RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14193
(239 letters)
>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 = 100 bits (250), Expect = 3e-27
Identities = 42/89 (47%), Positives = 55/89 (61%), Gaps = 4/89 (4%)
Query: 40 NPSLTKSKNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNA 99
N LT K + +FK +G +E+VRFRSVPV + LP+K K H+K+ N+NA
Sbjct: 7 NLPLTTKK----KDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62
Query: 100 YVRFKNLESVEKALEMNGHVIDEHTIRVD 128
YV FK ES EKAL++NG + H IRVD
Sbjct: 63 YVVFKEEESAEKALKLNGTEFEGHHIRVD 91
Score = 40.3 bits (95), Expect = 7e-05
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 17/69 (24%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRL---------IRDQHTNIGKGF--------G 183
+F+GN+P ++++L+K F+ G I++VR + + I K F
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62
Query: 184 YVNFKAEEE 192
YV FK EE
Sbjct: 63 YVVFKEEES 71
>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 = 95.7 bits (239), Expect = 8e-26
Identities = 33/60 (55%), Positives = 47/60 (78%), Gaps = 1/60 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
S+F+GN+PF+ EEEELRK FE CG+++ VR++RD+ T IGKGFGYV FK ++ + A +
Sbjct: 1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFK-TKDSVALALK 59
Score = 78.0 bits (193), Expect = 4e-19
Identities = 28/45 (62%), Positives = 35/45 (77%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + F EEEELRK FE CG+++ VR++RD+ T IGKGFGYV FK
Sbjct: 5 GNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFK 49
Score = 35.2 bits (82), Expect = 0.003
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 90 VHEKRTNMN---AYVRFKNLESVEKALEMNGHVIDEHTIRV 127
V +++T + YV FK +SV AL++NG + IRV
Sbjct: 32 VRDRKTGIGKGFGYVLFKTKDSVALALKLNGIKLKGRKIRV 72
>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 = 71.8 bits (176), Expect = 1e-16
Identities = 27/51 (52%), Positives = 35/51 (68%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAE 190
+F+GN+ FE EE L + F CG I+ VR++RD TN+GKGF YV FK E
Sbjct: 1 CVFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDE 51
Score = 60.3 bits (146), Expect = 3e-12
Identities = 23/45 (51%), Positives = 30/45 (66%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + F+ EE L + F CG I+ VR++RD TN+GKGF YV FK
Sbjct: 5 GNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFK 49
Score = 31.0 bits (70), Expect = 0.10
Identities = 14/31 (45%), Positives = 21/31 (67%), Gaps = 3/31 (9%)
Query: 90 VHEKRTNMN---AYVRFKNLESVEKALEMNG 117
V + +TN+ AYV+FK+ +VEKAL +N
Sbjct: 32 VRDPKTNVGKGFAYVQFKDENAVEKALLLNE 62
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 67.2 bits (165), Expect = 6e-15
Identities = 30/72 (41%), Positives = 47/72 (65%), Gaps = 3/72 (4%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++F+GN+P + EEELR+ F G++++VRL+RD+ T KGF +V F+ EE+ KA E
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFE-SEEDAEKALE 59
Query: 200 SCG--EIDNVRL 209
+ E+D L
Sbjct: 60 ALNGKELDGRPL 71
Score = 49.9 bits (120), Expect = 1e-08
Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ EEELR+ F G++++VRL+RD+ T KGF +V F+
Sbjct: 7 LPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFE 49
Score = 43.4 bits (103), Expect = 4e-06
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 18/75 (24%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ +F +G+VE+VR + +K K A+V F++ E EKAL
Sbjct: 16 LRELFSKFGKVESVR----------------LVRDKETGKSKGF-AFVEFESEEDAEKAL 58
Query: 114 E-MNGHVIDEHTIRV 127
E +NG +D ++V
Sbjct: 59 EALNGKELDGRPLKV 73
>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 = 66.2 bits (162), Expect = 1e-14
Identities = 29/73 (39%), Positives = 44/73 (60%), Gaps = 5/73 (6%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+GN+ F+A+E+ + +AF GEI +VRL D + KGFGYV F + +E + A ++
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEF-SSQEAAQAALDA 59
Query: 201 CGEID----NVRL 209
G D VRL
Sbjct: 60 LGGTDLLGRPVRL 72
Score = 45.4 bits (108), Expect = 6e-07
Identities = 20/44 (45%), Positives = 28/44 (63%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F A+E+ + +AF GEI +VRL D + KGFGYV F
Sbjct: 4 GNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEF 47
Score = 30.8 bits (70), Expect = 0.11
Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 18/77 (23%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKA 112
S+ F YGE+ +VR T P K YV F + E+ + A
Sbjct: 14 SIYEAFGEYGEISSVRL-------PTDPDSGRPKGF----------GYVEFSSQEAAQAA 56
Query: 113 LEMNGH-VIDEHTIRVD 128
L+ G + +R+D
Sbjct: 57 LDALGGTDLLGRPVRLD 73
>gnl|CDD|241113 cd12669, RRM1_Nop12p_like, RNA recognition motif 1 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM1 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
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 = 105
Score = 65.1 bits (159), Expect = 9e-14
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEK-ALEMN 116
P+G++E++RFRS+ A LPRK +H +R ++NAY+ +K K A ++N
Sbjct: 29 LAPFGKIESIRFRSISFATDALPRKVAFIKKDLHSERDSVNAYIVYKTPALAAKAAKKLN 88
Query: 117 GHVIDEHTIRVD 128
G V +RVD
Sbjct: 89 GTVFLGRHLRVD 100
>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 = 62.7 bits (153), Expect = 3e-13
Identities = 27/64 (42%), Positives = 43/64 (67%), Gaps = 2/64 (3%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++F+GN+ + AE+++L + F+ CGE+ +VR+ +D KGFG+V F A EE +KA E
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEF-ATEEGAQKALE 58
Query: 200 SCGE 203
GE
Sbjct: 59 KSGE 62
Score = 43.8 bits (104), Expect = 3e-06
Identities = 16/40 (40%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ AE+++L + F+ CGE+ +VR+ +D KGFG+V F
Sbjct: 9 WSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEF 47
Score = 33.1 bits (76), Expect = 0.017
Identities = 22/79 (27%), Positives = 30/79 (37%), Gaps = 18/79 (22%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEK 111
+ FK GEV VR I + + R+ +V F E +K
Sbjct: 14 DDLEEFFKECGEVVDVR----------------IAQD--DDGRSKGFGHVEFATEEGAQK 55
Query: 112 ALEMNGHVIDEHTIRVDKA 130
ALE +G + IRVD A
Sbjct: 56 ALEKSGEELLGREIRVDLA 74
>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 = 60.4 bits (147), Expect = 2e-12
Identities = 22/53 (41%), Positives = 35/53 (66%), Gaps = 1/53 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++F+ N+ + E+ELRK F CGEI +VRL+++ + KG+ YV F+ EE
Sbjct: 1 TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEES 52
Score = 48.4 bits (116), Expect = 5e-08
Identities = 18/41 (43%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ E+ELRK F CGEI +VRL+++ + KG+ YV F+
Sbjct: 9 YSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFE 48
Score = 29.9 bits (68), Expect = 0.24
Identities = 12/37 (32%), Positives = 26/37 (70%)
Query: 85 IKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVID 121
+++ K ++ ++ AYV F+N ESV++AL+++ +I
Sbjct: 29 VRLVKNYKGKSKGYAYVEFENEESVQEALKLDRELIK 65
>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 = 65.3 bits (159), Expect = 2e-12
Identities = 39/114 (34%), Positives = 59/114 (51%), Gaps = 14/114 (12%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVD-------------KALTTTKSNSHSIFIGN 145
AYV F ++ESV KAL + G ++ I V N +++GN
Sbjct: 134 AYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGN 193
Query: 146 IPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+ F E+ELR+ FE G+I++V+L RD T KGFG++ F + EE ++A E
Sbjct: 194 LHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFH-DAEEAKEALE 246
Score = 46.8 bits (111), Expect = 4e-06
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 128 DKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ LT + + ++F+ + +A E +L + F G++ +V+ I+D+++ KG YV F
Sbjct: 79 KEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEF 138
Query: 188 KAEEEELRKAFESCGE 203
+ E + KA G+
Sbjct: 139 Y-DVESVIKALALTGQ 153
Score = 39.1 bits (91), Expect = 0.001
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 188 KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
KA E +L + F G++ +V+ I+D+++ KG YV F
Sbjct: 100 KARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFY 139
>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 = 60.3 bits (147), Expect = 3e-12
Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+F+GNIP++A EE+L + F G + + RL+ D+ T KG+G+ F+ E
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIE 51
Score = 44.9 bits (107), Expect = 9e-07
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
G + + A EE+L + F G + + RL+ D+ T KG+G+ F+ T S+I
Sbjct: 4 GNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57
>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 = 59.2 bits (144), Expect = 5e-12
Identities = 25/59 (42%), Positives = 39/59 (66%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+++GN+ F E++LR FE GEI+ V+L RD T KG+G++ F A+ E+ +KA E
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQF-ADAEDAKKALE 58
Score = 49.2 bits (118), Expect = 3e-08
Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++F E++LR FE GEI+ V+L RD T KG+G++ F
Sbjct: 4 GNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFA 48
Score = 26.8 bits (60), Expect = 2.8
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 24/64 (37%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVEKALE 114
F+P+GE+E + L R + T + +++F + E +KALE
Sbjct: 19 FEPFGEIE----------FVQLQR----------DPETGRSKGYGFIQFADAEDAKKALE 58
Query: 115 -MNG 117
+NG
Sbjct: 59 QLNG 62
>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 = 59.2 bits (144), Expect = 6e-12
Identities = 28/71 (39%), Positives = 45/71 (63%), Gaps = 4/71 (5%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+GN+P + EE+LR+ F GEI++VR++RD+ KGF +V F+ E+ KA E+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFE-SPEDAEKALEA 58
Query: 201 CG--EIDNVRL 209
E+D +L
Sbjct: 59 LNGKELDGRKL 69
Score = 42.3 bits (100), Expect = 7e-06
Identities = 17/37 (45%), Positives = 26/37 (70%), Gaps = 1/37 (2%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
EE+LR+ F GEI++VR++RD+ KGF +V F+
Sbjct: 12 EEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFE 47
Score = 39.2 bits (92), Expect = 1e-04
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 19/78 (24%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEK 111
+ +F +GE+E+VR + + + ++ A+V F++ E EK
Sbjct: 13 EDLRELFSKFGEIESVR------------------IVRDKDGKSKGFAFVEFESPEDAEK 54
Query: 112 ALE-MNGHVIDEHTIRVD 128
ALE +NG +D ++V
Sbjct: 55 ALEALNGKELDGRKLKVS 72
>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2
and similar proteins. This subfamily corresponds to the
RRM1 of yeast protein gar2, a novel nucleolar protein
required for 18S rRNA and 40S ribosomal subunit
accumulation. It shares similar domain architecture with
nucleolin from vertebrates and NSR1 from Saccharomyces
cerevisiae. The highly phosphorylated N-terminal domain
of gar2 is made up of highly acidic regions separated
from each other by basic sequences, and contains
multiple phosphorylation sites. The central domain of
gar2 contains two closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
C-terminal RGG (or GAR) domain of gar2 is rich in
glycine, arginine and phenylalanine residues. .
Length = 76
Score = 59.3 bits (144), Expect = 6e-12
Identities = 24/67 (35%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+GN+ + ++E L+ FE G + R+I D+ T +GFGYV+F E+ +KA E+
Sbjct: 2 LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDF-ESPEDAKKAIEA 60
Query: 201 CG--EID 205
E+D
Sbjct: 61 MDGKELD 67
Score = 44.7 bits (106), Expect = 1e-06
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G +++ ++E L+ FE G + R+I D+ T +GFGYV+F
Sbjct: 5 GNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDF 48
Score = 30.0 bits (68), Expect = 0.19
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 100 YVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
YV F++ E +KA+E M+G +D I VD +
Sbjct: 45 YVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76
>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 = 59.1 bits (144), Expect = 6e-12
Identities = 24/61 (39%), Positives = 41/61 (67%), Gaps = 2/61 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+GN+P + EE+L+ F G I+++R++RD+ T KGF +V F+ +EE+ KA E+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFE-DEEDAEKALEA 58
Query: 201 C 201
Sbjct: 59 L 59
Score = 40.7 bits (96), Expect = 3e-05
Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + EE+L+ F G I+++R++RD+ T KGF +V F+
Sbjct: 4 GNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFE 47
Score = 36.8 bits (86), Expect = 8e-04
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 19/71 (26%)
Query: 57 MFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-M 115
+F +G +E++R + + A+V F++ E EKALE +
Sbjct: 18 LFSKFGPIESIRI-----------------VRDETGRSKGF-AFVEFEDEEDAEKALEAL 59
Query: 116 NGHVIDEHTIR 126
NG + +R
Sbjct: 60 NGKELGGRELR 70
>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 = 58.8 bits (143), Expect = 9e-12
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+++GN+P+ EE+L+ F GE+ + R+I D+ T +GFG+V EE A E
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEM-ETAEEANAAIE 59
Score = 43.0 bits (102), Expect = 5e-06
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + + EE+L+ F GE+ + R+I D+ T +GFG+V +
Sbjct: 5 GNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEME 49
Score = 28.7 bits (65), Expect = 0.60
Identities = 15/78 (19%), Positives = 30/78 (38%), Gaps = 18/78 (23%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ +F +GEV + R + ++ R+ +V + E A+
Sbjct: 16 LKDLFGQFGEVTSAR----------------VITDRE-TGRSRGFGFVEMETAEEANAAI 58
Query: 114 E-MNGHVIDEHTIRVDKA 130
E +NG T+ V++A
Sbjct: 59 EKLNGTDFGGRTLTVNEA 76
>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 = 58.6 bits (142), Expect = 9e-12
Identities = 28/72 (38%), Positives = 45/72 (62%), Gaps = 2/72 (2%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+++IGN+ ++ E+++R+ F EI +VRL D+ T KGFG+V+F A+EE L A +
Sbjct: 1 TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDF-ADEESLDAALK 58
Query: 200 SCGEIDNVRLIR 211
G + R IR
Sbjct: 59 LDGTVLCGRPIR 70
Score = 39.3 bits (92), Expect = 1e-04
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + + E+++R+ F EI +VRL D+ T KGFG+V+F
Sbjct: 5 GNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFA 48
Score = 27.0 bits (60), Expect = 2.5
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 83 ACIKMNKV--HEKRTNMN----AYVRFKNLESVEKALEMNGHVIDEHTIRVD 128
++ V + +V F + ES++ AL+++G V+ IR+
Sbjct: 21 KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLDGTVLCGRPIRIA 72
>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 = 58.5 bits (142), Expect = 1e-11
Identities = 22/52 (42%), Positives = 32/52 (61%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+ N+P +A+E L + F G + NV++IRD TN KG+G+V EE
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEE 55
Score = 44.6 bits (106), Expect = 1e-06
Identities = 16/37 (43%), Positives = 23/37 (62%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVN 225
A+E L + F G + NV++IRD TN KG+G+V
Sbjct: 13 ADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVT 49
>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 = 56.2 bits (136), Expect = 8e-11
Identities = 28/66 (42%), Positives = 39/66 (59%), Gaps = 4/66 (6%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+ N+PF EEELR+ FE+ GEI V L D+ T KGF +V+F E + KA+
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAV-KAYS- 59
Query: 201 CGEIDN 206
E+D
Sbjct: 60 --ELDG 63
Score = 44.6 bits (106), Expect = 1e-06
Identities = 20/42 (47%), Positives = 25/42 (59%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
F EEELR+ FE+ GEI V L D+ T KGF +V+F
Sbjct: 9 FTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMF 50
>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 = 54.8 bits (132), Expect = 2e-10
Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
+F+GNIP+EA EE+L+ F G + + RL+ D+ T KG+G+ +K +E L
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETAL 54
Score = 39.8 bits (93), Expect = 7e-05
Identities = 18/54 (33%), Positives = 32/54 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
G + ++A EE+L+ F G + + RL+ D+ T KG+G+ +K T LS++
Sbjct: 4 GNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAM 57
>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 = 54.7 bits (132), Expect = 3e-10
Identities = 25/71 (35%), Positives = 39/71 (54%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
IF+G++ E + E LR AF GEI + R+++D T KG+G+V+F +E+
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 201 CGEIDNVRLIR 211
G+ R IR
Sbjct: 62 NGQWLGGRAIR 72
Score = 45.8 bits (109), Expect = 4e-07
Identities = 16/37 (43%), Positives = 24/37 (64%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ E LR AF GEI + R+++D T KG+G+V+F
Sbjct: 12 DTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSF 48
>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 = 54.9 bits (133), Expect = 3e-10
Identities = 21/74 (28%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+ + ++ E +LR+ FE G I +RL+RD+ T +G+ ++ F+ E +++ A++
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFE-HERDMKAAYKY 62
Query: 201 CG--EIDNVRLIRD 212
+ID R++ D
Sbjct: 63 ADGKKIDGRRVLVD 76
Score = 43.8 bits (104), Expect = 4e-06
Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+N+ E +LR+ FE G I +RL+RD+ T +G+ ++ F+
Sbjct: 7 ARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFE 51
>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 = 54.5 bits (132), Expect = 4e-10
Identities = 14/58 (24%), Positives = 30/58 (51%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
+F+G + E +L + F G + +V +I+ + +GF Y++ + E +L+K
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCK 59
Score = 37.2 bits (87), Expect = 7e-04
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVS---FTTLSSIFSK 239
E +L + F G + +V +I+ + +GF Y++ + S S +
Sbjct: 13 ESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKSTLNG 64
>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 = 54.2 bits (131), Expect = 4e-10
Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
SIF+GN+ + EEL++ F+SCG I+ + ++ D+ T KGF Y+ F ++ + A
Sbjct: 1 SIFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEF-LDKSSVENA 57
Score = 42.3 bits (100), Expect = 8e-06
Identities = 17/44 (38%), Positives = 28/44 (63%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G V++ EEL++ F+SCG I+ + ++ D+ T KGF Y+ F
Sbjct: 5 GNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEF 48
Score = 33.8 bits (78), Expect = 0.009
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRV 127
AY+ F + SVE AL +N I+V
Sbjct: 44 AYIEFLDKSSVENALLLNESEFRGRQIKV 72
>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 = 54.0 bits (130), Expect = 5e-10
Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+GN+ FE E+ELR F G I VR++ + + KGF +V+F+ E E A +
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFE-EIEFATNALK- 58
Query: 201 CGEIDNVRLIRDQ 213
G+ N R +R +
Sbjct: 59 -GKHLNGRALRVE 70
Score = 39.4 bits (92), Expect = 1e-04
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++F+ E+ELR F G I VR++ + + KGF +V+F+
Sbjct: 4 GNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFE 48
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 53.3 bits (129), Expect = 8e-10
Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+++ N+P EE+LR+ F G+++ VRL+R + + +GF +V F A E+ A +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVR--NKDRPRGFAFVEF-ASPEDAEAALKK 57
Query: 201 CGEI 204
+
Sbjct: 58 LNGL 61
Score = 38.3 bits (90), Expect = 2e-04
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ EE+LR+ F G+++ VRL+R + + +GF +V F
Sbjct: 6 LPPSVTEEDLREFFSPYGKVEGVRLVR--NKDRPRGFAFVEFA 46
Score = 35.2 bits (82), Expect = 0.003
Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 20/74 (27%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL 113
+ F PYG+VE VR ++ R A+V F + E E AL
Sbjct: 15 LREFFSPYGKVEGVRLVR-------------------NKDRPRGFAFVEFASPEDAEAAL 55
Query: 114 EM-NGHVIDEHTIR 126
+ NG V+D T+R
Sbjct: 56 KKLNGLVLDGRTLR 69
>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 = 52.2 bits (126), Expect = 2e-09
Identities = 22/51 (43%), Positives = 31/51 (60%)
Query: 142 FIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
F+G +P A EE++R FE G I+ V +IRD+ T KG +V F + EE
Sbjct: 3 FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREE 53
Score = 40.6 bits (96), Expect = 4e-05
Identities = 18/45 (40%), Positives = 25/45 (55%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + A EE++R FE G I+ V +IRD+ T KG +V F
Sbjct: 5 GQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFS 49
>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 = 51.1 bits (123), Expect = 6e-09
Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++FI N+PF+A EEEL++ F GE+ R+++D+ T KG +V FK +E
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKES 54
Score = 35.6 bits (83), Expect = 0.003
Identities = 17/43 (39%), Positives = 26/43 (60%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ F A EEEL++ F GE+ R+++D+ T KG +V FK
Sbjct: 8 LPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFK 50
>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 = 50.5 bits (121), Expect = 9e-09
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+++G+I FE E+ +R+AF G I ++ + D T KGF +V ++ E
Sbjct: 3 VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPE 53
Score = 41.3 bits (97), Expect = 2e-05
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
G ++F+ E+ +R+AF G I ++ + D T KGF +V ++V
Sbjct: 6 GSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEV 51
>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 = 50.5 bits (121), Expect = 9e-09
Identities = 23/57 (40%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 146 IPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF-KAEEEELRKAFESC 201
IP EE+LR+ F+ G+I+ V +++D++T KGFGYV F K + A E+C
Sbjct: 8 IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAA--VALENC 62
Score = 44.7 bits (106), Expect = 1e-06
Identities = 19/47 (40%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF-KVSFTTLS 234
EE+LR+ F+ G+I+ V +++D++T KGFGYV F K S ++
Sbjct: 12 YTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVA 58
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++++G++ +E + AF CGE+ +V++IR++ T G+G+V F A E +A +
Sbjct: 1 TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEF-ATHEAAEQALQ 59
Query: 200 S 200
S
Sbjct: 60 S 60
Score = 42.2 bits (100), Expect = 1e-05
Identities = 14/36 (38%), Positives = 23/36 (63%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E + AF CGE+ +V++IR++ T G+G+V F
Sbjct: 13 EAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEF 48
>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 = 50.3 bits (121), Expect = 1e-08
Identities = 16/52 (30%), Positives = 29/52 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+F+ + E+EL F G ++ V L++D T +GFG+V F++ E+
Sbjct: 4 LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVED 55
Score = 41.8 bits (99), Expect = 1e-05
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++ + E+EL F G ++ V L++D T +GFG+V F
Sbjct: 9 LSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTF 50
Score = 27.6 bits (62), Expect = 1.6
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 18/74 (24%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKAL-EMN 116
F +G VE V + + + +V F+++E + A+ ++N
Sbjct: 22 FSKFGRVEEVL----------------LMKDP-ETGESRGFGFVTFESVEDADAAIRDLN 64
Query: 117 GHVIDEHTIRVDKA 130
G ++ I+V+KA
Sbjct: 65 GKELEGRVIKVEKA 78
>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 = 2e-08
Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++F+ + + E +L + F G++ +VR+IRD+++ KG YV F EE
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEE 52
Score = 44.5 bits (106), Expect = 1e-06
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 188 KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
K E +L + F G++ +VR+IRD+++ KG YV F
Sbjct: 10 KVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFY 49
Score = 29.9 bits (68), Expect = 0.22
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 99 AYVRFKNLESVEKALEMNG 117
AYV F + ESV AL + G
Sbjct: 44 AYVEFYDEESVPLALGLTG 62
>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 = 49.6 bits (119), Expect = 2e-08
Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 142 FIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESC 201
F+GN+PF + +L F+ + +VRL+RD+ T+ KGF YV F + E L++A E
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEF-EDVESLKEALEYD 62
Query: 202 GEIDNVRLIR 211
G + + R +R
Sbjct: 63 GALFDDRSLR 72
Score = 36.5 bits (85), Expect = 0.001
Identities = 14/32 (43%), Positives = 25/32 (78%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
YV F+++ES+++ALE +G + D+ ++RVD A
Sbjct: 45 CYVEFEDVESLKEALEYDGALFDDRSLRVDIA 76
Score = 32.7 bits (75), Expect = 0.022
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 203 EIDNVRLIRDQHTNIGKGFGYVNF 226
+ +VRL+RD+ T+ KGF YV F
Sbjct: 26 SVKSVRLVRDKETDKFKGFCYVEF 49
>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 = 48.9 bits (117), Expect = 4e-08
Identities = 16/46 (34%), Positives = 30/46 (65%)
Query: 146 IPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+P + +EELR FE+ G I++ +++RD+ T G+G+V++ E
Sbjct: 8 LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDEN 53
Score = 45.8 bits (109), Expect = 4e-07
Identities = 14/36 (38%), Positives = 26/36 (72%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+EELR FE+ G I++ +++RD+ T G+G+V++
Sbjct: 14 QEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDY 49
>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 = 49.9 bits (119), Expect = 4e-08
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++F+ N+P++A EE L F G + + D+ T KG G+V FK +
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYT 55
Score = 36.1 bits (83), Expect = 0.003
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFT 231
+ + A EE L F G + + D+ T KG G+V FK +T
Sbjct: 9 LPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYT 55
>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 = 49.2 bits (118), Expect = 4e-08
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
++F+G + + EE LR+ F G+I +RL+RD T KG+ +V ++ E + +A+
Sbjct: 4 LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYE-HERDALRAY 62
Query: 199 ESCGE--IDNVRLIRD 212
+ ID + D
Sbjct: 63 RDAHKLVIDGSEIFVD 78
Score = 37.6 bits (88), Expect = 5e-04
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++ + EE LR+ F G+I +RL+RD T KG+ +V ++
Sbjct: 9 GRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYE 53
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 52.3 bits (124), Expect = 5e-08
Identities = 29/114 (25%), Positives = 55/114 (48%), Gaps = 6/114 (5%)
Query: 82 KACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTTKSNSHSI 141
K + + E M + + E E + K+ +K ++++
