 VTQ-------RAHTPTPG-IYMGRPTYEQLNNTQSELGSLLSEKHAIKG 297
T+ A P P +Y+ P E+ + T+ EL + +H + G
Sbjct: 201 TTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNS---QHKLHG 246
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 29.0 bits (65), Expect = 4.6
Identities = 11/52 (21%), Positives = 15/52 (28%), Gaps = 4/52 (7%)
Query: 95 NGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRG 146
N + Y G + Y +R G G+ YGG G
Sbjct: 16 GPSNNYNSYGPYPDSSNPYGNYQANHQDNY----GGFRPGYGNYSGGYGGFG 63
>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM2 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 = 89
Score = 27.3 bits (60), Expect = 4.6
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 219 RSRGFCFVYFESRDDAAAAKDACTGMEID--GRQIRVDFS 256
++RGF FV +ES AA A+ I G QI VD++
Sbjct: 43 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWA 82
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 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 = 92
Score = 27.1 bits (60), Expect = 4.9
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 2/78 (2%)
Query: 179 SRCLGVFGLS-IYTTEQQINHIFSKYGPVERVEVVIDAKTGRSRGFCFVYFESRDDAAAA 237
S+CL V L + FSK ++ + G+ +GF + +ES + A
Sbjct: 2 SKCLCVDQLPPSLCDVGDLREAFSKIHAPTFCQLAC-GQDGQLKGFAVLEYESAEMAEMV 60
Query: 238 KDACTGMEIDGRQIRVDF 255
+ G+ + G IRV F
Sbjct: 61 QQQADGLSLAGSHIRVSF 78
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 29.2 bits (65), Expect = 5.2
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 2/70 (2%)
Query: 78 GSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGS 137
G+ + + + C NG G + + G+ + + R+ + K SS+ G +
Sbjct: 54 GTHESKEGKNKKECFDKNG-GIYNLGDAIR-MGKDTSVKIKQRTCPFHKEGSSFEMGSKN 111
Query: 138 RGDSYGGRGK 147
Y GK
Sbjct: 112 ITCFYPIHGK 121
>gnl|CDD|237539 PRK13878, PRK13878, conjugal transfer relaxase TraI; Provisional.
Length = 746
Score = 28.9 bits (65), Expect = 5.3
Identities = 11/49 (22%), Positives = 17/49 (34%)
Query: 98 GNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRG 146
R R + RGR G + + ++ R+G G G R
Sbjct: 519 TERPEHRGRTGRGRGGPGQRPAADQHAAGAAAVARAGDGRPAAGRGDRA 567
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 28.6 bits (64), Expect = 5.7
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 101 SRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGR 145
S R+++PR +GG R +S R + R S+
Sbjct: 23 SDKRTHNPRTGKGGGRPSGKSRADGGRRPA-RDDRNSQSRDRKWE 66
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to reconstitute
splicing in depleted nuclear extracts. Its function is
enhanced through interaction with U2 auxiliary factor
U2AF65. PUF60 also controls human c-myc gene expression
by binding and inhibiting the transcription factor far
upstream sequence element (FUSE)-binding-protein (FBP),
an activator of c-myc promoters. PUF60 contains two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal U2AF (U2 auxiliary factor)
homology motifs (UHM) that harbors another RRM and binds
to tryptophan-containing linear peptide motifs (UHM
ligand motifs, ULMs) in several nuclear proteins. The
research indicates that PUF60 binds FUSE as a dimer, and
only the first two RRM domains participate in the
single-stranded DNA recognition. .
Length = 98
Score = 27.0 bits (60), Expect = 5.8
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 6/69 (8%)
Query: 191 TTEQQINHIFSKYGPVERVEVVIDAKTGRSRGF-----CFVYFESRDDAAAAKDACTGME 245
E ++ K+G V RV ++ K G FV F +A A A G
Sbjct: 18 DLEGEVTEECGKFGAVNRV-IIYQEKQGEEEDAEIIVKIFVEFSLPSEAEKAIQALNGRW 76
Query: 246 IDGRQIRVD 254
GR+++ +
Sbjct: 77 FGGRKVKAE 85
>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown].
Length = 334
Score = 28.7 bits (64), Expect = 5.8
Identities = 16/39 (41%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 110 GRRGGYRSRSRSPGYRKRSSSYR--SGGGSRGDSYGGRG 146
GR GG R+P R S SGGG G Y G G
Sbjct: 51 GRIGG--GSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGG 87
>gnl|CDD|216205 pfam00937, Corona_nucleoca, Coronavirus nucleocapsid protein.
Length = 346
Score = 28.5 bits (64), Expect = 5.9
Identities = 25/83 (30%), Positives = 30/83 (36%), Gaps = 17/83 (20%)
Query: 98 GNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSRGDSYGGRGKIIIAVVTEVE 157
G R RSRS S R RS SR P S G SR +S +V V
Sbjct: 151 GFRGRSRSSS----RSSSRSNSRGP----------SRGSSRNNSRNRNSSSPDDLVAAV- 195
Query: 158 EEAEATAMVEEFADGRENPQPSR 180
A A + + +PSR
Sbjct: 196 --LAALAKLGFGKQKSSSKKPSR 216
>gnl|CDD|215814 pfam00242, DNA_pol_viral_N, DNA polymerase (viral) N-terminal
domain.