Sbjct: 65 KRLLSSERKEENEREMEEQNDGERGYTKEFEEE------LFRSSESPKSRQKSKEENNTL 118
Query: 142 FIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
F+GN+P++ EE+LR+ F+ G + VRL+RD+ T +GF +V F++EE +
Sbjct: 119 FVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEK 172
Score = 36.5 bits (83), Expect = 0.009
Identities = 41/189 (21%), Positives = 68/189 (35%), Gaps = 32/189 (16%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEK 111
+ +FK +G V+ VR + ++ K A+V F++ ES EK
Sbjct: 130 EDLRELFKKFGPVKRVR----------------LVRDRETGKSRGF-AFVEFESEESAEK 172
Query: 112 ALE-MNGHVIDEHTIRVDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRL 170
A+E +NG ++ +RV KA ++ S + F + +
Sbjct: 173 AIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKA------------- 219
Query: 171 IRDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSF 230
+ G + K EEEL F+S G+I L + I K +V + S
Sbjct: 220 -LLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASK 278
Query: 231 TTLSSIFSK 239
L S
Sbjct: 279 DALESNSRG 287
Score = 36.1 bits (82), Expect = 0.010
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ EE+LR+ F+ G + VRL+RD+ T +GF +V F+
Sbjct: 124 PYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFE 165
>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 = 48.5 bits (116), Expect = 5e-08
Identities = 24/61 (39%), Positives = 40/61 (65%), Gaps = 2/61 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQ-HTNIGKGFGYVNFKAEEEELRKAFE 199
I + NIPFEA +ELR+ F + GE+ VRL + T +GFG+V+F +++ ++AF+
Sbjct: 3 ILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDA-KRAFK 61
Query: 200 S 200
+
Sbjct: 62 A 62
Score = 32.4 bits (74), Expect = 0.032
Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQ-HTNIGKGFGYVNFK 227
F+A +ELR+ F + GE+ VRL + T +GFG+V+F
Sbjct: 10 FEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFI 51
>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 = 48.4 bits (116), Expect = 6e-08
Identities = 21/52 (40%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+G IP + EEELR F G + +V++I D + KG+G+V F+ +E+
Sbjct: 5 IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQED 55
Score = 35.7 bits (83), Expect = 0.002
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G + EEELR F G + +V++I D + KG+G+V F
Sbjct: 8 GGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTF 50
>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 = 48.4 bits (116), Expect = 6e-08
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE------EEL 194
IF+G +P+ ++ LRK F GEI+ +I D+ T +G+G+V FK +E ++
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62
Query: 195 RKAFESCGEIDNVRL 209
+ G NV L
Sbjct: 63 NPIID--GRKANVNL 75
Score = 31.4 bits (72), Expect = 0.072
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ LRK F GEI+ +I D+ T +G+G+V FK
Sbjct: 15 DSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFK 50
>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 = 48.4 bits (116), Expect = 7e-08
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 185
+S I+IG +P+E E ++ F GEI ++ L+RD+ T KGF ++
Sbjct: 7 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFL 56
Score = 34.5 bits (80), Expect = 0.006
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 224
G + ++ E ++ F GEI ++ L+RD+ T KGF ++
Sbjct: 14 IGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFL 56
>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 = 52.1 bits (125), Expect = 8e-08
Identities = 33/132 (25%), Positives = 56/132 (42%), Gaps = 29/132 (21%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNSHS----------------- 140
A+V F+ E KA+E MNG I + K L ++ +
Sbjct: 222 AFVNFEKHEDAAKAVEEMNGKKIGL--AKEGKKLYVGRAQKRAEREAELRRKFEELQQER 279
Query: 141 --------IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++ N+ +E+LR+ F CGEI + +++ D+ + +GFG+V F EE
Sbjct: 280 KMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEE 338
Query: 193 ELRKAFESCGEI 204
R E G +
Sbjct: 339 ANRAVTEMHGRM 350
Score = 51.7 bits (124), Expect = 9e-08
Identities = 27/109 (24%), Positives = 57/109 (52%), Gaps = 11/109 (10%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRV-------DKALTTTKSNSHSIFIGNIPFEA 150
+V F+ ES + A++ +NG ++++ + V ++ K ++++ N+
Sbjct: 132 GFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLK-KFTNLYVKNLDPSV 190
Query: 151 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
E++LR+ F GEI + +++D + +GF +VNF + E+ KA E
Sbjct: 191 NEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNF-EKHEDAAKAVE 237
Score = 48.6 bits (116), Expect = 1e-06
Identities = 48/225 (21%), Positives = 83/225 (36%), Gaps = 75/225 (33%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-MN 116
FKP+G V +VR C +R+ YV F+N E+ALE MN
Sbjct: 21 FKPFGPVLSVR--------------VCRDSVT---RRSLGYGYVNFQNPADAERALETMN 63
Query: 117 GHVIDEHTIRV---DKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRD 173
+ IR+ + + +S +IF+ N+ + + L F G I + ++ D
Sbjct: 64 FKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD 123
Query: 174 QHTNIGKGFGYVNFKAEE------------------------------------------ 191
+ +G+G+V+F+ EE
Sbjct: 124 E-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLY 182
Query: 192 ----------EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++LR+ F GEI + +++D + +GF +VNF
Sbjct: 183 VKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNF 226
Score = 38.6 bits (90), Expect = 0.002
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
S+++G++ + E +L F+ G + +VR+ RD T G+GYVNF+ + +A E
Sbjct: 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQ-NPADAERALE 60
Query: 200 SCGEIDNVRLIRDQHTNI 217
+ N + + + I
Sbjct: 61 TM----NFKRLGGKPIRI 74
Score = 33.6 bits (77), Expect = 0.077
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E +L F+ G + +VR+ RD T G+GYVNF
Sbjct: 14 EAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNF 49
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 49.7 bits (118), Expect = 8e-08
Identities = 27/85 (31%), Positives = 43/85 (50%)
Query: 127 VDKALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVN 186
V L + + S +FIG + + ++ LR AF G++ + ++I D+ T +GFG+VN
Sbjct: 23 VTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVN 82
Query: 187 FKAEEEELRKAFESCGEIDNVRLIR 211
F E E G+ N R IR
Sbjct: 83 FNDEGAATAAISEMDGKELNGRHIR 107
Score = 40.0 bits (93), Expect = 2e-04
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G +++ ++ LR AF G++ + ++I D+ T +GFG+VNF
Sbjct: 40 GGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNF 83
>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 = 47.8 bits (114), Expect = 1e-07
Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+ N+P+ +E++L K F GE+ V + D+ + KGF YV F E+ ++ E
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 201 CGEIDNVRLI 210
G++ RLI
Sbjct: 65 DGKVFQGRLI 74
Score = 37.8 bits (88), Expect = 4e-04
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+ +E++L K F GE+ V + D+ + KGF YV F
Sbjct: 12 YSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFL 52
>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 = 47.9 bits (114), Expect = 1e-07
Identities = 21/74 (28%), Positives = 38/74 (51%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+FIG + F+ E+ L + F G+I V +++D+ T +GFG+V F+ ++
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 201 CGEIDNVRLIRDQH 214
G+ + R IR
Sbjct: 63 NGKSVDGRQIRVDQ 76
Score = 41.8 bits (98), Expect = 2e-05
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 179 GKGF-GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
GK F G ++F E+ L + F G+I V +++D+ T +GFG+V F
Sbjct: 1 GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 49
Score = 30.2 bits (68), Expect = 0.23
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 93 KRTNMNAYVRFKNLESVEKALE-MNGHVIDEHTIRVDKA 130
+R+ +V F+N + + A+ MNG +D IRVD+A
Sbjct: 39 QRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQA 77
>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 = 47.5 bits (113), Expect = 1e-07
Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S+++GN+ + A EEL F CG ++ V ++ D+ + KGF Y+ F +++E +R A
Sbjct: 1 SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF-SDKESVRTA 57
Score = 39.4 bits (92), Expect = 9e-05
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G V++ A EEL F CG ++ V ++ D+ + KGF Y+ F
Sbjct: 5 GNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 48
>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 = 47.3 bits (113), Expect = 1e-07
Identities = 15/50 (30%), Positives = 30/50 (60%)
Query: 143 IGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ N+ + ++LR+ FE GE+ +V + RD++T +GF +V F + +
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRD 52
Score = 42.3 bits (100), Expect = 9e-06
Identities = 14/42 (33%), Positives = 27/42 (64%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ ++ ++LR+ FE GE+ +V + RD++T +GF +V F
Sbjct: 6 LTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRF 47
>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33)
and similar proteins. This subfamily corresponds to the
RRM of Cyp33, also termed peptidyl-prolyl cis-trans
isomerase E (PPIase E), or cyclophilin E, or rotamase E.
Cyp33 is a nuclear RNA-binding cyclophilin with an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal PPIase domain. Cyp33 possesses
RNA-binding activity and preferentially binds to
polyribonucleotide polyA and polyU, but hardly to polyG
and polyC. It binds specifically to mRNA, which can
stimulate its PPIase activity. Moreover, Cyp33 interacts
with the third plant homeodomain (PHD3) zinc finger
cassette of the mixed lineage leukemia (MLL)
proto-oncoprotein and a poly-A RNA sequence through its
RRM domain. It further mediates downregulation of the
expression of MLL target genes HOXC8, HOXA9, CDKN1B, and
C-MYC, in a proline isomerase-dependent manner. Cyp33
also possesses a PPIase activity that catalyzes
cis-trans isomerization of the peptide bond preceding a
proline, which has been implicated in the stimulation of
folding and conformational changes in folded and
unfolded proteins. The PPIase activity can be inhibited
by the immunosuppressive drug cyclosporin A. .
Length = 73
Score = 46.8 bits (112), Expect = 2e-07
Identities = 15/52 (28%), Positives = 30/52 (57%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++G + E +E+ L AF G+I ++++ D T +GF +V F+ E+
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPED 52
Score = 33.3 bits (77), Expect = 0.011
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E+ L AF G+I ++++ D T +GF +V F
Sbjct: 10 VDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEF 47
>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 = 47.0 bits (112), Expect = 2e-07
Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + +E ++ L+ F GEI + +++D +T +GFG+V F + E
Sbjct: 2 LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASE 53
Score = 40.4 bits (95), Expect = 5e-05
Identities = 13/48 (27%), Positives = 28/48 (58%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSF 230
G ++++ ++ L+ F GEI + +++D +T +GFG+V F +
Sbjct: 5 GGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASAS 52
>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 = 46.8 bits (112), Expect = 2e-07
Identities = 17/52 (32%), Positives = 29/52 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + ++ EE LR+ F GE+ + +++D T +GFG+V F
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSS 52
Score = 36.4 bits (85), Expect = 0.001
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
EE LR+ F GE+ + +++D T +GFG+V F
Sbjct: 12 EESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFA 48
Score = 29.9 bits (68), Expect = 0.22
Identities = 19/73 (26%), Positives = 26/73 (35%), Gaps = 17/73 (23%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKA 112
S+ F YGEV C+ M R+ +V F + SV+K
Sbjct: 14 SLREYFSKYGEVVD-----------------CVIMKDPITGRSRGFGFVTFADPSSVDKV 56
Query: 113 LEMNGHVIDEHTI 125
L HV+D I
Sbjct: 57 LAAKPHVLDGREI 69
>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 = 46.8 bits (111), Expect = 2e-07
Identities = 19/55 (34%), Positives = 33/55 (60%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
++++ N+P + E+ELRK FE+ G I L+RD+ T + +G +V + EE
Sbjct: 2 NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQ 56
Score = 37.2 bits (86), Expect = 7e-04
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+ELRK FE+ G I L+RD+ T + +G +V +
Sbjct: 14 EDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRY 49
>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 = 46.5 bits (111), Expect = 2e-07
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 6/53 (11%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++++GN+P EEEL++ F G I+ VR+ +D KG+ +V F E
Sbjct: 2 TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEA 48
Score = 33.7 bits (78), Expect = 0.009
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 6/36 (16%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EEEL++ F G I+ VR+ +D KG+ +V F
Sbjct: 14 EEELQRTFSPFGAIEEVRVFKD------KGYAFVRF 43
>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 = 46.8 bits (112), Expect = 2e-07
Identities = 18/53 (33%), Positives = 31/53 (58%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+I + N+ +A+E++LR+ F G I V L +D+ T +GF +V F E+
Sbjct: 1 TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTRED 53
Score = 39.4 bits (93), Expect = 8e-05
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
A+E++LR+ F G I V L +D+ T +GF +V F
Sbjct: 11 ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFH 49
Score = 27.1 bits (61), Expect = 2.5
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 8/47 (17%)
Query: 86 KMNKVH---EKRTNMN---AYVRFKNLESVEKALE-MNGHVIDEHTI 125
+++V+ +K T + A+V F E E+A+E +NG D + I
Sbjct: 25 PISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYD-NLI 70
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 150 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
E++LR+AF GEI ++ +++D+ T KG YV F
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKF 51
Score = 46.9 bits (112), Expect = 2e-07
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E++LR+AF GEI ++ +++D+ T KG YV F
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKF 51
Score = 32.7 bits (75), Expect = 0.027
Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 26/88 (29%)
Query: 46 SKNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVR 102
K+ + F P+GE++ + V +K+T + AYV+
Sbjct: 11 GKSVTEDDLREAFAPFGEIQDIWV--------------------VKDKQTKESKGVAYVK 50
Query: 103 FKNLESVEKALE-MNGHVIDEHT--IRV 127
F S +A+E MNG + T ++V
Sbjct: 51 FAKASSAARAMEEMNGKCLGGDTKPLKV 78
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 46.1 bits (110), Expect = 4e-07
Identities = 14/55 (25%), Positives = 30/55 (54%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ +GN+P E +E+ R+ G ++ L+ + T KG+G+V + ++ L+
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALK 56
Score = 30.7 bits (70), Expect = 0.11
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E+ R+ G ++ L+ + T KG+G+V +
Sbjct: 12 TDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEY 48
>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 = 46.2 bits (110), Expect = 4e-07
Identities = 19/55 (34%), Positives = 35/55 (63%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+F+G IP EE++LR FE G+I + +++D++T + KG ++ + A E L+
Sbjct: 8 LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALK 62
Score = 35.1 bits (81), Expect = 0.004
Identities = 12/37 (32%), Positives = 25/37 (67%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EE++LR FE G+I + +++D++T + KG ++ +
Sbjct: 18 EEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 54
>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 = 45.9 bits (109), Expect = 4e-07
Identities = 17/51 (33%), Positives = 34/51 (66%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
IF+G + E++++K F G++++ L+ D+ TN +GFG+V F++E+
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESED 52
Score = 37.8 bits (88), Expect = 4e-04
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E++++K F G++++ L+ D+ TN +GFG+V F
Sbjct: 13 EDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48
>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 = 45.8 bits (109), Expect = 4e-07
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+F+GN+P++ E+L F++ G +VRL+ D+ T KG +V F
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFD 50
Score = 34.6 bits (80), Expect = 0.005
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G + + E+L F++ G +VRL+ D+ T KG +V F
Sbjct: 6 GNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFD 50
>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 = 45.6 bits (109), Expect = 5e-07
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++IG++P E ELRK F G + +RL R + T KG+ +V F++ E
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE 52
Score = 36.4 bits (85), Expect = 0.001
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 176 TNIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
++ GF E ELRK F G + +RL R + T KG+ +V F+
Sbjct: 5 GHLPHGFY-------EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFE 49
>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 = 45.8 bits (109), Expect = 6e-07
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+ IF+G +P E +LRK F G + V ++ D +GFG++ F++E+
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESED 55
Score = 32.3 bits (74), Expect = 0.038
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E +LRK F G + V ++ D +GFG++ F
Sbjct: 16 ETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITF 51
>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 = 45.9 bits (108), Expect = 6e-07
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + FE ++ LR+ FE G + + ++RD T +GFG+V + EE
Sbjct: 5 LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEE 56
Score = 35.5 bits (81), Expect = 0.003
Identities = 14/44 (31%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ ++ LR+ FE G + + ++RD T +GFG+V +
Sbjct: 8 GGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTY 51
>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 = 45.8 bits (108), Expect = 6e-07
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + FE +E LR FE G + + ++RD +T +GFG+V + + EE
Sbjct: 5 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEE 56
Score = 35.8 bits (82), Expect = 0.002
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ +E LR FE G + + ++RD +T +GFG+V +
Sbjct: 8 GGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 51
>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 = 45.7 bits (109), Expect = 6e-07
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 5/75 (6%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGK---GFGYVNFKAEEEELR 195
I++ N+ F+ +E++LR F GE++++R+ + Q G+ GF +V FK +
Sbjct: 1 REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFK-DASSAE 59
Query: 196 KAFESCG-EIDNVRL 209
A + G E+ ++
Sbjct: 60 NALQLNGTELGGRKI 74
Score = 42.2 bits (100), Expect = 9e-06
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 14/72 (19%)
Query: 56 SMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEM 115
+F +GEVE I +P+K K +++ N A+V FK+ S E AL++
Sbjct: 19 GIFSKFGEVE----------SIRIPKKQDEKQGRLN----NGFAFVTFKDASSAENALQL 64
Query: 116 NGHVIDEHTIRV 127
NG + I V
Sbjct: 65 NGTELGGRKISV 76
Score = 37.6 bits (88), Expect = 5e-04
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 3/45 (6%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGK---GFGYVNFK 227
+FK +E++LR F GE++++R+ + Q G+ GF +V FK
Sbjct: 9 DFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFK 53
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 45.3 bits (108), Expect = 7e-07
Identities = 20/60 (33%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+ + N+PFEA ++ELR+ F G++ +VRL + + +GF +V F ++E + A E+
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEF-VTKQEAQNAMEA 60
Score = 31.4 bits (72), Expect = 0.060
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
V F+A ++ELR+ F G++ +VRL + + +GF +V F
Sbjct: 8 VPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEF 48
>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 = 45.4 bits (107), Expect = 7e-07
Identities = 21/60 (35%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+G + + EE++++ F + GEI+N+ L D TN +GF +V + +EE ++K ES
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTY-TDEEPVQKLLES 60
Score = 33.8 bits (77), Expect = 0.009
Identities = 14/36 (38%), Positives = 24/36 (66%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EE++++ F + GEI+N+ L D TN +GF +V +
Sbjct: 13 EEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTY 48
>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 = 45.5 bits (108), Expect = 8e-07
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S +FI N+ + EE+L K F G + V L D+ T KGF +V + E + KA
Sbjct: 2 SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAV-KA 60
Query: 198 F 198
F
Sbjct: 61 F 61
Score = 34.3 bits (79), Expect = 0.006
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+ EE+L K F G + V L D+ T KGF +V +
Sbjct: 12 YTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
>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 = 45.2 bits (108), Expect = 8e-07
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCG--EIDNVRLIRDQHTNIGKGFGYVNF 187
++++ + + EE++ +A + I +VRLIRD+ T +GF +V F
Sbjct: 2 TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEF 53
Score = 41.4 bits (98), Expect = 2e-05
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 191 EEELRKAFESCG--EIDNVRLIRDQHTNIGKGFGYVNF 226
EE++ +A + I +VRLIRD+ T +GF +V F
Sbjct: 16 EEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEF 53
>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 = 45.1 bits (107), Expect = 9e-07
Identities = 16/51 (31%), Positives = 32/51 (62%)
Query: 145 NIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+P++ E++L+ F + GE+ V++ +D T KGFG+V F E++++
Sbjct: 6 GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVK 56
Score = 40.8 bits (96), Expect = 3e-05
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+K E++L+ F + GE+ V++ +D T KGFG+V F
Sbjct: 9 WKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFA 49
>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 = 45.1 bits (107), Expect = 1e-06
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 6/50 (12%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
S +++IGN+P EEELR+ E G ID ++++++ K +V+F
Sbjct: 3 SRNVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE------KNIAFVHF 46
Score = 31.6 bits (72), Expect = 0.059
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EEELR+ E G ID ++++++ K +V+F
Sbjct: 15 YSEEELREDLEKFGPIDQIKIVKE------KNIAFVHF 46
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 20/61 (32%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++F+ N+P++ +E+L + F G I +++D+ + +GFGYV F A EE+ ++A E
Sbjct: 1 TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTF-ALEEDAKRALE 59
Query: 200 S 200
Sbjct: 60 E 60
Score = 31.0 bits (71), Expect = 0.093
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
+ +E+L + F G I +++D+ + +GFGYV F +
Sbjct: 9 YDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFAL 50
>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 = 45.1 bits (107), Expect = 1e-06
Identities = 17/44 (38%), Positives = 29/44 (65%)
Query: 152 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
++E+R F S GEI++ +LIRD+ T G+G+VN+ E+ +
Sbjct: 15 QDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEK 58
Score = 43.2 bits (102), Expect = 5e-06
Identities = 16/36 (44%), Positives = 26/36 (72%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++E+R F S GEI++ +LIRD+ T G+G+VN+
Sbjct: 15 QDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNY 50
>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 = 44.8 bits (106), Expect = 1e-06
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
I+IG++P E+EL+K F G + NVR+ R + T K +G++ F E
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPE 52
Score = 37.5 bits (87), Expect = 5e-04
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+EL+K F G + NVR+ R + T K +G++ F
Sbjct: 12 LEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQF 48
>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 = 1e-06
Identities = 24/59 (40%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
IF+G + EA EE++R+ F GEI+ + L D TN +GF ++ FK EE+ ++K E
Sbjct: 7 IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFK-EEDPVKKVLE 64
Score = 35.0 bits (80), Expect = 0.004
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G +N +A EE++R+ F GEI+ + L D TN +GF ++ FK
Sbjct: 10 GGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFK 54
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 44.9 bits (107), Expect = 1e-06
Identities = 15/52 (28%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++ N+ + ++E+L++ F G+I + ++++D KGFG+VNF+ E
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGK-SKGFGFVNFENHEA 54
Score = 38.3 bits (90), Expect = 3e-04
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 4/47 (8%)
Query: 184 YV-NFKAE--EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
YV N + +E+L++ F G+I + ++++D KGFG+VNF+
Sbjct: 5 YVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGK-SKGFGFVNFE 50
>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 = 44.7 bits (106), Expect = 1e-06
Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+++G IP+ + E+E+R F CGEI+ + L+ T +G ++ FK EE R A
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKR-ALAL 59
Query: 201 CGEIDNVRLIRDQ 213
GE R ++ +
Sbjct: 60 DGEDMGGRFLKVE 72
Score = 30.0 bits (68), Expect = 0.18
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
G + + + E+E+R F CGEI+ + L+ T +G ++ FK
Sbjct: 4 GGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKT 49
>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 = 44.3 bits (104), Expect = 2e-06
Identities = 19/52 (36%), Positives = 30/52 (57%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FIG + FE EE LR +E G++ + ++RD + +GFG+V F E
Sbjct: 5 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNE 56
Score = 35.9 bits (82), Expect = 0.002
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++F+ EE LR +E G++ + ++RD + +GFG+V F
Sbjct: 8 GGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the RRM
of SLIRP, a widely expressed small steroid receptor RNA
activator (SRA) binding protein, which binds to STR7, a
functional substructure of SRA. SLIRP is localized
predominantly to the mitochondria and plays a key role
in modulating several nuclear receptor (NR) pathways. It
functions as a co-repressor to repress SRA-mediated
nuclear receptor coactivation. It modulates SHARP- and
SKIP-mediated co-regulation of NR activity. SLIRP
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is required for SLIRP's corepression activities. .
Length = 73
Score = 43.8 bits (104), Expect = 2e-06
Identities = 17/57 (29%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+F+GN+P+ +EL++ F G++ + + D+ T + KG+G+V+F + + L A
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSF-SSRDGLENA 57
Score = 29.6 bits (67), Expect = 0.32
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 193 ELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EL++ F G++ + + D+ T + KG+G+V+F
Sbjct: 15 ELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSF 48
>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 = 43.9 bits (104), Expect = 2e-06
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 153 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
L + F SCGEI V + D+ T KGF Y+ FK + + KA E
Sbjct: 18 RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFK-SVDGVEKALE 63
Score = 41.6 bits (98), Expect = 2e-05
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 183 GYVNFKAEEE---ELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G+ + E++ L + F SCGEI V + D+ T KGF Y+ FK
Sbjct: 6 GFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFK 53
Score = 32.0 bits (73), Expect = 0.049
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 17/79 (21%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEK 111
S+T F GE+ V +P T K AY+ FK+++ VEK
Sbjct: 18 RSLTEHFSSCGEITRVS---IPTDRETGASKGF--------------AYIEFKSVDGVEK 60
Query: 112 ALEMNGHVIDEHTIRVDKA 130
ALE++G + + VD+A
Sbjct: 61 ALELDGSDLGGGNLVVDEA 79
>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 = 44.1 bits (104), Expect = 2e-06
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
S+++GN+ + + EEL F CG I+ V ++ D+ + KG+ Y+ F R + E
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF-----ATRDSVE 55
Query: 200 SCGEID 205
+ +D
Sbjct: 56 AAVALD 61
Score = 37.2 bits (86), Expect = 6e-04
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G V++ + EEL F CG I+ V ++ D+ + KG+ Y+ F
Sbjct: 5 GNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF 48
>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 = 43.8 bits (104), Expect = 3e-06
Identities = 14/52 (26%), Positives = 30/52 (57%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+FI ++P E +++L + F G + + ++ D++T K FG+V++ E
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPES 52
Score = 33.8 bits (78), Expect = 0.010
Identities = 9/37 (24%), Positives = 22/37 (59%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+++L + F G + + ++ D++T K FG+V++
Sbjct: 12 DQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYD 48
>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 = 43.8 bits (104), Expect = 3e-06
Identities = 18/59 (30%), Positives = 32/59 (54%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
N IF+G++ E +E L +AF +++RD+ T KG+G+V+F + L+
Sbjct: 5 NDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLK 63
Score = 35.7 bits (83), Expect = 0.002
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+E L +AF +++RD+ T KG+G+V+F
Sbjct: 20 DEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFS 56
>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 = 43.7 bits (103), Expect = 3e-06
Identities = 18/72 (25%), Positives = 38/72 (52%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+IF+G++ E + L AF + + R++ D + +G+G+V+F+++++ E
Sbjct: 1 NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60
Query: 200 SCGEIDNVRLIR 211
G+ R IR
Sbjct: 61 MNGKWLGSRPIR 72
Score = 30.9 bits (70), Expect = 0.11
Identities = 10/45 (22%), Positives = 24/45 (53%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++ + + L AF + + R++ D + +G+G+V+F+
Sbjct: 5 GDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFR 49
>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 = 43.8 bits (104), Expect = 4e-06
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
++F+GNIP ++ +RK E CG++ + + ++D T K FG+ F+ E LR
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALR 57
>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 = 46.9 bits (111), Expect = 4e-06
Identities = 32/140 (22%), Positives = 54/140 (38%), Gaps = 50/140 (35%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE- 192
+K+N + + +P +EE+R F S GEI++ +L+RD+ T G+G+VN+ E+
Sbjct: 2 SKTN---LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDA 58
Query: 193 ----------------------------------------------ELRKAFESCGEIDN 206
EL F G+I
Sbjct: 59 EKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIIT 118
Query: 207 VRLIRDQHTNIGKGFGYVNF 226
R++ D T + KG G++ F
Sbjct: 119 SRILSDNVTGLSKGVGFIRF 138
Score = 41.8 bits (98), Expect = 1e-04
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+ N+ + +E L + F G + NV++IRD TN KG+G+V+ +E
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDE 323
Score = 41.8 bits (98), Expect = 2e-04
Identities = 34/144 (23%), Positives = 62/144 (43%), Gaps = 25/144 (17%)
Query: 54 VTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLESVE 110
+ S+F GE+E+ + V +K T + +V + E E
Sbjct: 20 IRSLFTSIGEIESCKL--------------------VRDKVTGQSLGYGFVNYVRPEDAE 59
Query: 111 KALE-MNGHVIDEHTIRVDKALTTTKS-NSHSIFIGNIPFEAEEEELRKAFESCGEIDNV 168
KA+ +NG + TI+V A ++ S ++++ +P + EL F G+I
Sbjct: 60 KAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITS 119
Query: 169 RLIRDQHTNIGKGFGYVNFKAEEE 192
R++ D T + KG G++ F +E
Sbjct: 120 RILSDNVTGLSKGVGFIRFDKRDE 143
Score = 34.1 bits (78), Expect = 0.048
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 224
+E L + F G + NV++IRD TN KG+G+V
Sbjct: 282 DETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFV 316
>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 = 43.5 bits (103), Expect = 4e-06
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCG-EIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+++I + +P EE++R A S G E +VRL+R + T +GF +V F + EE R
Sbjct: 2 NNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60
Score = 34.7 bits (80), Expect = 0.006
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 191 EEELRKAFESCG-EIDNVRLIRDQHTNIGKGFGYVNFK 227
EE++R A S G E +VRL+R + T +GF +V F
Sbjct: 16 EEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFM 53
>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 = 43.0 bits (102), Expect = 5e-06
Identities = 12/49 (24%), Positives = 29/49 (59%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ I++ ++ + E++++ FE+ G+I + L D T KG+G++ +
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEY 49
Score = 33.8 bits (78), Expect = 0.009
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E++++ FE+ G+I + L D T KG+G++ +
Sbjct: 14 EDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEY 49
>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 = 43.2 bits (102), Expect = 6e-06
Identities = 18/55 (32%), Positives = 30/55 (54%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+SH +F+GN+P + E+EL++ F+ G + VR+ FG+V F E
Sbjct: 2 DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPE 56
>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 = 43.0 bits (102), Expect = 6e-06
Identities = 24/64 (37%), Positives = 37/64 (57%), Gaps = 4/64 (6%)
Query: 151 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESC--GEIDNVR 208
E +LR+ F G I+ V+++ DQ T +GFG+V F++ E+ ++A E EID R
Sbjct: 12 TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDA-KEAKERLNGMEIDG-R 69
Query: 209 LIRD 212
IR
Sbjct: 70 RIRV 73
Score = 39.1 bits (92), Expect = 1e-04
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E +LR+ F G I+ V+++ DQ T +GFG+V F
Sbjct: 12 TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYF 48
Score = 29.9 bits (68), Expect = 0.26
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 4/53 (7%)
Query: 84 CIKMNKVHEKRTNMN---AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALT 132
K+ V++++T + +V F+++E ++A E +NG ID IRVD ++T
Sbjct: 26 IEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDYSIT 78
>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 = 42.7 bits (101), Expect = 6e-06
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
I +G I E++L++ F +CGE+ VRL D+ + F +V F A+ E A
Sbjct: 3 IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSA--RFAFVEF-ADAESALSALNL 59
Query: 201 CGEIDNVRLIR 211
G + +R
Sbjct: 60 SGTLLGGHPLR 70
Score = 31.2 bits (71), Expect = 0.082
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQH 214
G ++ E++L++ F +CGE+ VRL D+
Sbjct: 6 GGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQ 37
Score = 29.2 bits (66), Expect = 0.43
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 88 NKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRV 127
++ H R A+V F + ES AL ++G ++ H +RV
Sbjct: 35 DRQHSAR---FAFVEFADAESALSALNLSGTLLGGHPLRV 71
>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 = 43.0 bits (102), Expect = 6e-06
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++ N+ ++E LR+ F G I + +++ D+ KGFG+V F + EE
Sbjct: 4 LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGR-SKGFGFVCFSSPEE 54
Score = 36.4 bits (85), Expect = 0.001
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E LR+ F G I + +++ D+ KGFG+V F
Sbjct: 15 DERLREEFSPFGTITSAKVMTDEKGR-SKGFGFVCF 49
>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 = 42.7 bits (100), Expect = 6e-06
Identities = 22/59 (37%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
IF+G + + EE++R+ F + GE++++ L D TN +GF ++ FK EEE ++K E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFK-EEEPVKKIME 59
Score = 32.7 bits (74), Expect = 0.027
Identities = 14/37 (37%), Positives = 25/37 (67%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
EE++R+ F + GE++++ L D TN +GF ++ FK
Sbjct: 13 EEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFK 49
>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 = 43.0 bits (101), Expect = 6e-06
Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+FIG + +E ++ LR+ F GE+ + ++RD T +GFG++ FK
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFK 48
Score = 37.9 bits (88), Expect = 3e-04
Identities = 15/45 (33%), Positives = 28/45 (62%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G +N++ ++ LR+ F GE+ + ++RD T +GFG++ FK
Sbjct: 4 GGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFK 48
>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 = 42.6 bits (101), Expect = 6e-06
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+F+G + + EE+LR+ F G +++V ++ D+ T +GF +V F
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48
Score = 37.2 bits (87), Expect = 6e-04
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EE+LR+ F G +++V ++ D+ T +GF +V F
Sbjct: 12 TEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTF 48
>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 = 42.9 bits (101), Expect = 7e-06
Identities = 27/82 (32%), Positives = 45/82 (54%), Gaps = 12/82 (14%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE---LRKA 197
IF+G I F+ E +LRK F G + V+++ D+ + KG+G+V F+ +E+ L++A
Sbjct: 5 IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQEA 63
Query: 198 FESCGEIDNVRLIRDQHTNIGK 219
C RD+ NIG+
Sbjct: 64 NRLC--------FRDKKLNIGQ 77
>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 = 42.7 bits (101), Expect = 7e-06
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
IF+G + E EE++R+ F G I + L D+ TN +GF ++ F +EE
Sbjct: 2 IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52
Score = 31.6 bits (72), Expect = 0.064
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
EE++R+ F G I + L D+ TN +GF ++ F
Sbjct: 13 EEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFD 49
Score = 26.2 bits (58), Expect = 5.3
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 73 PVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
+ +I LP M+K KR ++ F + E V+K LE HVI + V KA
Sbjct: 25 NIVEIELP------MDKKTNKRRGF-CFITFDSEEPVKKILETQFHVIGGKKVEVKKA 75
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 42.7 bits (101), Expect = 7e-06
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 139 HSIFIGNIPFEAEEEEL----RKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
HSIF+G++ + + L R + S +++ D T KG+G+V F E+E
Sbjct: 2 HSIFVGDLAPDVTDYMLQETFRARYPSV---RGAKVVMDPVTGRSKGYGFVRFGDEDERD 58
Query: 195 RKAFESCGEIDNVRLIR 211
R E G + R +R
Sbjct: 59 RALTEMNGVYCSSRPMR 75
Score = 27.6 bits (62), Expect = 1.5
Identities = 10/36 (27%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E R + S +++ D T KG+G+V F
Sbjct: 19 QETFRARYPSV---RGAKVVMDPVTGRSKGYGFVRF 51
>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 = 42.6 bits (101), Expect = 7e-06
Identities = 14/50 (28%), Positives = 29/50 (58%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+ IFIG +P E+++++ ES G++ L++D T + KG+ + +
Sbjct: 1 NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYL 50
>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 = 42.5 bits (101), Expect = 7e-06
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+F+G IP + E+EL FE G I +RL+ D +G+ +V +
Sbjct: 4 VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTY 49
Score = 31.8 bits (73), Expect = 0.058
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+EL FE G I +RL+ D +G+ +V +
Sbjct: 15 EDELVPLFEKAGPIYELRLMMDFSGL-NRGYAFVTY 49
>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 = 42.8 bits (100), Expect = 8e-06
Identities = 16/47 (34%), Positives = 31/47 (65%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+F+G++ E E+++ AF G+I + R+++D T KG+G+V+F
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 50
Score = 35.4 bits (81), Expect = 0.003
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+++ AF G+I + R+++D T KG+G+V+F
Sbjct: 16 EDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 50
>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 = 42.3 bits (99), Expect = 1e-05
Identities = 20/51 (39%), Positives = 31/51 (60%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
IF+G IP + E+EL FE G I ++RL+ D T + +G+ +V F +E
Sbjct: 4 IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKE 54
Score = 31.1 bits (70), Expect = 0.083
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+EL FE G I ++RL+ D T + +G+ +V F
Sbjct: 15 EDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTF 50
>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 = 42.4 bits (100), Expect = 1e-05
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
S+++ N+ ++LR+ F G I +V + D +T +GF YV F E++R A +
Sbjct: 2 SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQF----EDVRDAED 57
Query: 200 SCGEIDNVRL 209
+ +D R
Sbjct: 58 ALYYLDRTRF 67
Score = 30.8 bits (70), Expect = 0.13
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++LR+ F G I +V + D +T +GF YV F
Sbjct: 15 DDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQF 49
>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 = 42.4 bits (99), Expect = 1e-05
Identities = 23/52 (44%), Positives = 32/52 (61%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IFI N+ +A+E L + F G + NV++IRD +TN KGFG+V EE
Sbjct: 4 IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEE 55
Score = 33.9 bits (77), Expect = 0.010
Identities = 19/51 (37%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV---NFKVSFTTLSSI 236
A+E L + F G + NV++IRD +TN KGFG+V N++ + ++S+
Sbjct: 13 ADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63
>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 = 42.0 bits (98), Expect = 1e-05
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+F+G I + EE LR FE G+ID + +I D+ + +GFG+V F
Sbjct: 3 LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49
Score = 36.2 bits (83), Expect = 0.002
Identities = 17/44 (38%), Positives = 25/44 (56%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G + EE LR FE G+ID + +I D+ + +GFG+V F
Sbjct: 6 GGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTF 49
>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 = 42.0 bits (99), Expect = 1e-05
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 142 FIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFKAEEEELRKAFE 199
++GN+P++ EE++++ F + +VRL R+ + G +GFGY F+ + + L +A
Sbjct: 5 YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREP-GDPGRLRGFGYAEFE-DRDSLLQALS 61
Query: 200 SCGEIDNVRLIR 211
E R IR
Sbjct: 62 LNDESLKNRRIR 73
Score = 32.4 bits (74), Expect = 0.030
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 69 FRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVD 128
FR + V+ + LPR+ R Y F++ +S+ +AL +N + IRVD
Sbjct: 22 FRGLNVSSVRLPREPG------DPGRLRGFGYAEFEDRDSLLQALSLNDESLKNRRIRVD 75
Query: 129 KA 130
A
Sbjct: 76 IA 77
>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 = 42.0 bits (99), Expect = 1e-05
Identities = 17/53 (32%), Positives = 31/53 (58%)
Query: 143 IGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
I +P +EE R F + G + N +++RD+ T GFG+V++++ E+ R
Sbjct: 5 INYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQR 57
Score = 37.8 bits (88), Expect = 4e-04
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+EE R F + G + N +++RD+ T GFG+V++
Sbjct: 14 DEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDY 49
>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 = 42.0 bits (98), Expect = 1e-05
Identities = 22/52 (42%), Positives = 31/52 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+ N+ EA+E L + F G + NV++IRD TN KGFG+V +E
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDE 55
Score = 34.3 bits (78), Expect = 0.007
Identities = 17/37 (45%), Positives = 24/37 (64%)
Query: 188 KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 224
+A+E L + F G + NV++IRD TN KGFG+V
Sbjct: 12 EADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFV 48
>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 = 42.0 bits (99), Expect = 1e-05
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+++ +P A E L+ F G + V L R +HT KGF ++ F+ EE +KA +
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFE-TPEEAQKACKH 60
Score = 33.5 bits (77), Expect = 0.012
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
A E L+ F G + V L R +HT KGF ++ F+
Sbjct: 11 ATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFE 49
>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 = 41.6 bits (98), Expect = 1e-05
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAE 190
IF+G +P + EEE ++ F G++ + +L++D T +GFG+V F +E
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE 51
Score = 30.8 bits (70), Expect = 0.11
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EEE ++ F G++ + +L++D T +GFG+V F
Sbjct: 12 TEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTF 48
>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 = 42.0 bits (98), Expect = 2e-05
Identities = 21/52 (40%), Positives = 32/52 (61%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+ N+ +A+E L + F G + NV++IRD +TN KGFG+V +E
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDE 57
Score = 35.1 bits (80), Expect = 0.004
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 224
A+E L + F G + NV++IRD +TN KGFG+V
Sbjct: 15 ADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFV 50
>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 = 41.4 bits (98), Expect = 2e-05
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
S+++G++ + E L + F G + ++R+ RD T G+ YVNF+
Sbjct: 1 SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQ 49
Score = 34.0 bits (79), Expect = 0.008
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E L + F G + ++R+ RD T G+ YVNF+
Sbjct: 13 EAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQ 49
Score = 28.7 bits (65), Expect = 0.74
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRV 127
AYV F+N E+AL +N VI IR+
Sbjct: 44 AYVNFQNPADAERALDTLNFDVIKGKPIRI 73
>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 = 41.7 bits (98), Expect = 2e-05