Length = 379
Score = 28.2 bits (63), Expect = 7.2
Identities = 23/111 (20%), Positives = 31/111 (27%), Gaps = 11/111 (9%)
Query: 29 SHVSGRLLPKEP-AQTSSDQCYYRLSPARSGSAGSIDDKKYRKSITRSRSGSPHRRSKRP 87
H + EP SS + A + K S +RS+
Sbjct: 192 QHSHLQRHGDEPFGAQSSGILSRSENRRTRNLANNTSRKSDTSRSVGPVRQSQIQRSRLG 251
Query: 88 QVACGRDNGLGNRSRSRSYSPRGR-----RGGYRSR---SRSPGYRKRSSS 130
L + + RS S RGR R + S R SSS
Sbjct: 252 L--QANQGKLAHGQQGRSGSIRGRKHSTTRRPFGVEPSSSGVTTNRASSSS 300
>gnl|CDD|218425 pfam05091, eIF-3_zeta, Eukaryotic translation initiation factor 3
subunit 7 (eIF-3). This family is made up of eukaryotic
translation initiation factor 3 subunit 7 (eIF-3
zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is
a multi-subunit complex that is required for binding of
mRNA to 40 S ribosomal subunits, stabilisation of
ternary complex binding to 40 S subunits, and
dissociation of 40 and 60 S subunits. These functions
and the complex nature of eIF3 suggest multiple
interactions with many components of the translational
machinery. The gene coding for the protein has been
implicated in cancer in mammals.
Length = 517
Score = 28.4 bits (64), Expect = 7.4
Identities = 19/76 (25%), Positives = 29/76 (38%), Gaps = 12/76 (15%)
Query: 65 DKKYRKSITRSRSGSPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGY 124
D + R ++ G RR G+ R + P+G+RG R++ G
Sbjct: 81 DDRSRLKARTTKHGKRKRR--------GKQTRTQRRGQG----PQGKRGMTSRRAKRGGQ 128
Query: 125 RKRSSSYRSGGGSRGD 140
RK+ GG RG
Sbjct: 129 RKQKRFQTGRGGRRGA 144
>gnl|CDD|188044 TIGR00350, lytR_cpsA_psr, cell envelope-related function
transcriptional attenuator common domain. This model
describes a domain of unknown function that is found in
the predicted extracellular domain of a number of
putative membrane-bound proteins. One of these is
proteins psr, described as a penicillin binding protein
5 (PDP-5) synthesis repressor. Another is Bacillus
subtilis LytR, described as a transcriptional attenuator
of itself and the LytABC operon, where LytC is
N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a
putative regulatory protein involved in exocellular
polysaccharide biosynthesis. Besides the region of
strong similarily represented by This model, these
proteins share the property of having a short putative
N-terminal cytoplasmic domain and transmembrane domain
forming a signal-anchor [Regulatory functions, Other].
Length = 152
Score = 27.7 bits (62), Expect = 7.7
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 186 GLSIYTTEQQINHIFSKYGPVERVEVV 212
G +E +IN +S GP V+ V
Sbjct: 33 GCRTPNSETKINSAYSFGGPQCTVKTV 59
>gnl|CDD|217770 pfam03868, Ribosomal_L6e_N, Ribosomal protein L6, N-terminal
domain.
Length = 58
Score = 25.8 bits (57), Expect = 8.4
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 79 SPHRRSKRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKR 127
RS+ P +A G+G SRS Y RR Y+ +++ G + +
Sbjct: 6 KKKHRSRNPDLA----RGIGRYSRSAMYH---RRALYKRKAKKGGTKPK 47
>gnl|CDD|182958 PRK11096, ansB, L-asparaginase II; Provisional.
Length = 347
Score = 28.1 bits (63), Expect = 8.7
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 170 ADGRENPQPSRCLGVFGLSIYTTEQQINHIFSKY 203
A G NPQ +R L L+ QQI +F++Y
Sbjct: 314 ASGTLNPQKARVLLQLALTQTKDPQQIQQMFNQY 347
>gnl|CDD|215494 PLN02915, PLN02915, cellulose synthase A [UDP-forming], catalytic
subunit.
Length = 1044
Score = 28.4 bits (63), Expect = 9.0
Identities = 28/98 (28%), Positives = 42/98 (42%), Gaps = 15/98 (15%)
Query: 80 PHRRSKRPQVACGRDN---------GLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSS 130
P KRP++ C D G G R +S+ S +G++G RS G +KR
Sbjct: 581 PPVSEKRPKMTC--DCWPSWCCCCCGGGRRGKSKK-SKKGKKG---RRSLLGGLKKRKKK 634
Query: 131 YRSGGGSRGDSYGGRGKIIIAVVTEVEEEAEATAMVEE 168
GG G YG + + + E+EE E +E+
Sbjct: 635 GGGGGSMMGKKYGRKKSQAVFDLEEIEEGLEGYDELEK 672
>gnl|CDD|237695 PRK14376, PRK14376, hypothetical protein; Provisional.
Length = 176
Score = 27.6 bits (61), Expect = 9.0
Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 85 KRPQVACGRDNGLGNRSRSRSYSPRGRRGGYRSRSRSPGYRKRSSSYRSGGGSR 138
++P+ R G + R RR + S RS S G+R
Sbjct: 123 RKPRGRT-RTAGGPVGAVDAGTPHRSRRPTGGHGTASLHRGTRSEIVGSRRGTR 175
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
0.316 0.134 0.399
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,560,447
Number of extensions: 1970447
Number of successful extensions: 2680
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2394
Number of HSP's successfully gapped: 454
Length of query: 403
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 304
Effective length of database: 6,546,556
Effective search space: 1990153024
Effective search space used: 1990153024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (27.1 bits)