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 139 HSIFIGNIPFEAEEEEL----RKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
+SIF+G++ E E +L + F SC + +++ D T + +G+G+V F E ++
Sbjct: 2 YSIFVGDLSPEVNESDLVSLFQSRFPSC---KSAKIMTDPVTGVSRGYGFVRFSDENDQQ 58
Query: 195 RKAFESCGEIDNVRLIR 211
R E G R +R
Sbjct: 59 RALIEMQGVYCGGRPMR 75
>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 = 41.3 bits (97), Expect = 2e-05
Identities = 18/48 (37%), Positives = 32/48 (66%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+F+G + +E +E LR+ F GE+ + +++D+ TN +GFG+V FK
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFK 49
Score = 32.9 bits (75), Expect = 0.023
Identities = 16/45 (35%), Positives = 30/45 (66%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++++ +E LR+ F GE+ + +++D+ TN +GFG+V FK
Sbjct: 5 GGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFK 49
>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 = 41.2 bits (96), Expect = 2e-05
Identities = 20/52 (38%), Positives = 33/52 (63%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+ N+ +++E L + F G ++NV++IRD +TN KGFG+V +E
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDE 57
Score = 34.7 bits (79), Expect = 0.006
Identities = 16/36 (44%), Positives = 25/36 (69%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 224
++E L + F G ++NV++IRD +TN KGFG+V
Sbjct: 15 SDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFV 50
>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 = 40.8 bits (95), Expect = 3e-05
Identities = 18/51 (35%), Positives = 34/51 (66%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
IF+G + E++++ FE G++D+ L+ D+ TN +GFG+V F++E+
Sbjct: 2 IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
Score = 33.1 bits (75), Expect = 0.017
Identities = 14/36 (38%), Positives = 26/36 (72%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E++++ FE G++D+ L+ D+ TN +GFG+V F+
Sbjct: 14 EDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFE 49
>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 = 41.2 bits (97), Expect = 3e-05
Identities = 17/57 (29%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGE-IDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S+++G++ +E +++AF S GE + +V++IR++ T G+ +V F E R
Sbjct: 1 SLWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAER 57
Score = 36.5 bits (85), Expect = 0.001
Identities = 13/37 (35%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 191 EEELRKAFESCGE-IDNVRLIRDQHTNIGKGFGYVNF 226
E +++AF S GE + +V++IR++ T G+ +V F
Sbjct: 13 ENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEF 49
>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 = 41.1 bits (96), Expect = 3e-05
Identities = 17/55 (30%), Positives = 31/55 (56%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+F+G++P E+E+R FE G + V +I+D+ T +G +V + +E R
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADR 56
Score = 29.9 bits (67), Expect = 0.28
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVS 229
G V E+E+R FE G + V +I+D+ T +G +V +
Sbjct: 5 GSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTR 51
>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 = 41.1 bits (97), Expect = 3e-05
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIR-----DQHTNIGKGFGYVNFKAEEE 192
++F+ N+ F+ EE L+K FE CG + +V + + + G+G+V FK++E
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEA 59
Score = 36.4 bits (85), Expect = 0.001
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIR-----DQHTNIGKGFGYVNFKVSFTTLSSI 236
+NFK EE L+K FE CG + +V + + + G+G+V FK ++
Sbjct: 8 LNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKAL 64
Score = 27.6 bits (62), Expect = 1.8
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 100 YVRFKNLESVEKAL-EMNGHVIDEHTI 125
+V FK+ E+ +KAL + G V+D H +
Sbjct: 51 FVEFKSKEAAQKALKRLQGTVLDGHAL 77
>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 = 40.3 bits (95), Expect = 4e-05
Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 5/54 (9%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKG--FGYVNFKAEEE 192
I + N+P E+ LR+ FES GE+ +V+++R T GK FG+V FK+EE+
Sbjct: 3 IIVKNLPKYVTEDRLREHFESKGEVTDVKVMR---TRDGKSRRFGFVGFKSEED 53
Score = 30.3 bits (69), Expect = 0.17
Identities = 18/39 (46%), Positives = 26/39 (66%), Gaps = 5/39 (12%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKG--FGYVNFK 227
E+ LR+ FES GE+ +V+++R T GK FG+V FK
Sbjct: 14 EDRLREHFESKGEVTDVKVMR---TRDGKSRRFGFVGFK 49
>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 = 40.5 bits (95), Expect = 4e-05
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+FIG + ++ E LR+ F GEI ++RD T +GFG+V F
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFS 48
Score = 34.3 bits (79), Expect = 0.006
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E LR+ F GEI ++RD T +GFG+V F
Sbjct: 13 EGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFS 48
Score = 27.8 bits (62), Expect = 1.4
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 82 KACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTI 125
K C+ M KR+ +V F + SV+K L H +D I
Sbjct: 26 KECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKI 69
>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 = 40.6 bits (95), Expect = 5e-05
Identities = 20/62 (32%), Positives = 39/62 (62%), Gaps = 2/62 (3%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
+++F+G I +E E+R F G + V++I D+ T + KG+G+V+F ++ +++K
Sbjct: 6 NTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSF-YDDVDVQKIV 63
Query: 199 ES 200
ES
Sbjct: 64 ES 65
Score = 35.2 bits (81), Expect = 0.004
Identities = 15/44 (34%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++ + +E E+R F G + V++I D+ T + KG+G+V+F
Sbjct: 11 GGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSF 53
>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 = 40.3 bits (94), Expect = 5e-05
Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 6/75 (8%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE--ELRKA 197
++F+ + + EE L+++F+ G I R++ D+ T KGFG+V+F +EE+ ++A
Sbjct: 2 TLFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEA 58
Query: 198 FESCGEIDNVRLIRD 212
E GEID ++ D
Sbjct: 59 MED-GEIDGNKVTLD 72
Score = 31.5 bits (71), Expect = 0.076
Identities = 15/36 (41%), Positives = 24/36 (66%), Gaps = 3/36 (8%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EE L+++F+ G I R++ D+ T KGFG+V+F
Sbjct: 14 EETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDF 46
>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 = 40.4 bits (95), Expect = 6e-05
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNF 187
+FIGN+ E +E+ L F + G I +++RD T KGF ++++
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY 51
Score = 30.0 bits (68), Expect = 0.27
Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 190 EEEELRKAFESCGEI-DNVRLIRDQHTNIGKGFGYVNF 226
+E+ L F + G I +++RD T KGF ++++
Sbjct: 14 DEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY 51
>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 = 39.9 bits (94), Expect = 6e-05
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 9/59 (15%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+++ N+P EE+LR+ F GE++ V+ I+D + +V+F E ++ KA E
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHF-EERDDAVKAME 53
Score = 31.1 bits (71), Expect = 0.091
Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 8/37 (21%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
EE+LR+ F GE++ V+ I+D + +V+F+
Sbjct: 15 EEQLRELFSEYGEVERVKKIKD--------YAFVHFE 43
Score = 25.7 bits (57), Expect = 7.4
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRV 127
A+V F+ + KA+E MNG ++ I V
Sbjct: 38 AFVHFEERDDAVKAMEEMNGKELEGSPIEV 67
>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 = 40.1 bits (93), Expect = 7e-05
Identities = 17/48 (35%), Positives = 31/48 (64%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++ + +P +EEL+ F S GEI++ +L+RD+ T G+G+VN+
Sbjct: 6 NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 53
Score = 37.8 bits (87), Expect = 4e-04
Identities = 17/43 (39%), Positives = 28/43 (65%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ +EEL+ F S GEI++ +L+RD+ T G+G+VN+
Sbjct: 11 YLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 53
>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 = 40.1 bits (93), Expect = 7e-05
Identities = 15/47 (31%), Positives = 30/47 (63%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+F+G++ E ++++ AF G I + R+++D T KG+G+V+F
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50
Score = 32.7 bits (74), Expect = 0.025
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++++ AF G I + R+++D T KG+G+V+F
Sbjct: 16 DDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 50
>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 = 39.6 bits (92), Expect = 8e-05
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F+G IP + E+EL FE G I ++RL+ D + +G+ ++ F +E ++A +
Sbjct: 4 VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITF-CGKEAAQEAVKL 62
Query: 201 CGEIDNVRLIRDQHTNI 217
C DN + +H +
Sbjct: 63 C---DNYEIRPGKHLGV 76
Score = 28.8 bits (64), Expect = 0.56
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+EL FE G I ++RL+ D + +G+ ++ F
Sbjct: 15 EDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITF 50
>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 = 39.8 bits (93), Expect = 9e-05
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTN--IGKGFGYVNFKAEEEELRKAF 198
+F+G IP E++LR+ FE G + + ++RD+ N KG +V F + A
Sbjct: 4 MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTR----KAAL 59
Query: 199 ESCGEIDNVRLIRDQHTNI 217
E+ + N++ + H I
Sbjct: 60 EAQNALHNMKTLPGMHHPI 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 = 39.7 bits (92), Expect = 9e-05
Identities = 17/48 (35%), Positives = 30/48 (62%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++ + +P +EE R F S GEI++ +L+RD+ T G+G+VN+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 51
Score = 37.8 bits (87), Expect = 5e-04
Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ +EE R F S GEI++ +L+RD+ T G+G+VN+
Sbjct: 9 YLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 51
>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 = 39.6 bits (93), Expect = 9e-05
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLI 171
S +++IG++ + EE+L+ FE GEI ++ +I
Sbjct: 2 STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI 35
Score = 28.5 bits (64), Expect = 0.85
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLI 210
G+++ K EE+L+ FE GEI ++ +I
Sbjct: 8 GHLSKKVTEEDLKNLFEEYGEIQSIDMI 35
Score = 27.7 bits (62), Expect = 1.6
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 24/87 (27%)
Query: 46 SKNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKN 105
SK + ++F+ YGE++++ +P + C AYV +
Sbjct: 11 SKKVTEEDLKNLFEEYGEIQSIDM---------IPPRGC--------------AYVCMET 47
Query: 106 LESVEKAL-EMNGHVIDEHTIRVDKAL 131
+ +AL ++ + I+V A
Sbjct: 48 RQDAHRALQKLRNVKLAGKKIKVAWAP 74
>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 = 39.4 bits (92), Expect = 1e-04
Identities = 14/58 (24%), Positives = 27/58 (46%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
++F+ N+ F +E+L F I + ++ D T +G+G+V F E+
Sbjct: 1 TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEAL 58
Score = 26.7 bits (59), Expect = 3.9
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
F +E+L F I + ++ D T +G+G+V F +
Sbjct: 9 FSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAM 50
>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 = 39.4 bits (92), Expect = 1e-04
Identities = 13/53 (24%), Positives = 29/53 (54%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+F+G + + + LR+ F G++ ++ D +T +GFG++ F + +E
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADE 56
Score = 34.8 bits (80), Expect = 0.005
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G +N K + LR+ F G++ ++ D +T +GFG++ F
Sbjct: 8 GGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITF 51
Score = 29.0 bits (65), Expect = 0.54
Identities = 12/47 (25%), Positives = 25/47 (53%)
Query: 84 CIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
C+ M + KR+ ++ F + + ++A+E H ID + I + +A
Sbjct: 32 CVVMVDPNTKRSRGFGFITFSSADEADEAMEAQPHSIDGNQIELKRA 78
>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 = 39.3 bits (91), Expect = 1e-04
Identities = 17/47 (36%), Positives = 26/47 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+FIG + ++ + LR F GEI ++RD T +GFG+V F
Sbjct: 2 MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48
Score = 33.5 bits (76), Expect = 0.012
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++++ + LR F GEI ++RD T +GFG+V F
Sbjct: 5 GGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48
>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 = 38.7 bits (91), Expect = 1e-04
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
I + N+PF EEELR+ FE G + + L+ T V F E + RKAF+S
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSLGRL-LLPPSRT-----IALVEF-LEPSDARKAFKS 55
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+++GN+ A + EL FE G + +V + R+ GF +V F E+ R A ++
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP-----PGFAFVEF----EDPRDAEDA 52
Query: 201 CGEIDNVRL 209
+D R+
Sbjct: 53 VRALDGRRI 61
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLI-RDQHTNIGKGFGYVNFKAEE 191
+ +SIF+G + + +EEL + F G+I V LI R HTN F ++ F+ E+
Sbjct: 1 IDKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA---FAFIKFEREQ 54
Score = 28.1 bits (63), Expect = 1.3
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLI-RDQHTNIGKGFGYVNFK 227
G ++ +EEL + F G+I V LI R HTN F ++ F+
Sbjct: 9 GQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNA---FAFIKFE 51
>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 = 41.9 bits (98), Expect = 2e-04
Identities = 26/82 (31%), Positives = 39/82 (47%), Gaps = 14/82 (17%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE-------- 192
+F+G IP + E+EL FE G I +RL+ D +G+ +V F +EE
Sbjct: 61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQ-NRGYAFVTFCGKEEAKEAVKLL 119
Query: 193 ---ELR--KAFESCGEIDNVRL 209
E+R + C +DN RL
Sbjct: 120 NNYEIRPGRLLGVCISVDNCRL 141
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF-KAEEEE 193
+++ +P ++EL F G I R++ D T + +G G++ F K E E
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAE 56
Score = 35.4 bits (82), Expect = 0.003
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++EL F G I R++ D T + +G G++ F
Sbjct: 14 QQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF 49
>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 = 38.9 bits (90), Expect = 2e-04
Identities = 16/48 (33%), Positives = 30/48 (62%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++ + +P ++ELR F S GE+++ +LIRD+ G+G+VN+
Sbjct: 3 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 50
Score = 37.0 bits (85), Expect = 9e-04
Identities = 16/43 (37%), Positives = 27/43 (62%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ ++ELR F S GE+++ +LIRD+ G+G+VN+
Sbjct: 8 YLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNY 50
>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 = 38.9 bits (90), Expect = 2e-04
Identities = 17/56 (30%), Positives = 35/56 (62%)
Query: 136 SNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+ + IF+G + E++++ FE G++++ L+ D+ TN +GFG+V F+ E+
Sbjct: 1 TRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENED 56
Score = 33.1 bits (75), Expect = 0.020
Identities = 13/37 (35%), Positives = 26/37 (70%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
E++++ FE G++++ L+ D+ TN +GFG+V F+
Sbjct: 18 EDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFEN 54
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
++I +P +E+L K + G+I + + I D+ TN KG+G+V+F E KA E
Sbjct: 3 VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDF-DSPEAALKAIEG 61
Score = 35.3 bits (82), Expect = 0.003
Identities = 14/36 (38%), Positives = 24/36 (66%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E+L K + G+I + + I D+ TN KG+G+V+F
Sbjct: 14 DEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDF 49
>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 = 2e-04
Identities = 16/62 (25%), Positives = 33/62 (53%)
Query: 134 TKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
T ++ ++ + +P + + EL F + G I+ R++RD T G+ +V+F +E +
Sbjct: 103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADS 162
Query: 194 LR 195
R
Sbjct: 163 QR 164
Score = 36.5 bits (84), Expect = 0.008
Identities = 27/111 (24%), Positives = 55/111 (49%), Gaps = 6/111 (5%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKS-NSHSIFIGNIPFEAEEEELR 156
A+V F + ++A++ +NG + ++V A +S ++++ N+P +++L
Sbjct: 152 AFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLD 211
Query: 157 KAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNV 207
F G+I ++RD+ T +G +V F EE A E+ ++NV
Sbjct: 212 TIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREE----AQEAISALNNV 258
Score = 31.1 bits (70), Expect = 0.45
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
+ EL F + G I+ R++RD T G+ +V+F + +I
Sbjct: 120 TDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAI 166
>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 = 38.3 bits (90), Expect = 2e-04
Identities = 17/52 (32%), Positives = 32/52 (61%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++GN+ + EE L + F G + NV + +D+ T +G+G+V F +EE+
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEED 52
Score = 29.5 bits (67), Expect = 0.27
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 188 KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
K EE L + F G + NV + +D+ T +G+G+V F
Sbjct: 9 KVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFL 48
>gnl|CDD|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface
Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX)
proteins. This subgroup corresponds to the conserved
RNA recognition motif (RRM) in ECTO-NOX proteins (also
termed ENOX), comprising a family of plant and animal
NAD(P)H oxidases exhibiting both, oxidative and protein
disulfide isomerase-like, activities. They are
growth-related and drive cell enlargement, and may play
roles in aging and neurodegenerative diseases. ENOX
proteins function as terminal oxidases of plasma
membrane electron transport (PMET) through catalyzing
electron transport from plasma membrane quinones to
extracellular oxygen, forming water as a product. They
are also hydroquinone oxidases that oxidize externally
supplied NADH, hence NOX. ENOX proteins harbor a
di-copper center that lack flavin. ENOX proteins display
protein disulfide interchange activity that is also
possessed by protein disulfide isomerase. In contrast to
the classic protein disulfide isomerases, ENOX proteins
lack the double CXXC motif. This family includes two
ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed
candidate growth-related and time keeping constitutive
hydroquinone [NADH] oxidase (cCNOX), or cell
proliferation-inducing gene 38 protein, or Constitutive
Ecto-NOX (cNOX), is the constitutively expressed cell
surface NADH (ubiquinone) oxidase that is ubiquitous and
refractory to drugs. ENOX2, also termed APK1 antigen, or
cytosolic ovarian carcinoma antigen 1, or
tumor-associated hydroquinone oxidase (tNOX), is a
cancer-specific variant of ENOX1 and plays a key role in
cell proliferation and tumor progression. In contrast to
ENOX1, ENOX2 is drug-responsive and harbors a drug
binding site to which the cancer-specific S-peptide
tagged pan-ENOX2 recombinant (scFv) is directed.
Moreover, ENOX2 is specifically inhibited by a variety
of quinone site inhibitors that have anticancer activity
and is unique to the surface of cancer cells. ENOX
proteins contain many functional motifs.
Length = 84
Score = 38.5 bits (90), Expect = 2e-04
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++F+G +P A EE +R+ FE CGEI +R+ + K F ++ F E
Sbjct: 8 TVFVGGLPENATEEIIREVFEQCGEIIAIRMSK-------KNFCHIRFAEEF 52
Score = 28.9 bits (65), Expect = 0.56
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 189 AEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSIF 237
A EE +R+ FE CGEI +R+ + K F ++ F F +I+
Sbjct: 18 ATEEIIREVFEQCGEIIAIRMSK-------KNFCHIRFAEEFAVDKAIY 59
>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 = 38.1 bits (89), Expect = 2e-04
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 12/69 (17%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
++IG +P+ A E ++ + F+ G I + N+ GFG+V F E+ R A ++
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREI--------NLKNGFGFVEF----EDPRDADDA 49
Query: 201 CGEIDNVRL 209
E++ L
Sbjct: 50 VYELNGKEL 58
>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 = 38.3 bits (89), Expect = 3e-04
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 11/55 (20%)
Query: 138 SHSIFIGNIPFEAE-----EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
S +++IGN+ + E+ELRK E GEI+++R++R+ K ++NF
Sbjct: 2 SRNVYIGNVSDVGDERNLPEKELRKECEKYGEIESIRILRE------KACAFINF 50
Score = 30.3 bits (68), Expect = 0.22
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 6/36 (16%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+ELRK E GEI+++R++R+ K ++NF
Sbjct: 21 EKELRKECEKYGEIESIRILRE------KACAFINF 50
>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 = 38.1 bits (88), Expect = 3e-04
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+FIG + ++ +E LR+ F GE+ ++RD T +GFG+V F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 32.3 bits (73), Expect = 0.033
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++++ +E LR+ F GE+ ++RD T +GFG+V F
Sbjct: 6 GGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>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 = 38.0 bits (88), Expect = 3e-04
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
IF+G I + EE LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 3 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49
Score = 30.3 bits (68), Expect = 0.15
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G + EE LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 6 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 49
>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 = 38.0 bits (88), Expect = 3e-04
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
IF+G I + EE LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 3 IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49
Score = 30.7 bits (69), Expect = 0.14
Identities = 14/44 (31%), Positives = 24/44 (54%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G + EE LR FE G+I+ + ++ D+ + +GF +V F
Sbjct: 6 GGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTF 49
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich
splicing factor 10 (SRSF10) and similar proteins. This
subgroup corresponds to the RRM of SRSF10, also termed
40 kDa SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). SRSF10 is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 38.0 bits (88), Expect = 3e-04
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 4/66 (6%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
S+F+ NI + E+LR+ F G I +V + D +T +GF YV F E++R A +
Sbjct: 2 SLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQF----EDVRDAED 57
Query: 200 SCGEID 205
+ +D
Sbjct: 58 ALHNLD 63
Score = 28.0 bits (62), Expect = 1.5
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 192 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E+LR+ F G I +V + D +T +GF YV F+
Sbjct: 15 EDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFE 50
>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 = 37.8 bits (88), Expect = 4e-04
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAE 190
H +F+ +PF +EEL K F+ G + +VRL+ ++ + KG YV ++ E
Sbjct: 3 HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENE 53
Score = 26.2 bits (58), Expect = 5.0
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 99 AYVRFKNLESVEKA-LEMNGHVIDEHTIRV 127
AYV ++N S +A L+M+G I E TI V
Sbjct: 46 AYVEYENESSASQAVLKMDGTEIKEKTISV 75
Score = 25.8 bits (57), Expect = 6.6
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 186 NFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
F +EEL K F+ G + +VRL+ ++ + KG YV +
Sbjct: 11 PFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEY 50
>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 = 37.6 bits (88), Expect = 4e-04
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 6/45 (13%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 185
+F+GN+P + EEE ++ F GE+ V L N KGFG++
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFI 42
Score = 28.4 bits (64), Expect = 0.73
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 6/34 (17%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYV 224
EEE ++ F GE+ V L N KGFG++
Sbjct: 15 EEEFKELFSKYGEVSEVFL------NKEKGFGFI 42
>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 = 40.6 bits (95), Expect = 4e-04
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 132 TTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
TT + I+IGN+P E+++++ ES G++ LI+D T + KG+ + +K
Sbjct: 289 TTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYK 345
Score = 27.2 bits (60), Expect = 9.7
Identities = 11/37 (29%), Positives = 23/37 (62%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E+++++ ES G++ LI+D T + KG+ + +K
Sbjct: 309 EDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYK 345
>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 = 37.8 bits (88), Expect = 4e-04
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+ + NIPF + +LR+ F G I +V +I ++ + KGFG+V F + R
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS--KGFGFVTFANSADADR 55
Score = 29.3 bits (66), Expect = 0.34
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
F+ + +LR+ F G I +V +I ++ + KGFG+V F
Sbjct: 10 FRFRDPDLRQMFGQFGPILDVEIIFNERGS--KGFGFVTF 47
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 37.3 bits (86), Expect = 6e-04
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+F+G IP + E+EL FES G I +RL+ D +G+ +V + + E R E
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD-FDGKNRGYAFVMYTQKHEAKRAVRE 61
>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 = 37.2 bits (87), Expect = 6e-04
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 151 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLI 210
+E+L F G+I + +IRD+ T + ++ F+ +E+ F ++DNV LI
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYF----KMDNV-LI 70
Query: 211 RD 212
D
Sbjct: 71 DD 72
Score = 33.4 bits (77), Expect = 0.014
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E+L F G+I + +IRD+ T + ++ F
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEF 52
Score = 30.7 bits (70), Expect = 0.13
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 99 AYVRFKNLESVEKA-LEMNGHVIDEHTIRVD 128
A++ F+ E E+A +M+ +ID+ I VD
Sbjct: 48 AFIEFETKEDCEEAYFKMDNVLIDDRRIHVD 78
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La) family.
It is expressed predominantly in neurons and muscle in
vertebrates. LARP6 functions as a key regulatory protein
that may play a role in mediating a variety of
developmental and homeostatic processes in animals,
including myogenesis, neurogenesis and possibly
metastasis. LARP6 binds to Ca2+/calmodulin-dependent
serine protein kinase (CASK), and forms a complex with
inhibitor of differentiation transcription factors. It
is structurally related to the La autoantigen and
contains a La motif (LAM), nuclear localization and
export (NLS and NES) signals, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 37.2 bits (87), Expect = 8e-04
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 12/82 (14%)
Query: 51 LSSVTSMFKPYGEVETVR----FRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNL 106
+ SV +F G + +R R++P D+ ++ ++ + T A V F+ L
Sbjct: 15 IESVLELFSTCGVIALIRILRPGRTIP-PDL---KRY---SSRHPQLGTKECAVVEFEKL 67
Query: 107 ESVEKALE-MNGHVIDEHTIRV 127
E+ KA+E ++ I+V
Sbjct: 68 EAARKAVEELSARDDWRDGIKV 89
>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 = 36.8 bits (86), Expect = 9e-04
Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 25/81 (30%)
Query: 52 SSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AYVRFKNLES 108
S + +F+ YGE+ ++RF S R N YV+F + ES
Sbjct: 15 SDIRDLFEQYGEILSIRFPS---------------------LRFNKTRRFCYVQFTSPES 53
Query: 109 VEKALE-MNGHVIDEHTIRVD 128
A+ +NG + + + + V
Sbjct: 54 AAAAVALLNGKLGEGYKLVVK 74
Score = 36.4 bits (85), Expect = 0.001
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++ N P ++ ++R FE GEI ++R N + F YV F + E
Sbjct: 3 LWVTNFPPSFDQSDIRDLFEQYGEILSIRF-PSLRFNKTRRFCYVQFTSPES 53
Score = 29.1 bits (66), Expect = 0.42
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 184 YV-NF--KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+V NF ++ ++R FE GEI ++R N + F YV F
Sbjct: 4 WVTNFPPSFDQSDIRDLFEQYGEILSIRF-PSLRFNKTRRFCYVQFT 49
>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 = 39.7 bits (92), Expect = 9e-04
Identities = 17/51 (33%), Positives = 31/51 (60%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+++G+I FE E+ +R+AF+ G I ++ + D T KGF +V ++ E
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPE 160
Score = 38.9 bits (90), Expect = 0.001
Identities = 23/102 (22%), Positives = 49/102 (48%), Gaps = 13/102 (12%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDKALTTTKSNS------------HSIFIGN 145
A+V ++ E+ + ALE MNG ++ I+V + ++ + I++ +
Sbjct: 152 AFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVAS 211
Query: 146 IPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ + E +++ FE+ GEI +L R KG+G++ +
Sbjct: 212 VHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEY 253
Score = 33.9 bits (77), Expect = 0.072
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E +++ FE+ GEI +L R KG+G++ +
Sbjct: 218 ETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEY 253
Score = 32.7 bits (74), Expect = 0.16
Identities = 15/46 (32%), Positives = 28/46 (60%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKV 228
G ++F+ E+ +R+AF+ G I ++ + D T KGF +V ++V
Sbjct: 113 GSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEV 158
>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 = 36.9 bits (86), Expect = 0.001
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESC-GEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ + N+P E EL++ F GEI +V+L+R + + ++ +K EEE
Sbjct: 3 LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDG-KSRRIAFIGYKTEEE 54
>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 = 36.4 bits (84), Expect = 0.001
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE-EELRKA 197
+F+GN+P + E+E +K F GE V + N GKGFG++ ++ E+ KA
Sbjct: 4 LFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKA 55
>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 = 36.8 bits (86), Expect = 0.001
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
IF+ + EA+EE++ F GEI N+ L D+ T KG+ + ++ ++E
Sbjct: 9 IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKE 60
Score = 27.6 bits (62), Expect = 1.9
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
V+ +A+EE++ F GEI N+ L D+ T KG+ + +
Sbjct: 14 VHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEY 55
>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 = 36.3 bits (84), Expect = 0.001
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
I + N+PFEA ++++R F S G++ +VR+ + + +GF +V F +E L A +
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPK-KFDQSARGFAFVEFSTAKEAL-NAMNA 60
>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 = 36.3 bits (84), Expect = 0.001
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
S+F+GN+ + +EL+ A N+ ++D K FGYV+F E+L KA E
Sbjct: 2 SLFVGNLNPNKDFDELKTAISEFFSKKNLA-VQDVRIGSSKKFGYVDF-ESAEDLEKALE 59
Query: 200 SCG 202
G
Sbjct: 60 LTG 62
Score = 29.0 bits (65), Expect = 0.50
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 90 VHEKRTNMN---AYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
V + R + YV F++ E +EKALE+ G + + I+++KA
Sbjct: 32 VQDVRIGSSKKFGYVDFESAEDLEKALELTGKKLLGNEIKLEKA 75
>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 = 36.2 bits (83), Expect = 0.002
Identities = 16/48 (33%), Positives = 30/48 (62%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++ + +P +EE + F S GEI++ +L+RD+ T G+G+VN+
Sbjct: 5 NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 52
Score = 33.9 bits (77), Expect = 0.010
Identities = 16/43 (37%), Positives = 27/43 (62%)
Query: 184 YVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
Y+ +EE + F S GEI++ +L+RD+ T G+G+VN+
Sbjct: 10 YLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNY 52
>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 = 35.6 bits (82), Expect = 0.002
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
IF+GN+ + +EELR FE+ G + + ++R F +V+ + E R
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADR 49
>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 = 35.6 bits (82), Expect = 0.002
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRK 196
++ ++F+ N+P+ +EL++ FE +I RL KG Y+ FK E E K
Sbjct: 2 DARTLFVKNLPYNITVDELKEVFEDAVDI---RLPS-GKDGSSKGIAYIEFKT-EAEAEK 56
Query: 197 AFE 199
A E
Sbjct: 57 ALE 59
Score = 26.3 bits (58), Expect = 4.7
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVD 128
AY+ FK EKALE G +D +I VD
Sbjct: 44 AYIEFKTEAEAEKALEEKQGAEVDGRSIVVD 74
>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 = 35.7 bits (82), Expect = 0.002
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 8/72 (11%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE-EELRKAFE 199
+F+GN+P + EE+ +K FE GE V + RD +GFG++ ++ E+ KA E
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA-E 56
Query: 200 SCGEIDNVRLIR 211
G I R +R
Sbjct: 57 LDGTILKNRPLR 68
>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 = 35.7 bits (83), Expect = 0.002
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEI 165
S ++F+ NI E+EELR FE G+I
Sbjct: 1 SRTLFVRNINSNVEDEELRALFEQFGDI 28
Score = 26.5 bits (59), Expect = 3.5
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 185 VNFKAEEEELRKAFESCGEI 204
+N E+EELR FE G+I
Sbjct: 9 INSNVEDEELRALFEQFGDI 28
>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 = 35.5 bits (82), Expect = 0.002
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 6/50 (12%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
S +++IGNI EE+LR F GEI++V +R+ K +VNF
Sbjct: 3 SRNVYIGNIDDSLTEEKLRNDFSQYGEIESVNYLRE------KNCAFVNF 46
Score = 28.2 bits (63), Expect = 0.98
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 182 FGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
G ++ EE+LR F GEI++V +R+ K +VNF
Sbjct: 8 IGNIDDSLTEEKLRNDFSQYGEIESVNYLRE------KNCAFVNF 46
>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 = 35.7 bits (82), Expect = 0.003
Identities = 15/53 (28%), Positives = 29/53 (54%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++++ +P ++EL + F G I R++RDQ T + +G G++ F E
Sbjct: 2 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIE 54
Score = 28.4 bits (63), Expect = 0.82
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++EL + F G I R++RDQ T + +G G++ F
Sbjct: 14 QKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRF 49
>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 = 35.7 bits (82), Expect = 0.003
Identities = 14/51 (27%), Positives = 28/51 (54%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+F+G + + E +L + F G ++ +I D+ T +GFG+V F+ +
Sbjct: 2 LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHD 52
Score = 29.5 bits (66), Expect = 0.42
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E +L + F G ++ +I D+ T +GFG+V F+
Sbjct: 12 GEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQ 49
Score = 27.2 bits (60), Expect = 2.6
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 100 YVRFKNLESVEKALEMNGHVIDEHTIRVDKALT 132
+V F+N +S +KA + H I+ H + V KA+
Sbjct: 45 FVYFQNHDSADKAAVVKFHPINGHRVEVKKAVP 77
>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 = 35.4 bits (82), Expect = 0.003
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++F+GN+ EE L + F G ++ V++ +D + K F +V FK E
Sbjct: 3 TLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFKHEV 53
Score = 28.4 bits (64), Expect = 0.85
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++ + EE L + F G ++ V++ +D + K F +V FK
Sbjct: 7 GNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFK 50
>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 = 35.2 bits (82), Expect = 0.003
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 141 IFIGNIPFEAEEEELRKAFESCG-EIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+ + +PF A EE++R F D + ++ D G YV F E+ R+A
Sbjct: 2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGR-PTGEAYVEFA-SPEDARRA 57
Score = 34.8 bits (81), Expect = 0.004
Identities = 11/48 (22%), Positives = 18/48 (37%)
Query: 80 PRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRV 127
I + + R AYV F + E +AL + + + I V
Sbjct: 25 IPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNKMGGRYIEV 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 = 35.2 bits (82), Expect = 0.003
Identities = 13/52 (25%), Positives = 30/52 (57%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+ +G + ++ L++ F + G + +V L D+ N+ +G+ YV F++ E+
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPED 52
Score = 32.5 bits (75), Expect = 0.028
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 190 EEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
++ L++ F + G + +V L D+ N+ +G+ YV F+
Sbjct: 11 NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFE 48
Score = 31.0 bits (71), Expect = 0.080
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 74 VADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-MNGHVIDEHTIRV 127
V D+ LP + + + + AYV F++ E EKA++ M+G ID + V
Sbjct: 25 VKDVDLPIDREVNLPRGY-------AYVEFESPEDAEKAIKHMDGGQIDGQEVTV 72
>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 = 35.5 bits (81), Expect = 0.003
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF--KAEEEELRKA 197
++++ +P ++EL + F G I R++ DQ T + +G G++ F + E EE K
Sbjct: 7 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66
Query: 198 F 198
Sbjct: 67 L 67
Score = 30.5 bits (68), Expect = 0.22
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++EL + F G I R++ DQ T + +G G++ F
Sbjct: 19 QKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 54
>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa
nuclear RNA- and DNA-binding protein (p54nrb). This
subgroup corresponds to the RRM1 of p54nrb, also termed
non-POU domain-containing octamer-binding protein
(NonO), or 55 kDa nuclear protein (NMT55), or
DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a
multifunctional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. It is ubiquitously expressed and highly
conserved in vertebrates. p54nrb binds both, single- and
double-stranded RNA and DNA, and also possesses inherent
carbonic anhydrase activity. It forms a heterodimer with
paraspeckle component 1 (PSPC1 or PSP1), localizing to
paraspeckles in an RNA-dependent manneras well as with
polypyrimidine tract-binding protein-associated-splicing
factor (PSF). p54nrb contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 35.2 bits (81), Expect = 0.003
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 12/70 (17%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE-EELRKAFE 199
+F+GN+P + EEE+RK FE G+ + + +D KGFG++ + E+ KA
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKA-- 55
Query: 200 SCGEIDNVRL 209
E+DN+ L
Sbjct: 56 ---ELDNMPL 62
>gnl|CDD|240842 cd12396, RRM1_Nop13p_fungi, RNA recognition motif 1 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM1 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both, Nop12p and Nop13p, are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 85
Score = 35.2 bits (81), Expect = 0.003
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 141 IFIGNIPFEAEEEELRKAFES-------CGEIDNVRLIRDQHTNIG----KGFGYVNFKA 189
++IGN+ F +E LR+ F S +I V + + G KGF YV+F +
Sbjct: 1 VWIGNLSFTTTKEMLRQFFVSKSGDRITDEQITRVHMPDSKAKRKGVKQNKGFAYVDFTS 60
Query: 190 EE 191
+E
Sbjct: 61 QE 62
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This subfamily
corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a
specific nucleolar component of the spliceosomal small
nuclear ribonucleoproteins (snRNPs), possibly
coordinating their transition through the nucleolus. It
specifically associates with U1, U2, U4, U5, and U6
small nuclear RNAs (snRNAs), and may play a role in the
maturation of both small nuclear and ribosomal RNAs.
RBM28 has four RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W
from Saccharomyces cerevisiae. It is an essential
nucleolar protein involved in processing and maturation
of 27S pre-rRNA and biogenesis of 60S ribosomal
subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 34.9 bits (81), Expect = 0.004
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF--KAEEEELRKAF 198
+ + N+PF+ E +L+K F G + V + R KGF +V F KA+ E+ K
Sbjct: 2 LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKGV 60
Query: 199 ES 200
Sbjct: 61 NG 62
Score = 34.5 bits (80), Expect = 0.006
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 19/75 (25%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-MN 116
F P+G V ++T+PRK K A+V+F + EKA++ +N
Sbjct: 20 FSPFGFVW----------EVTIPRKPDGKKKGF--------AFVQFTSKADAEKAIKGVN 61
Query: 117 GHVIDEHTIRVDKAL 131
G I + VD A+
Sbjct: 62 GKKIKGRPVAVDWAV 76
Score = 30.7 bits (70), Expect = 0.12
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 187 FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
FK E +L+K F G + V + R KGF +V F
Sbjct: 9 FKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFT 48
>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 = 35.1 bits (80), Expect = 0.004
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF--KAEEEELRKA 197
++++ +P ++EL + F G I R++ DQ T + +G G++ F + E EE K
Sbjct: 4 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63
Query: 198 F 198
Sbjct: 64 L 64
Score = 29.7 bits (66), Expect = 0.28
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++EL + F G I R++ DQ T + +G G++ F
Sbjct: 16 QKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 51
>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras
GTPase-activating protein-binding protein 1 (G3BP1) and
similar proteins. This subgroup corresponds to the RRM
of G3BP1, also termed ATP-dependent DNA helicase VIII
(DH VIII), or GAP SH3 domain-binding protein 1, which
has been identified as a phosphorylation-dependent
endoribonuclease that interacts with the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity. The acidic RasGAP binding domain of G3BP1
harbors an arsenite-regulated phosphorylation site and
dominantly inhibits stress granule (SG) formation. G3BP1
also contains an N-terminal nuclear transfer factor 2
(NTF2)-like domain, an RNA recognition motif (RRM
domain), and an Arg-Gly-rich region (RGG-rich region, or
arginine methylation motif). The RRM domain and RGG-rich
region are canonically associated with RNA binding.
G3BP1 co-immunoprecipitates with mRNAs. It binds to and
cleaves the 3'-untranslated region (3'-UTR) of the c-myc
mRNA in a phosphorylation-dependent manner. Thus, G3BP1
may play a role in coupling extra-cellular stimuli to
mRNA stability. It has been shown that G3BP1 is a novel
Dishevelled-associated protein that is methylated upon
Wnt3a stimulation and that arginine methylation of G3BP1
regulates both Ctnnb1 mRNA and canonical
Wnt/beta-catenin signaling. Furthermore, G3BP1 can be
associated with the 3'-UTR of beta-F1 mRNA in
cytoplasmic RNA-granules, demonstrating that G3BP1 may
specifically repress the translation of the transcript.
Length = 80
Score = 34.9 bits (80), Expect = 0.004
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 7/57 (12%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGK--GFGYVNFKAEE 191
+SH +F+GN+P + ++ EL++ F+ G + +R+ + GK FG+V F E
Sbjct: 2 DSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI-----NSGGKLPNFGFVVFDDSE 53
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 34.0 bits (79), Expect = 0.005
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 23/74 (31%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALE-MN 116
F P+G VE ++ K+ A+V F E+ EKA++ +N
Sbjct: 5 FSPFGNVEKIKL----------------------LKKKPGFAFVEFSTEEAAEKAVQYLN 42
Query: 117 GHVIDEHTIRVDKA 130
G + +RVD +
Sbjct: 43 GVLFGGRPLRVDYS 56
Score = 28.2 bits (64), Expect = 0.50
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 6/47 (12%)
Query: 155 LRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESC 201
L K F G ++ ++L++ GF +V F + EE KA +
Sbjct: 1 LYKLFSPFGNVEKIKLLKK-----KPGFAFVEF-STEEAAEKAVQYL 41
>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 = 34.6 bits (80), Expect = 0.005
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+F+G + + EE+LR+ F GE+ +V + + + F +V F
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTF 44
Score = 25.7 bits (57), Expect = 7.6
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
EE+LR+ F GE+ +V + + + F +V F
Sbjct: 14 EEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTF 44
>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 = 34.6 bits (79), Expect = 0.005
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+FIG + ++ +++L+ F GE+ + L D T +GFG+V FK E E + K +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFK-ESESVDKVMD 58
Score = 26.9 bits (59), Expect = 2.7
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVS 229
G +++ +++L+ F GE+ + L D T +GFG+V FK S
Sbjct: 4 GGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES 50
>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 = 34.6 bits (79), Expect = 0.005
Identities = 14/48 (29%), Positives = 30/48 (62%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++FI ++P E + +L + F G + + ++ D+ TN+ K FG+V++
Sbjct: 6 NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSY 53
Score = 28.8 bits (64), Expect = 0.72
Identities = 11/46 (23%), Positives = 26/46 (56%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
+ +L + F G + + ++ D+ TN+ K FG+V++ + ++I
Sbjct: 18 DTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAI 63
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 34.5 bits (79), Expect = 0.005
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 11/58 (18%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF---KAEEEELR 195
+F+GN+P EA E+E+R FE G++ +I K +G+V+ A +E +R
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIR 52
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating
protein-binding protein 2 (G3BP2) and similar proteins.
This subgroup corresponds to the RRM of G3BP2, also
termed GAP SH3 domain-binding protein 2, a cytoplasmic
protein that interacts with both IkappaBalpha and
IkappaBalpha/NF-kappaB complexes, indicating that G3BP2
may play a role in the control of nucleocytoplasmic
distribution of IkappaBalpha and cytoplasmic anchoring
of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an
N-terminal nuclear transfer factor 2 (NTF2)-like domain,
an acidic domain, a domain containing five PXXP motifs,
an RNA recognition motif (RRM domain), and an
Arg-Gly-rich region (RGG-rich region, or arginine
methylation motif). It binds to the SH3 domain of
RasGAP, a multi-functional protein controlling Ras
activity, through its N-terminal NTF2-like domain. The
acidic domain is sufficient for the interaction of G3BP2
with the IkappaBalpha cytoplasmic retention sequence.
Furthermore, G3BP2 might influence stability or
translational efficiency of particular mRNAs by binding
to RNA-containing structures within the cytoplasm
through its RNA-binding domain.
Length = 83
Score = 34.6 bits (79), Expect = 0.006
Identities = 18/55 (32%), Positives = 30/55 (54%)
Query: 137 NSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+SH +F+GN+P + +E EL++ F S G + +R+ FG+V F E
Sbjct: 4 DSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSE 58
>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 = 34.2 bits (79), Expect = 0.006
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++F+G + E+ELR F GEI V++ GKG G+V F
Sbjct: 3 TVFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQF 44
Score = 30.7 bits (70), Expect = 0.10
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 6/36 (16%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+ELR F GEI V++ GKG G+V F
Sbjct: 15 EDELRSLFGPFGEIVYVKI------PPGKGCGFVQF 44
>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 = 34.6 bits (79), Expect = 0.006
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
IFIG +P + E+EL E G+I +R++ D + N +G+ +V F + ++E + A +
Sbjct: 4 IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGN-NRGYAFVTF-SNKQEAKNAIKQ 61
Query: 201 CG--EIDNVRLI 210
EI N RL+
Sbjct: 62 LNNYEIRNGRLL 73
>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 = 34.8 bits (79), Expect = 0.006
Identities = 15/50 (30%), Positives = 31/50 (62%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
+++I +P +++L K + G+I + + I D+ TN KG+G+V+F +
Sbjct: 9 NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS 58
Score = 29.8 bits (66), Expect = 0.31
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+++L K + G+I + + I D+ TN KG+G+V+F
Sbjct: 21 DQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 56
>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 = 34.3 bits (79), Expect = 0.007
Identities = 24/62 (38%), Positives = 38/62 (61%), Gaps = 7/62 (11%)
Query: 141 IFIGNIPFEAEEEELRKAF-ESCGEIDNVRLIRDQHTNIGK--GFGYVNFKAEEEELRKA 197
+FI NIP++ + ++L+ F E GE+ V L +D+ GK G G V FK ++E ++KA
Sbjct: 2 VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEE---GKSRGCGVVEFK-DKESVQKA 57
Query: 198 FE 199
E
Sbjct: 58 LE 59
>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate
RNA-binding motif, single-stranded-interacting protein 3
(RBMS3). This subgroup corresponds to the RRM2 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
contain 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 = 88
Score = 34.7 bits (79), Expect = 0.007
Identities = 13/53 (24%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++I N+P +E+EL + G + + R++RD + + +G G+ ++ E+
Sbjct: 3 NLYISNLPVSMDEQELENMLKPFGHVISTRILRDAN-GVSRGVGFARMESTEK 54
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 34.1 bits (78), Expect = 0.007
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+F+G IP + E+EL FE G+I RL+ + + +G+ +V + +EE
Sbjct: 4 VFVGKIPRDMYEDELVPLFERAGKIYEFRLMM-EFSGENRGYAFVMYTTKEEAQL 57
>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative
RNA exonuclease NEF-sp. This subfamily corresponds to
the RRM1 of NEF-sp., including uncharacterized putative
RNA exonuclease NEF-sp found in vertebrates. Although
its cellular functions remains unclear, NEF-sp contains
an exonuclease domain and two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), suggesting it may possess
both exonuclease and RNA-binding activities. .
Length = 71
Score = 33.9 bits (78), Expect = 0.008
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 22/85 (25%)
Query: 46 SKNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKN 105
+ LS V +F+ G V V S + +A++ F+N
Sbjct: 8 PTSFCLSDVKRLFETCGPVRKVTMLS---------------------RTVQPHAFITFEN 46
Query: 106 LESVEKALE-MNGHVIDEHTIRVDK 129
LE+ + A+E +NG +D + I+V +
Sbjct: 47 LEAAQLAIETLNGASVDGNCIKVQR 71
Score = 25.5 bits (56), Expect = 7.3
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNV 168
+++ G P ++++ FE+CG + V
Sbjct: 1 TVYAGPFPTSFCLSDVKRLFETCGPVRKV 29
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 33.8 bits (78), Expect = 0.009
Identities = 22/54 (40%), Positives = 35/54 (64%), Gaps = 5/54 (9%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGK--GFGYVNFKAEEE 192
+ + N+P +E++LRK FE+ G I +V+L ++T GK FG+V +K EEE
Sbjct: 3 LIVKNLPKGIKEDKLRKLFEAFGTITDVQL---KYTKDGKFRKFGFVGYKTEEE 53
Score = 26.5 bits (59), Expect = 3.4
Identities = 17/39 (43%), Positives = 26/39 (66%), Gaps = 5/39 (12%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGK--GFGYVNFK 227
E++LRK FE+ G I +V+L ++T GK FG+V +K
Sbjct: 14 EDKLRKLFEAFGTITDVQL---KYTKDGKFRKFGFVGYK 49
>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 = 34.0 bits (77), Expect = 0.009
Identities = 15/50 (30%), Positives = 32/50 (64%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
+++I +P +++L K + G+I + + I D++TN KG+G+V+F +
Sbjct: 6 NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDS 55
Score = 30.2 bits (67), Expect = 0.21
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+++L K + G+I + + I D++TN KG+G+V+F
Sbjct: 18 DQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDF 53
>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 = 33.8 bits (77), Expect = 0.009
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF--KAEEEELRKA 197
++++ +P ++E+ + F G I R++ DQ T I +G G++ F + E EE K
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62
Query: 198 F 198
Sbjct: 63 L 63
Score = 28.8 bits (64), Expect = 0.57
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
++E+ + F G I R++ DQ T I +G G++ F
Sbjct: 15 QKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRF 50
>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 = 33.8 bits (77), Expect = 0.010
Identities = 15/59 (25%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+F+G + ++ +++L+ F GE+ + + D +T +GFG++ FK + + K E
Sbjct: 2 MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFK-DASSVEKVLE 59
Score = 28.0 bits (62), Expect = 1.2
Identities = 12/45 (26%), Positives = 26/45 (57%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G +++ +++L+ F GE+ + + D +T +GFG++ FK
Sbjct: 5 GGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFK 49
Score = 26.1 bits (57), Expect = 5.3
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 85 IKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
IKM+ + R+ ++ FK+ SVEK LE H +D I KA
Sbjct: 31 IKMDP-NTGRSRGFGFILFKDASSVEKVLEQKEHRLDGRLIDPKKA 75
>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 = 33.7 bits (77), Expect = 0.013
Identities = 12/51 (23%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+F+G + +A E+E+ + F G ++++ ++RD+ +G +V + ++E
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKE 51
Score = 32.1 bits (73), Expect = 0.043
Identities = 12/54 (22%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
G +N +A E+E+ + F G ++++ ++RD+ +G +V + ++I
Sbjct: 5 GCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEMAQAAI 57
>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-1. This
subgroup corresponds to the RRM2 of MSSP-1, also termed
RNA-binding motif, single-stranded-interacting protein 1
(RBMS1), or suppressor of CDC2 with RNA-binding motif 2
(SCR2). MSSP-1 is 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 = 85
Score = 33.5 bits (76), Expect = 0.014
Identities = 13/53 (24%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++I N+P +E+EL + G++ + R++RD + +G G+ ++ E+
Sbjct: 2 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEK 53
>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 = 33.5 bits (76), Expect = 0.015
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S+F+ N+ E+LR+ F G I +V + D +T +GF Y+ F E++R A
Sbjct: 2 SLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQF----EDVRDA 55
>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 = 33.0 bits (76), Expect = 0.016
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 10/63 (15%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIR-DQHTNIG---KGFGYVNFKAEEEELRK 196
IF+ N+PF ++L+ F CG + +R D T+ KGFG V F E+ ++
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNV-----LRADVKTDNDGRSKGFGTVLF-ESPEDAQR 54
Query: 197 AFE 199
A E
Sbjct: 55 AIE 57
Score = 27.2 bits (61), Expect = 2.2
Identities = 12/46 (26%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 83 ACIKMNKVHEKRTNMNAYVRFKNLESVEKALEM-NGHVIDEHTIRV 127
A +K + ++ R+ V F++ E ++A+EM NG+ ++ + V
Sbjct: 28 ADVKTD--NDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71
>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 = 33.5 bits (76), Expect = 0.016
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 152 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCG-EIDNVRLI 210
E +LR+ F G I +V ++ DQ + +GF +V F+ ++ + G E+D R+
Sbjct: 23 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 82
Query: 211 RD 212
D
Sbjct: 83 VD 84
Score = 31.5 bits (71), Expect = 0.084
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E +LR+ F G I +V ++ DQ + +GF +V F+
Sbjct: 23 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 59
>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 = 33.4 bits (76), Expect = 0.016
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 152 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCG--EIDNVRL 209
E +LR+ F G + V ++ DQ T +GF +V F+ ++ ++A E E+D R+
Sbjct: 13 ERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDS-KEAMEHANGMELDGRRI 71
Query: 210 IRD 212
D
Sbjct: 72 RVD 74
Score = 31.1 bits (70), Expect = 0.11
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
E +LR+ F G + V ++ DQ T +GF +V F+
Sbjct: 13 ERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFE 49
>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 = 33.5 bits (76), Expect = 0.016
Identities = 14/48 (29%), Positives = 31/48 (64%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++FI ++P E +++L + F G + + ++ D+ TN+ K FG+V++
Sbjct: 9 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 56
Score = 26.9 bits (59), Expect = 3.3
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+++L + F G + + ++ D+ TN+ K FG+V++
Sbjct: 21 DQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 56
>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 = 32.9 bits (76), Expect = 0.020
Identities = 15/52 (28%), Positives = 29/52 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++GN+ F EE++ + F CG+I + + D+ T GF +V + E+
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTRED 52
Score = 26.4 bits (59), Expect = 4.6
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++F EE++ + F CG+I + + D+ T GF +V +
Sbjct: 4 GNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYY 48
Score = 25.6 bits (57), Expect = 9.2
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 99 AYVRFKNLESVEKALE-MNGHVIDEHTIRVDK 129
+V + E E A++ +NG +D+ IRVD
Sbjct: 43 CFVEYYTREDAENAVKYLNGTKLDDRIIRVDW 74
>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 = 33.1 bits (76), Expect = 0.020
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 6/81 (7%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++F+GN+ EEELR+AFE G +++V + R G + +V F + R
Sbjct: 4 TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQ-GNAYAFVKFLNLDMAHRAKVA 62
Query: 200 SCGEIDNVRLIRDQHTNIGKG 220
G + I IG G
Sbjct: 63 MSG-----QYIGRNQIKIGYG 78
>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 = 32.9 bits (75), Expect = 0.021
Identities = 14/48 (29%), Positives = 29/48 (60%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+F+G + ++ +++L++ F GE+ + + D T +GFG+V FK
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFK 48
Score = 26.0 bits (57), Expect = 5.5
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G +++ +++L++ F GE+ + + D T +GFG+V FK
Sbjct: 4 GGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFK 48
Score = 26.0 bits (57), Expect = 5.7
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 73 PVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
V D T IK++ V R+ +V FK+ SVEK L+ H +D I +A
Sbjct: 24 EVVDCT------IKIDPV-TGRSRGFGFVLFKDAASVEKVLDQKEHKLDGRVIDPKRA 74
>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 = 33.1 bits (76), Expect = 0.022
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRL-IRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
I++G IP + ELR+ F+ GEI+ + L RD G +G+V + + +A E
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDD----GDNYGFVTY-RYACDAFRAIE 59
Query: 200 S 200
Sbjct: 60 H 60
>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 = 33.4 bits (77), Expect = 0.023
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 16/78 (20%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRD-------------QHTNIGKGF--G 183
++F+ N+P EE L++ F CG++++V L KGF
Sbjct: 1 RTLFVLNVPPYCTEESLKRLFSRCGKVESVELQEKPGPAESEDLTSKFFPPKPIKGFKVA 60
Query: 184 YVNFKAEEEELRKAFESC 201
YV FK + L +A +
Sbjct: 61 YVVFK-KPSSLSRALKLK 77
Score = 32.7 bits (75), Expect = 0.037
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 2/62 (3%)
Query: 58 FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEMNG 117
F G+VE+V + P K + AYV FK S+ +AL++
Sbjct: 21 FSRCGKVESVELQEKPGPAE--SEDLTSKFFPPKPIKGFKVAYVVFKKPSSLSRALKLKS 78
Query: 118 HV 119
Sbjct: 79 TE 80
>gnl|CDD|241083 cd12639, RRM3_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
RRM3 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, 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 contains
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. 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 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 = 79
Score = 32.9 bits (75), Expect = 0.023
Identities = 16/48 (33%), Positives = 29/48 (60%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
++FI ++P E + EL + F G + + ++ D+ TN K FG+V+F
Sbjct: 6 NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSF 53
>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 = 32.6 bits (74), Expect = 0.026
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++F+GN+ EE L + F G + V + +D+ K FG+V FK E
Sbjct: 3 TLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGK-PKSFGFVCFKHSE 53
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 32.6 bits (75), Expect = 0.028
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
+I++GN+ ++L + F GE+ VR+ D+ + +V F AE+ + A +
Sbjct: 6 TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQP--TRYAFVEF-AEQTSVINALK 62
Query: 200 SCGEIDNVRLIRDQHTN 216
G + R ++ H+N
Sbjct: 63 LNGAMFGGRPLKVNHSN 79
Score = 28.0 bits (63), Expect = 1.2
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRV 127
A+V F SV AL++NG + ++V
Sbjct: 47 AFVEFAEQTSVINALKLNGAMFGGRPLKV 75
>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 = 32.7 bits (74), Expect = 0.030
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF--KAEEEELRKA 197
+++I +P ++++ F G I N R++ DQ T + +G ++ F ++E EE +
Sbjct: 2 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61
Query: 198 F 198
F
Sbjct: 62 F 62
>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type
and RNA-binding motif-containing protein 1 (ZCRB1) and
similar proteins. This subfamily corresponds to the RRM
of ZCRB1, also termed MADP-1, or U11/U12 small nuclear
ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or
U11/U12-31K), a novel multi-functional nuclear factor,
which may be involved in morphine dependence, cold/heat
stress, and hepatocarcinoma. It is located in the
nucleoplasm, but outside the nucleolus. ZCRB1 is one of
the components of U11/U12 snRNPs that bind to U12-type
pre-mRNAs and form a di-snRNP complex, simultaneously
recognizing the 5' splice site and branchpoint sequence.
ZCRB1 is characterized by an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a CCHC-type Zinc finger
motif. In addition, it contains core nucleocapsid
motifs, and Lys- and Glu-rich domains. .
Length = 78
Score = 32.3 bits (74), Expect = 0.030
Identities = 14/53 (26%), Positives = 29/53 (54%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++++ N+PF +L K F G++ V +++D+ T KG ++ F E+
Sbjct: 3 TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDRED 55
Score = 26.1 bits (58), Expect = 5.2
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 180 KGFGYVN---FKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
K YV+ F +L K F G++ V +++D+ T KG ++ F
Sbjct: 1 KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILF 50
>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 = 32.3 bits (74), Expect = 0.032
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFKAEE 191
+++GN+ + +E+L A G +D + +H G KGF YV F +E
Sbjct: 1 LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEA 53
Score = 26.9 bits (60), Expect = 2.4
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFK 227
+E+L A G +D + +H G KGF YV F
Sbjct: 12 DEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFA 50
>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM2 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 82
Score = 32.1 bits (73), Expect = 0.039
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFES-CGEIDNVRLIRDQH--TNIGKGFGYVNFKAEE 191
+ +I+ NI + + +++ FES CGE+ +RL+ D H T I +V F E
Sbjct: 4 ARTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYHHSTRI----AFVEFAMAE 56
Score = 30.5 bits (69), Expect = 0.15
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 14/64 (21%)
Query: 176 TNIGKGFGYVNFKAEEEELRKAFES-CGEIDNVRLIRDQH--TNIGKGFGYVNFKVSFTT 232
TNI K K + +++ FES CGE+ +RL+ D H T I +V F ++ +
Sbjct: 10 TNIDK-------KVTQSDVKLFFESLCGEVSRLRLLGDYHHSTRI----AFVEFAMAESA 58
Query: 233 LSSI 236
++++
Sbjct: 59 IAAL 62
>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 = 32.2 bits (73), Expect = 0.040
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
++F+GN+ + EE + + F G + V++ +D+ K F +VNFK E
Sbjct: 3 TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGK-PKQFAFVNFKHEV 53
>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate
single-stranded DNA-binding protein MSSP-2. This
subgroup corresponds to the RRM2 of MSSP-2, also termed
RNA-binding motif, single-stranded-interacting protein 2
(RBMS2), or suppressor of CDC2 with RNA-binding motif 3
(SCR3). MSSP-2 is 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 = 86
Score = 32.3 bits (73), Expect = 0.040
Identities = 13/53 (24%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+++I N+P +E+EL + G++ + R++RD + +G G+ ++ E+
Sbjct: 2 NLYISNLPLSMDEQELESMLKPFGQVISTRILRDA-SGTSRGVGFARMESTEK 53
>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 = 32.3 bits (74), Expect = 0.042
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 138 SHSIFIGNIPFEAEEEELRKAF----ESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEE 193
S+F+G++ + ++ +L + F SC +++ DQ +G+G+V F E E+
Sbjct: 1 EFSLFVGDLTPDVDDYQLYEFFSKRYPSC---KGAKVVLDQ-NGNSRGYGFVRFSDESEQ 56
Query: 194 LR 195
R
Sbjct: 57 KR 58
>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 = 32.1 bits (73), Expect = 0.044
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+F+G + + E ++R F G I+ ++RDQ+ +G +V F
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTF 49
Score = 31.3 bits (71), Expect = 0.078
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSFTTLSSI 236
G ++ K E ++R F G I+ ++RDQ+ +G +V F L++I
Sbjct: 7 GMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQCALNAI 59
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 31.9 bits (72), Expect = 0.048
Identities = 13/50 (26%), Positives = 27/50 (54%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ ++F + +L + F + G++ +VR+I D+++ KG YV F
Sbjct: 1 ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEF 50
Score = 30.4 bits (68), Expect = 0.17
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 193 ELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+L + F + G++ +VR+I D+++ KG YV F
Sbjct: 17 DLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEF 50
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 31.9 bits (73), Expect = 0.048
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNV-RLIRDQHTNIGKGFGY--VNFKAEEE 192
++IGN+ E L K F G+I L G+ GY V F+ +EE
Sbjct: 2 LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEE 56
>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 = 31.6 bits (72), Expect = 0.053
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
+++ P + E +R+ F G + V++I F +V F++ E +R
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIR 48
>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 = 31.9 bits (72), Expect = 0.058
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 9/65 (13%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+++GN+ + EL +AF G + +V + R+ GF +V F E+ R A ++
Sbjct: 7 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEF----EDPRDAADA 57
Query: 201 CGEID 205
E+D
Sbjct: 58 VRELD 62
>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM1 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5). SFSF5 is an essential splicing regulatory
serine/arginine (SR) protein that 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 it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains 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. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 70
Score = 31.5 bits (71), Expect = 0.069
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 12/75 (16%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+FIG + A E+++ + F+ G I ++ L R GFG+V F ++ R A ++
Sbjct: 2 VFIGRLNPAAREKDVERFFKGYGRIRDIDLKR--------GFGFVEF----DDPRDADDA 49
Query: 201 CGEIDNVRLIRDQHT 215
E+D L ++ T
Sbjct: 50 VYELDGKELCNERVT 64
>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subgroup corresponds to the
RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, being highly expressed
throughout the brain and in glandular tissues,
moderately expressed in heart, skeletal muscle, and
liver, is also known as bruno-like protein 4 (BRUNOL-4),
or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4
also contain three highly conserved RRMs. The splicing
activation or repression activity of CELF-4 on some
specific substrates is mediated by its RRM1/RRM2. On the
other hand, both RRM1 and RRM2 of CELF-4 can activate
cardiac troponin T (cTNT) exon 5 inclusion. CELF-5,
expressed in brain, is also known as bruno-like protein
5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5.
Although its biological role remains unclear, CELF-5
shares same domain architecture with CELF-3. CELF-6,
being strongly expressed in kidney, brain, and testis,
is also known as bruno-like protein 6 (BRUNOL-6), or
CUG-BP- and ETR-3-like factor 6. It activates exon
inclusion of a cardiac troponin T minigene in transient
transfection assays in a muscle-specific splicing
enhancer (MSE)-dependent manner and can activate
inclusion via multiple copies of a single element, MSE2.
CELF-6 also promotes skipping of exon 11 of insulin
receptor, a known target of CELF activity that is
expressed in kidney. In addition to three highly
conserved RRMs, CELF-6 also possesses numerous potential
phosphorylation sites, a potential nuclear localization
signal (NLS) at the C terminus, and an alanine-rich
region within the divergent linker region. .
Length = 81
Score = 31.6 bits (72), Expect = 0.070
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+F+G + + E+++R+ FE G I+ ++R N KG +V F + E
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGN-SKGCAFVKFSSHAE 54
Score = 27.8 bits (62), Expect = 1.4
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 183 GYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
G ++ + E+++R+ FE G I+ ++R N KG +V F
Sbjct: 7 GMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGN-SKGCAFVKFS 50
>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 = 31.0 bits (71), Expect = 0.070
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 14/55 (25%)
Query: 141 IFIGNIPFEAEEEELRKAFESCG---EIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
+F+GN+P EELR FE G E D V K +G+V+ + EE+
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVV-----------KNYGFVHMEEEED 45
>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 = 31.5 bits (71), Expect = 0.080
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+ ++FIGN+ E ELR+AF+ G I+ V +I+ G + ++ F+
Sbjct: 8 TRNLFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKFQ 57
>gnl|CDD|241007 cd12563, RRM2_RBM6, RNA recognition motif 2 in vertebrate
RNA-binding protein 6 (RBM6). This subgroup corresponds
to the RRM2 of RBM6, also termed lung cancer antigen
NY-LU-12, or protein G16, or RNA-binding protein DEF-3,
which has been predicted to be a nuclear factor based on
its nuclear localization signal. It shows high sequence
similarity to RNA-binding protein 5 (RBM5 or LUCA15 or
NY-REN-9). Both, RBM6 and RBM5, 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. In contrast to RBM5, RBM6 has two additional
unique domains: the decamer repeat occurring more than
20 times, and the POZ (poxvirus and zinc finger) domain.
The POZ domain may be involved in protein-protein
interactions and inhibit binding of target sequences by
zinc fingers. .
Length = 87
Score = 31.3 bits (71), Expect = 0.092
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEID--NVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S +I + I E + KA + + NVR+I+++ GK FG+++ + E LR
Sbjct: 2 SKTIILKRIKRSTPPEVIVKALDPYVRLSTSNVRIIKNKPGPGGKTFGFIDLDSHAEALR 61
>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 = 30.8 bits (70), Expect = 0.10
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 152 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+E+L + F+ ++ L RD +T KGF YV +
Sbjct: 13 QEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTY 48
Score = 30.8 bits (70), Expect = 0.10
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+E+L + F+ ++ L RD +T KGF YV +
Sbjct: 13 QEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTY 48
>gnl|CDD|241198 cd12754, RRM2_RBM10, RNA recognition motif 2 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM2 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 87
Score = 31.1 bits (70), Expect = 0.11
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 167 NVRLIRDQHTNIGKGFGYVNFKAEEE 192
NVR+I+D+ T + +GF ++ E
Sbjct: 33 NVRVIKDKQTQLNRGFAFIQLSTIVE 58
Score = 30.0 bits (67), Expect = 0.28
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 206 NVRLIRDQHTNIGKGFGYVNF 226
NVR+I+D+ T + +GF ++
Sbjct: 33 NVRVIKDKQTQLNRGFAFIQL 53
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable
RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 30.8 bits (69), Expect = 0.13
Identities = 13/50 (26%), Positives = 26/50 (52%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ ++F + +L F + G++ +VR+I D+++ KG YV F
Sbjct: 1 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 50
Score = 30.0 bits (67), Expect = 0.26
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 193 ELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+L F + G++ +VR+I D+++ KG YV F
Sbjct: 17 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 50
>gnl|CDD|240891 cd12445, RRM2_CPEBs, RNA recognition motif 2 in cytoplasmic
polyadenylation element-binding protein CPEB-1, CPEB-2,
CPEB-3, CPEB-4 and similar protiens. This subfamily
corresponds to the RRM2 of CPEB family of proteins that
bind to defined groups of mRNAs and act as either
translational repressors or activators to regulate their
translation. CPEB proteins are well conserved in both,
vertebrates and invertebrates. Based on sequence
similarity, RNA-binding specificity, and functional
regulation of translation, the CPEB proteins has been
classified into two subfamilies. The first subfamily
includes CPEB-1 and related proteins. CPEB-1 is an
RNA-binding protein that interacts with the cytoplasmic
polyadenylation element (CPE), a short U-rich motif in
the 3' untranslated regions (UTRs) of certain mRNAs. It
functions as a translational regulator that plays a
major role in the control of maternal CPE-containing
mRNA in oocytes, as well as of subsynaptic
CPE-containing mRNA in neurons. Once phosphorylated and
recruiting the polyadenylation complex, CPEB-1 may
function as a translational activator stimulating
polyadenylation and translation. Otherwise, it may
function as a translational inhibitor when
dephosphorylated and bound to a protein such as maskin
or neuroguidin, which blocks translation initiation
through interfering with the assembly of eIF-4E and
eIF-4G. Although CPEB-1 is mainly located in cytoplasm,
it can shuttle between nucleus and cytoplasm. The second
subfamily includes CPEB-2, CPEB-3, CPEB-4, and related
protiens. Due to the high sequence similarity, members
in this subfamily may share similar expression patterns
and functions. CPEB-2 is an RNA-binding protein that is
abundantly expressed in testis and localized in
cytoplasm in transfected HeLa cells. It preferentially
binds to poly(U) RNA oligomers and may regulate the
translation of stored mRNAs during spermiogenesis.
Moreover, CPEB-2 impedes target RNA translation at
elongation. It directly interacts with the elongation
factor, eEF2, to reduce eEF2/ribosome-activated GTP
hydrolysis in vitro and inhibit peptide elongation of
CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific
translational regulatory protein that regulates
translation in a polyadenylation-independent manner. It
functions as a translational repressor that governs the
synthesis of the AMPA receptor GluR2 through binding
GluR2 mRNA. It also represses translation of a reporter
RNA in transfected neurons and stimulates translation in
response to NMDA. CPEB-4 is an RNA-binding protein that
mediates meiotic mRNA cytoplasmic polyadenylation and
translation. It is essential for neuron survival and
present on the endoplasmic reticulum (ER). It is
accumulated in the nucleus upon ischemia or the
depletion of ER calcium. CPEB-4 is overexpressed in a
large variety of tumors and is associated with many
mRNAs in cancer cells. All CPEB proteins are
nucleus-cytoplasm shuttling proteins. They contain an
N-terminal unstructured region, followed by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
Zn-finger motif. CPEB-2, -3, and -4 have conserved
nuclear export signals that are not present in CPEB-1. .
Length = 81
Score = 30.8 bits (70), Expect = 0.14
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 4/77 (5%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESC-GEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR-- 195
++F+G +P EL E G + V + D+ G V F E+ ++
Sbjct: 1 RTVFVGGLPLPLTAAELAAILERLYGGVCYVEIDTDEFYLYPTGCARVTFNNEQSYIKAV 60
Query: 196 -KAFESCGEIDNVRLIR 211
+ F D + +R
Sbjct: 61 SEVFVELPFNDINKRVR 77
>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 = 30.4 bits (68), Expect = 0.15
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 140 SIFIGNIPFEAEEEELRKAF-ESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
FI NIPF+ + + L+ E GE+ V L+ D +G V FK EE ++KA
Sbjct: 1 RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGK-SRGCAVVEFKM-EESMKKAV 58
Query: 199 E 199
E
Sbjct: 59 E 59
>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 = 30.6 bits (69), Expect = 0.15
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 167 NVRLIRDQHTNIGKGFGYVNFKAEEE 192
N+RLI+D+ T +GF +V + E
Sbjct: 33 NIRLIKDKQTQQNRGFAFVQLSSALE 58
Score = 30.2 bits (68), Expect = 0.20
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 206 NVRLIRDQHTNIGKGFGYV 224
N+RLI+D+ T +GF +V
Sbjct: 33 NIRLIKDKQTQQNRGFAFV 51
>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate
RNA-binding protein 10 (RBM10). This subgroup
corresponds to the RRM1 of RBM10, also termed G patch
domain-containing protein 9, or RNA-binding protein S1-1
(S1-1), a paralog of putative tumor suppressor
RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may
play an important role in mRNA generation, processing
and degradation in several cell types. The rat homolog
of human RBM10 is protein S1-1, a hypothetical RNA
binding protein with poly(G) and poly(U) binding
capabilities. RBM10 is structurally related to RBM5 and
RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or
DEF-3). It contains two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 85
Score = 30.4 bits (68), Expect = 0.18
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCG-EIDNVRLIRDQHTNIGKGFGYVNFKAEEEELR 195
S+ I + +P A E ++R + G + VRL+R++ + +GF +V F ++ R
Sbjct: 2 SNIIMLRMLPQNATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATR 60
Score = 27.0 bits (59), Expect = 3.7
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 189 AEEEELRKAFESCG-EIDNVRLIRDQHTNIGKGFGYVNFKV 228
A E ++R + G + VRL+R++ + +GF +V F
Sbjct: 14 ATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNH 54
>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 = 30.4 bits (68), Expect = 0.19
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+FIG + ++ +++L + GE+ + + D T +GFG+V FK
Sbjct: 2 MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAA 52
Score = 26.5 bits (58), Expect = 3.7
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 94 RTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
R+ +V FK+ SV+K LE+ H +D I +A
Sbjct: 39 RSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRA 75
>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 = 29.8 bits (67), Expect = 0.21
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 12/71 (16%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFES 200
+F GN ++A + E+ + F G +D V ++ GF +V + E R A ++
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRV--------DMKSGFAFVYMEDE----RDAEDA 50
Query: 201 CGEIDNVRLIR 211
+DN R
Sbjct: 51 IRGLDNFEFGR 61
>gnl|CDD|224252 COG1333, ResB, ResB protein required for cytochrome c biosynthesis
[Posttranslational modification, protein turnover,
chaperones].
Length = 478
Score = 32.4 bits (74), Expect = 0.21
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 69 FRSVPVADITLPRKACIKMNKVH-EKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRV 127
FR+ P AD T+ C+++N+ + AY ++ + E + E+TIRV
Sbjct: 195 FRAGPTADGTILLPFCVRVNRFGIDYLPTGQAYSFASDISVTDGQGE----EVAEYTIRV 250
Query: 128 DKALT 132
+ L
Sbjct: 251 NHPLR 255
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM3
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 72
Score = 30.0 bits (68), Expect = 0.21
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNV 168
I + N P+ EELR FE G++ V
Sbjct: 3 ILVKNFPYGTTAEELRDLFEPHGKLTRV 30
Score = 25.8 bits (57), Expect = 5.8
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 9/55 (16%)
Query: 53 SVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN--AYVRFKN 105
+ +F+P+G++ V +P A A ++ + R AY RFK+
Sbjct: 16 ELRDLFEPHGKLTRVL---MPPAGTI----AIVEFANPQQARLAFKALAYRRFKD 63
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It 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. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain. .
Length = 96
Score = 30.5 bits (69), Expect = 0.23
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 140 SIFIGNIPFEAEEEELRKAFES-CGEIDNVR 169
++F+ N+P + E LRK F S G I++V
Sbjct: 2 TLFLVNLPVDTTERHLRKLFGSGGGIIESVV 32
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein
19 (RBM19) and similar proteins. This subfamily
corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 72
Score = 29.6 bits (67), Expect = 0.24
Identities = 17/59 (28%), Positives = 35/59 (59%), Gaps = 3/59 (5%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
++ + PF +E+ +R+ F S + +R++++ H GF +V+ K+ EE+L+KA
Sbjct: 1 FTVKMRGAPFNVKEKHIRE-FFSPLKPVAIRIVKNDHGR-KTGFAFVDLKS-EEDLKKA 56
>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 = 30.0 bits (68), Expect = 0.24
Identities = 12/52 (23%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++I N+P +E++L + G++ + R++RD +G G+ ++ E+
Sbjct: 3 LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQ-SRGVGFARMESREK 53
>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 = 29.8 bits (67), Expect = 0.25
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S S+F+ N+P + E LR+ FE G++ V Q I +G V+F ++R A
Sbjct: 1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGV-----QTERISEGIVTVHFY----DIRDA 51
Query: 198 FESCGEIDNVRLIRD 212
+ E+ + +
Sbjct: 52 KRAVRELCGRHMQQQ 66
>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 = 29.7 bits (66), Expect = 0.26
Identities = 14/52 (26%), Positives = 30/52 (57%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKA 189
+++I + +++L K + G+I + + I D+ TN KG+G+V+F +
Sbjct: 1 KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDS 52
Score = 29.7 bits (66), Expect = 0.31
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
+++L K + G+I + + I D+ TN KG+G+V+F
Sbjct: 15 DQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 50
>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 = 29.4 bits (66), Expect = 0.30
Identities = 14/47 (29%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+++GN+ E+ L++ F+ G + NV++I D++ N G +G+V +
Sbjct: 1 LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKN-NKGVNYGFVEY 46
Score = 25.6 bits (56), Expect = 7.5
Identities = 12/36 (33%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 191 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 226
E+ L++ F+ G + NV++I D++ N G +G+V +
Sbjct: 12 EDILKQIFQVGGPVQNVKIIPDKN-NKGVNYGFVEY 46
>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 = 29.5 bits (67), Expect = 0.32
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNV 168
++ + N+P + E ++R+ F+ CGEI V
Sbjct: 2 TVKVKNLPKDTTENKIRQFFKDCGEIREV 30
>gnl|CDD|240970 cd12526, RRM1_EAR1_like, RNA recognition motif 1 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM1 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 = 29.2 bits (66), Expect = 0.33
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 15/77 (19%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S ++ + +P E +LR+ E G + V++ + +G V+F +LR A
Sbjct: 1 SRALLLSGVPPHIPETQLRRDLEQWGAVRAVQMDA-----MAEGIVTVHFY----DLRHA 51
Query: 198 FESCGEIDNVRLIRDQH 214
D +R IR QH
Sbjct: 52 ------EDALRDIRAQH 62
>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 = 29.5 bits (66), Expect = 0.34
Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S + + N+ + A E+ L++ FE I Q+ KG+ +V F E+ ++A
Sbjct: 1 SKVLVVNNLSYSASEDSLQEVFEKATSIR-----IPQNNGRPKGYAFVEF-ESAEDAKEA 54
Query: 198 FESCGEID 205
SC +
Sbjct: 55 LNSCNNTE 62
>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 = 29.3 bits (66), Expect = 0.34
Identities = 8/33 (24%), Positives = 21/33 (63%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIR 172
+++GN+P EE + + F+ G +++V+++
Sbjct: 1 HLWVGNLPENVREERISEHFKRYGRVESVKILP 33
Score = 29.0 bits (65), Expect = 0.53
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 19/78 (24%)
Query: 51 LSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVE 110
++ FK YG VE+V+ LP++ + A+V F +++S +
Sbjct: 13 EERISEHFKRYGRVESVKI---------LPKRG---------SDGGVAAFVDFVDIKSAQ 54
Query: 111 KALEMNGHVIDEHTIRVD 128
KA + + + +R D
Sbjct: 55 KAHNAV-NKMGDRDLRTD 71
>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 = 29.5 bits (67), Expect = 0.37
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 178 IGKGFGYVNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
+G K EE LR+ F G+I+++R++ KG +V +K
Sbjct: 6 VGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLP------SKGIAFVRYK 49
Score = 28.0 bits (63), Expect = 0.99
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 18/80 (22%)
Query: 140 SIFIGNI----PFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK------- 188
++++G I + EE LR+ F G+I+++R++ KG +V +K
Sbjct: 3 TLYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLP------SKGIAFVRYKYRASAEF 56
Query: 189 AEEEELRKAFESCGEIDNVR 208
A+E ++ + GE+ NVR
Sbjct: 57 AKEAMADQSLDG-GEVLNVR 75
>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 = 29.2 bits (66), Expect = 0.37
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 152 EEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCGEIDNVRLI 210
E+ELRK F G++ +V ++ + KG V F +++ CG N L+
Sbjct: 18 EDELRKIFSKYGDVSDV-VVSSKK----KGSAIVEFASKKAAEAAVENECGLPSNPLLV 71
>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 = 29.2 bits (66), Expect = 0.40
Identities = 9/36 (25%), Positives = 20/36 (55%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQH 175
++++G + E++LR F GEI ++ ++ Q
Sbjct: 3 TLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQ 38
>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 = 29.2 bits (65), Expect = 0.41
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDN-VRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
++ + N+P E L +AF G+++ V ++ D+ GKG V F A + RKA
Sbjct: 1 ALTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGI--VEF-AGKPSARKAL 57
Query: 199 ESCGE 203
+ C +
Sbjct: 58 DRCSD 62
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 29.3 bits (66), Expect = 0.42
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++++ +I + EE+L F +CG++ + R+ D N F ++ F +EE R A
Sbjct: 4 TVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEF-TDEEGARAALS 60
Query: 200 SCG 202
G
Sbjct: 61 LSG 63
Score = 26.6 bits (59), Expect = 3.9
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRV 127
A++ F + E AL ++G ++ + +RV
Sbjct: 45 AFIEFTDEEGARAALSLSGTMLGFYPVRV 73
>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 = 29.1 bits (65), Expect = 0.43
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 10/62 (16%)
Query: 140 SIFIGNI-PFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF 198
++F+ N P +L + FE G++ NVR I + F +V ++ +E+ KA
Sbjct: 1 TLFVINFDPINTRTRDLERHFEPYGKLVNVR--------IRRNFAFVQYETQEDA-TKAL 51
Query: 199 ES 200
ES
Sbjct: 52 ES 53
>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate
dead end protein homolog 1 (DND1). This subgroup
corresponds to the RRM1 of DND1, also termed RNA-binding
motif, single-stranded-interacting protein 4, an
RNA-binding protein that 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. For instance, DND1 binds cell cycle
inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle
regulator and tumor suppressor, LATS2 (large tumor
suppressor, homolog 2 of Drosophila). It helps maintain
their protein expression through blocking the inhibitory
function of microRNAs (miRNA) from these transcripts.
DND1 may also impose another level of translational
regulation to modulate expression of critical factors in
embryonic stem (ES) cells. DND1 interacts specifically
with apolipoprotein B editing complex 3 (APOBEC3), a
multi-functional protein inhibiting retroviral
replication. The DND1-APOBEC3 interaction may play a
role in maintaining viability of germ cells and for
preventing germ cell tumor development. DND1 contains
two conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 29.0 bits (65), Expect = 0.48
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+FIG IP + E+ L F+S G + RL+ + + +GF Y +
Sbjct: 4 VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMT-FSGLNRGFAYAKY 49
>gnl|CDD|215293 PLN02534, PLN02534, UDP-glycosyltransferase.
Length = 491
Score = 31.0 bits (70), Expect = 0.49
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 119 VIDEHTIRVDKALTTTKSNSHSIFIGNIP--FEAEEEELRKAFESCGEIDNVR 169
++ H IR+ A + S+S + +P E +L AF S ++D+VR
Sbjct: 154 LLSSHNIRLHNAHLSVSSDSEPFVVPGMPQSIEITRAQLPGAFVSLPDLDDVR 206
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 30.8 bits (70), Expect = 0.51
Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
++ + N+ +A E ++++ F G+I+ V + + + YV FK
Sbjct: 5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERS---QIAYVTFK 51
Score = 27.3 bits (61), Expect = 6.5
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 185 VNFKAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 227
V+ KA E ++++ F G+I+ V + + + YV FK
Sbjct: 12 VSLKATERDIKEFFSFSGDIEYVEMQSENERS---QIAYVTFK 51
>gnl|CDD|241068 cd12624, RRM_PRC, RNA recognition motif in peroxisome
proliferator-activated receptor gamma
coactivator-related protein 1 (PRC) and similar
proteins. This subgroup corresponds to the RRM of PRC,
also termed PGC-1-related coactivator, one of the
members of PGC-1 transcriptional coactivators family,
including peroxisome proliferator-activated receptor
gamma coactivators PGC-1alpha and PGC-1beta. Unlike
PGC-1alpha and PGC-1beta, PRC is ubiquitous and more
abundantly expressed in proliferating cells than in
growth-arrested cells. PRC has been implicated in the
regulation of several metabolic pathways, mitochondrial
biogenesis, and cell growth. It functions as a
growth-regulated transcriptional cofactor activating
many nuclear genes specifying mitochondrial respiratory
function. PRC directly interacts with nuclear
transcriptional factors implicated in respiratory chain
expression including nuclear respiratory factors 1 and 2
(NRF-1 and NRF-2), CREB (cAMP-response element-binding
protein), and estrogen-related receptor alpha
(ERRalpha). It interacts indirectly with the NRF-2beta
subunit through host cell factor (HCF), a cellular
protein involved in herpes simplex virus (HSV) infection
and cell cycle regulation. Furthermore, like PGC-1alpha
and PGC-1beta, PRC can transactivate a number of
NRF-dependent nuclear genes required for mitochondrial
respiratory function, including those encoding
cytochrome c, 5-aminolevulinate synthase, Tfam, and
TFB1M, and TFB2M. Further research indicates that PRC
may also act as a sensor of metabolic stress that
orchestrates a redox-sensitive program of inflammatory
gene expression. PRC is a multi-domain protein
containing an N-terminal activation domain, an LXXLL
coactivator signature, a central proline-rich region, a
tetrapeptide motif (DHDY) responsible for HCF binding, a
C-terminal arginine/serine-rich (SR) domain, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 91
Score = 29.1 bits (65), Expect = 0.54
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRL-IRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++IG IP EL+ F GEI+ + R + G +G+V ++ EE A E
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSE----GDNYGFVTYRYTEEAF-AAIE 59
Query: 200 SCGEI 204
+ ++
Sbjct: 60 NGHKL 64
>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 = 28.7 bits (65), Expect = 0.56
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
IFI N+ + + L F + G I + ++ D KG+G+V+F+ EE
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEE 54
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 29.0 bits (66), Expect = 0.58
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 9/59 (15%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHT-------NIGKGFGYVNFKAEEE 192
+++GN+P EEEL F + L + N K F +V F+ EE
Sbjct: 4 LYVGNLPPGITEEELVDFFNQA--MLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEE 60
>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM1 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
highly acidic carboxyl-terminal half. The family also
includes CUS2, a yeast homolog of human Tat-SF1. CUS2
interacts with U2 RNA in splicing extracts and functions
as a splicing factor that aids assembly of the
splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the conserved
splicing factor SF3a. Like Tat-SF1, CUS2 contains two
RRMs as well. .
Length = 92
Score = 29.0 bits (66), Expect = 0.62
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 9/61 (14%)
Query: 139 HSIFIGNIPFEAEEEELRKAFESCGEIDN--------VRLIRDQHTNIGKGFGYVNFKAE 190
++++ +P + EE + F CG I ++L RD++ N+ KG + E
Sbjct: 2 TNVYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNL-KGDALCCYLKE 60
Query: 191 E 191
E
Sbjct: 61 E 61
>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 = 28.6 bits (64), Expect = 0.69
Identities = 13/48 (27%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
I++GN+P + E++L F G I ++ L +++ + F +V F+
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIEL-KNRRGLV--PFAFVRFE 46
>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 = 28.8 bits (64), Expect = 0.73
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCG---EIDNVRLIRDQHTNIGKGFGYVNFK 188
++F+GN+ E +LR+AF+ G E+D R R Q + +G++ F+
Sbjct: 9 TLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTST----YGFLKFE 56
>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 = 28.7 bits (64), Expect = 0.74
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 100 YVRFKNLESVEKALE-MNGHVIDEHTIRV 127
+V FK E + AL+ M+G V+D HT+ V
Sbjct: 51 FVGFKTKEQAQAALKAMDGFVLDGHTLVV 79
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM4 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 = 76
Score = 28.4 bits (64), Expect = 0.79
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 143 IGNIPFEAEEEELRKAFESC-GEIDNVR 169
+ NIP EE+L++ F G + +
Sbjct: 4 LSNIPPSVTEEDLKELFTQTGGTVKAFK 31
>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 = 28.3 bits (64), Expect = 0.82
Identities = 16/53 (30%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++++ P +A +++++ FE G+++N+R+ RD KG +V FK EE+
Sbjct: 1 TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKF-KGSVFVEFKTEED 52
Score = 27.2 bits (61), Expect = 1.9
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 18/77 (23%)
Query: 51 LSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLESVE 110
L + F+ +G+V I+M + +K+ + +V FK E +
Sbjct: 13 LDDIQEFFEKFGKVN------------------NIRMRRDLDKKFKGSVFVEFKTEEDAK 54
Query: 111 KALEMNGHVIDEHTIRV 127
K LE E + V
Sbjct: 55 KFLEKEKLKYKEKELTV 71
>gnl|CDD|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53
and similar proteins. This subfamily corresponds to the
RRM domain of nucleoporin Nup53, also termed mitotic
phosphoprotein 44 (MP-44), or nuclear pore complex
protein Nup53, required for normal cell growth and
nuclear morphology in vertebrate. It tightly associates
with the nuclear envelope membrane and the nuclear
lamina where it interacts with lamin B. It may also
interact with a group of nucleoporins including Nup93,
Nup155, and Nup205 and play a role in the association of
the mitotic checkpoint protein Mad1 with the nuclear
pore complex (NPC). The family also includes
Saccharomyces cerevisiae Nup53p, an ortholog of
vertebrate nucleoporin Nup53. A unique property of yeast
Nup53p is that it contains an additional Kap121p-binding
domain and interacts specifically with the karyopherin
Kap121p, which is involved in the assembly of Nup53p
into NPCs. Both, vertebrate Nup35 and yeast Nup53p,
contain an atypical RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a C-terminal amphipathic
alpha-helix and several FG repeats. This family
corresponds to the RRM domain which lacks the conserved
residues that typically bind RNA in canonical RRM
domains.
Length = 73
Score = 28.3 bits (64), Expect = 0.85
Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 89 KVHEKRTNMNAYVRFKNLESVEKALEMNGHVI-DEHTIRV 127
+V ++++ + E+AL NG +I + V
Sbjct: 29 EVRYPPGANWIHLKYSSRLEAERALSKNGTIINGGVMVGV 68
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 28.3 bits (63), Expect = 0.88
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVR-LIRDQHTNIGKGFGYVNFKAEE 191
I+I N+ EL+K FE GEI+ + LI+ + G+ +G++ ++ E
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSR----GEKYGFITYRHSE 52
>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 = 28.4 bits (63), Expect = 0.97
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIG--KGFGYVNFKAEEEELRKAF 198
IF+ N+PF+ + L+ F CG + L D G KG G V F++ E R
Sbjct: 2 IFVRNLPFDFTWKMLKDKFNECGHV----LYADIKMENGKSKGCGVVRFESPEVAER--- 54
Query: 199 ESCGEIDNVRL 209
+C ++ +L
Sbjct: 55 -ACRMMNGYKL 64
>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 = 28.1 bits (62), Expect = 0.97
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 6/52 (11%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
+++ G + E+ +R+ F G+I VR+ D KG+ +V F + E
Sbjct: 2 TVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHE 47
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 28.1 bits (63), Expect = 0.97
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEI 165
+ ++FIGN+ +LR+AFE GEI
Sbjct: 2 TRTLFIGNLEKTTTYSDLREAFERFGEI 29
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family including
yeast cell wall integrity protein scw1, yeast Whi3
protein, yeast Whi4 protein and similar proteins. The
strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates septation
and cell-wall structure in fission yeast. It may
function as an inhibitor of septum formation, such that
its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a
G1 cyclin that promotes transcription of many genes to
trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict Cln3
synthesis to modulate cell cycle progression. Moreover,
Whi3 plays a key role in cell fate determination in
budding yeast. The RRM domain is essential for Whi3
function. Whi4 is a partially redundant homolog of Whi3,
also containing one RRM. Some uncharacterized family
members of this subfamily contain two RRMs; their RRM1
shows high sequence homology to the RRM of RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 28.3 bits (64), Expect = 1.0
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 141 IFIGNIPFEAEEEELRKAFESC 162
+F+ N+ EEELR+ F
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQ 26
>gnl|CDD|240777 cd12331, RRM_NRD1_SEB1_like, RNA recognition motif in Saccharomyces
cerevisiae protein Nrd1, Schizosaccharomyces pombe
Rpb7-binding protein seb1 and similar proteins. This
subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1
is a novel heterogeneous nuclear ribonucleoprotein
(hnRNP)-like RNA-binding protein encoded by gene NRD1
(for nuclear pre-mRNA down-regulation) from yeast S.
cerevisiae. It is implicated in 3' end formation of
small nucleolar and small nuclear RNAs transcribed by
polymerase II, and plays a critical role in pre-mRNA
metabolism. Nrd1 contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a short arginine-, serine-,
and glutamate-rich segment similar to the regions rich
in RE and RS dipeptides (RE/RS domains) in many metazoan
splicing factors, and a proline- and glutamine-rich
C-terminal domain (P+Q domain) similar to domains found
in several yeast hnRNPs. Disruption of NRD1 gene is
lethal to yeast cells. Its N-terminal domain is
sufficient for viability, which may facilitate
interactions with RNA polymerase II where Nrd1 may
function as an auxiliary factor. By contrast, the RRM,
RE/RS domains, and P+Q domain are dispensable. Seb1 is
an RNA-binding protein encoded by gene seb1 (for seven
binding) from fission yeast S. pombe. It is essential
for cell viability and bound directly to Rpb7 subunit of
RNA polymerase II. Seb1 is involved in processing of
polymerase II transcripts. It also contains one RRM
motif and a region rich in arginine-serine dipeptides
(RS domain).
Length = 79
Score = 28.3 bits (63), Expect = 1.0
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
S ++F G + F E +LR F GE+ + L D+ F + + + E R+A
Sbjct: 3 SRTLFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKR----HAFVKMYNRRDAENAREA 58
Query: 198 FESCGEIDNVRLIRDQHTNIGKGFG 222
E D +R T G GFG
Sbjct: 59 MEQYKSGDMQ--LR---TRWGVGFG 78
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 28.4 bits (64), Expect = 1.1
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 99 AYVRFKNLESVEKA-LEMNGHVIDEHTIRV 127
A+V + E E+A +NGH + IRV
Sbjct: 47 AFVEYATAEDAEEAQQALNGHSLQGSPIRV 76
>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 = 28.1 bits (62), Expect = 1.1
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+FIG + + E ++R F G+I+ R++R + +G +V F
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTF 49
>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 = 27.8 bits (62), Expect = 1.1
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 140 SIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++++GNIP + +L F++ G I R D +GF +V E+
Sbjct: 2 TVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQ 48
>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 = 28.1 bits (62), Expect = 1.3
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE 191
IF+ N+PF+ ++L++ F CG + + + + KG G V F + E
Sbjct: 2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMENGKS--KGCGTVRFDSPE 50
>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 = 28.0 bits (62), Expect = 1.3
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 165 IDNVRLIRDQHTNIGKGFGYVNFKAEEE 192
++N+RLI+D+ T +GF +V + E
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFVQLSSALE 58
Score = 28.0 bits (62), Expect = 1.5
Identities = 9/21 (42%), Positives = 16/21 (76%)
Query: 204 IDNVRLIRDQHTNIGKGFGYV 224
++N+RLI+D+ T +GF +V
Sbjct: 31 VNNIRLIKDKQTQQNRGFAFV 51
>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 = 27.6 bits (62), Expect = 1.5
Identities = 10/33 (30%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRVDKA 130
+V F+ +ES ++A+ E+NG + ++V A
Sbjct: 41 GFVTFEKMESADRAIAELNGTTVQGVQLKVSLA 73
>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 = 27.2 bits (61), Expect = 2.0
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 10/58 (17%)
Query: 141 IFIGNIP-FEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKA 197
+F+GN+ + +E+L + F G+I + L H KG+G+V F EE+ R A
Sbjct: 3 VFVGNLNTDKVSKEDLEEIFSKYGKILGISL----H----KGYGFVQF-DNEEDARAA 51
>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 = 27.4 bits (61), Expect = 2.0
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 87 MNKVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRV 127
MN + +K + A V F + E V+K L H ++ H +RV
Sbjct: 30 MNVIMDKDKGVYAIVEFDSKEGVDKVLSEPQHTLNGHRLRV 70
>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 = 26.7 bits (59), Expect = 2.4
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEEL 194
IF+GN+ +ELR FE G R + K + +V+ + EEE L
Sbjct: 3 IFVGNVSATCTSDELRGLFEEFG--------RVVECDKVKDYAFVHMEREEEAL 48
>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 = 27.2 bits (61), Expect = 2.5
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGE-IDNVRLIRD-QHTNIGKGFGYVNFK 188
+F+G IP +EE+ + F E + +V + R N +GF +V ++
Sbjct: 4 LFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYE 53
>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar
proteins. This subgroup corresponds to the RRM of
PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect
modulator 6, a member of a family of transcription
coactivators that plays a central role in the regulation
of cellular energy metabolism. As an inducible
transcription coactivator, PGC-1alpha can interact with
a broad range of transcription factors involved in a
wide variety of biological responses, such as adaptive
thermogenesis, skeletal muscle fiber type switching,
glucose/fatty acid metabolism, and heart development.
PGC-1alpha stimulates mitochondrial biogenesis and
promotes oxidative metabolism. It participates in the
regulation of both carbohydrate and lipid metabolism and
plays a role in disorders such as obesity, diabetes, and
cardiomyopathy. PGC-1alpha is a multi-domain protein
containing an N-terminal activation domain region, a
central region involved in the interaction with at least
a nuclear receptor, and a C-terminal domain region. The
N-terminal domain region consists of three leucine-rich
motifs (L1, NR box 2 and 3), among which the two last
are required for interaction with nuclear receptors,
potential nuclear localization signals (NLS), and a
proline-rich region overlapping a putative repression
domain. The C-terminus of PGC-1alpha is composed of two
arginine/serine-rich regions (SR domains), a putative
dimerization domain, and an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). PGC-1alpha could interact
favorably with single-stranded RNA. .
Length = 91
Score = 27.2 bits (60), Expect = 2.5
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRL-IRDQHTNIGKGFGYVNFK 188
I++G I + ELR FE GEI+ + +RD G +G++ ++
Sbjct: 5 IYVGKIRPDTTRTELRDRFEVFGEIEECTVNLRDD----GDSYGFITYR 49
>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 = 27.0 bits (60), Expect = 2.6
Identities = 12/34 (35%), Positives = 14/34 (41%)
Query: 94 RTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRV 127
R AYV+F E KAL + I I V
Sbjct: 41 RKTGEAYVQFATPEMANKALLKHREEIGNRYIEV 74
>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 = 26.8 bits (60), Expect = 2.6
Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 12/64 (18%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEE------EEL 194
+++G + EL + F+ G I + G+ + Y+ +++ E E L
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDP------GRNYAYIEYESIEAAQAAKEAL 54
Query: 195 RKAF 198
R
Sbjct: 55 RGFP 58
>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 = 27.0 bits (60), Expect = 2.6
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 99 AYVRFKNLESVEKAL-EMNGHVIDEHTIRV 127
AY F + E EK + ++NG V + V
Sbjct: 49 AYAEFSSPEQAEKVVKDLNGKVFKNRKLFV 78
>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 = 26.9 bits (60), Expect = 2.9
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDN-VRLIRDQHTNIGKGFG--YVNFKAEEEELR 195
I I NIPF+ + E+ F + + ++ D GK G YV F +EE+ +R
Sbjct: 2 IKIKNIPFDVTKGEVLAFFAGIAIAEQGIHILYD---KTGKTLGEAYVEFVSEEDAMR 56
>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 = 26.8 bits (59), Expect = 2.9
Identities = 14/61 (22%), Positives = 28/61 (45%)
Query: 143 IGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFESCG 202
+ N+P EE + + G I+ L+ + T KG+G+V + ++ + E G
Sbjct: 4 VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63
Query: 203 E 203
+
Sbjct: 64 K 64
>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of
RNA-binding proteins. This subfamily corresponds to the
RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family
of RNA-binding proteins. This ubiquitously expressed
family of similarly structured proteins predominantly
localizing to the nuclear, includes FUS (also known as
TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1),
TAF15 (also known as hTAFII68 or TAF2N or RPB56), and
Drosophila Cabeza (also known as SARFH). The
corresponding coding genes of these proteins are
involved in deleterious genomic rearrangements with
transcription factor genes in a variety of human
sarcomas and acute leukemias. All FET proteins interact
with each other and are therefore likely to be part of
the very same protein complexes, which suggests a
general bridging role for FET proteins coupling RNA
transcription, processing, transport, and DNA repair.
The FET proteins contain multiple copies of a degenerate
hexapeptide repeat motif at the N-terminus. The
C-terminal region consists of a conserved nuclear import
and retention signal (C-NLS), a putative zinc-finger
domain, and a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is flanked by 3
arginine-glycine-glycine (RGG) boxes. FUS and EWS might
have similar sequence specificity; both bind
preferentially to GGUG-containing RNAs. FUS has also
been shown to bind strongly to human telomeric RNA and
to small low-copy-number RNAs tethered to the promoter
of cyclin D1. To date, nothing is known about the RNA
binding specificity of TAF15. .
Length = 81
Score = 26.9 bits (60), Expect = 3.3
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 9/49 (18%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEID--------NVRLIRDQHTNIGKG 181
I+I +P + E+ L + F G I +++ D+ T KG
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETE-PKG 48
>gnl|CDD|240947 cd12503, RRM1_hnRNPH_GRSF1_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, G-rich sequence factor 1 (GRSF-1) and
similar proteins. This subfamily corresponds to the
RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein
family includes hnRNP H (also termed mcs94-1), hnRNP H2
(also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3
(also termed hnRNP 2H9), which represent a group of
nuclear RNA binding proteins that are involved in
pre-mRNA processing. These proteins have similar RNA
binding affinities and specifically recognize the
sequence GGGA. They can either stimulate or repress
splicing upon binding to a GGG motif. hnRNP H binds to
the RNA substrate in the presence or absence of these
proteins, whereas hnRNP F binds to the nuclear mRNA only
in the presence of cap-binding proteins. hnRNP H and
hnRNP H2 are almost identical; both have been found to
bind nuclear-matrix proteins. hnRNP H activates exon
inclusion by binding G-rich intronic elements downstream
of the 5' splice site in the transcripts of c-src, human
immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and
myelin. It silences exons when bound to exonic elements
in the transcripts of beta-tropomyosin, HIV-1, and
alpha-tropomyosin. hnRNP H2 has been implicated in
pre-mRNA 3' end formation. hnRNP H3 may be involved in
splicing arrest induced by heat shock. Most family
members contain three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), except for hnRNP H3, in
which the RRM1 is absent. RRM1 and RRM2 are responsible
for the binding to the RNA at DGGGD motifs, and play an
important role in efficiently silencing the exon.
Members in this family can regulate the alternative
splicing of fibroblast growth factor receptor 2 (FGFR2)
transcripts, and function as silencers of FGFR2 exon
IIIc through an interaction with the exonic GGG motifs.
The lack of RRM1 could account for the reduced silencing
activity within hnRNP H3. Members in this family have an
extensive glycine-rich region near the C-terminus, which
may allow them to homo- or heterodimerize. They also
include a cytoplasmic poly(A)+ mRNA binding protein,
GRSF-1, which interacts with RNA in a G-rich
element-dependent manner. They may function in RNA
packaging, stabilization of RNA secondary structure, or
other macromolecular interactions. GRSF-1 contains three
potential RRMs responsible for the RNA binding, and two
auxiliary domains (an acidic alpha-helical domain and an
N-terminal alanine-rich region) that may play a role in
protein-protein interactions and provide binding
specificity. .
Length = 77
Score = 26.6 bits (59), Expect = 3.6
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 85 IKMNKVHEKRTNMNAYVRFKNLESVEKALEMN 116
I E R + A++ ++ E VEKALE +
Sbjct: 32 IHFTYSREGRPSGEAFIELESEEDVEKALEKH 63
>gnl|CDD|240901 cd12455, RRM_like_Smg4_UPF3, RNA recognition motif-like Smg4_UPF3
domain in yeast up-frameshift suppressor 3 (Upf3p),
Caenorhabditis elegans SMG-4, their human orthologs
Upf3A and Upf3B, and similar proteins. This subfamily
corresponds to the RRM-like Smg4_UPF3 domain found in
yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis
elegans SMG-4, their human orthologs Upf3A and Upf3B,
and similar proteins. Upf3p, also termed
nonsense-mediated mRNA decay protein 3, or Sua6p, a
surveillance factor encoded by UPF3 gene from
Saccharomyces cerevisiae. It is required for
nonsense-mediated mRNA decay (NMD) in yeast. Upf3p is
primarily cytoplasmic but accumulates inside the
nucleus. Its nuclear import is mediated by the Srp1p
(importin-alpha)/beta heterodimer while its nuclear
export is mediated by a leucine-rich nuclear export
sequence (NES-A), but not the Crm1p exportin. C. elegans
SMG-4 is a nuclear shuttling protein that shuttles
between the cytoplasm and nucleus through nuclear import
and export signals similar to that of the yeast Upf3p.
It is regulated by phosphorylation. Human orthologs of
yeast Upf3p and C. elegans SMG-4 include Upf3A and
Upf3B, which derive from two genes, UPF3A and X-linked
UPF3B, respectively. Both, Upf3A (Up-frameshift
suppressor 3 homolog A, also termed regulator of
nonsense transcripts 3A, or nonsense mRNA reducing
factor 3A) and Upf3B (Up-frameshift suppressor 3 homolog
B on chromosome X, also termed regulator of nonsense
transcripts 3B, or nonsense mRNA reducing factor 3B),
are nucleocytoplasmic shuttling proteins. They associate
selectively with spliced beta-globin mRNA in vivo, and
tethering of any human Upf protein to the 3'UTR of
beta-globin mRNA prevents NMD. The function of the Upf
proteins in identifying and targeting nonsense mRNAs for
rapid decay is conserved among eukaryotes. Besides, all
Upf proteins in this family contain a conserved
Smg4_UPF3 domain with some similarity to an RNA
recognition motif (RRM), indicating that they may be RNA
binding proteins. .
Length = 88
Score = 26.8 bits (60), Expect = 3.7
Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 19/85 (22%)
Query: 41 PSLTKSKNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAY 100
PSLT+ + L V+ + KP TV + + K I AY
Sbjct: 9 PSLTEEE--FLEQVSPLIKP-----TVDWYYFVGGKSSKDFKPPI----------YSRAY 51
Query: 101 VRFKNLESVEK-ALEMNGHV-IDEH 123
+ FKN E + + A +GHV +D
Sbjct: 52 INFKNPEDLLEFARRFDGHVFVDSK 76
>gnl|CDD|223488 COG0411, LivG, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 250
Score = 27.9 bits (63), Expect = 3.8
Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 165 IDNVRLIRDQHTNIGKGFGYVNFKAEEEELR-KAFESCGEID 205
++NV + + G + EE E R +A E +
Sbjct: 97 LENVAVGAHARLGLSGLLGRPRARKEEREARERARELLEFVG 138
>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM1 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a
splicing regulatory serine/arginine (SR) protein that
plays an important role in both constitutive splicing
and alternative splicing of many pre-mRNAs. For
instance, it interacts with heterogeneous nuclear
ribonucleoproteins, hnRNP G and hnRNP E2, and further
regulates the 5' splice site of tau exon 10, whose
misregulation causes frontotemporal dementia. SFSF4 also
induces production of HIV-1 vpr mRNA through the
inhibition of the 5'-splice site of exon 3. In addition,
it activates splicing of the cardiac troponin T (cTNT)
alternative exon by direct interactions with the cTNT
exon 5 enhancer RNA. SRSF4 can shuttle between the
nucleus and cytoplasm. It contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a
glycine-rich region, an internal region homologous to
the RRM, and a very long, highly phosphorylated
C-terminal SR domains rich in serine-arginine
dipeptides. .
Length = 74
Score = 26.5 bits (58), Expect = 3.8
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 13/68 (19%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAF-- 198
++IG + ++A E ++ + F+ G+I V ++ G+G+V F + +
Sbjct: 2 VYIGRLSYQARERDVERFFKGYGKILEV--------DLKNGYGFVEFDDLRDADDAVYEL 53
Query: 199 ---ESCGE 203
+ CGE
Sbjct: 54 NGKDLCGE 61
>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 = 26.3 bits (58), Expect = 3.9
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 6/36 (16%)
Query: 99 AYVRFKNLESVEKALEMNGHVIDEHTIRVDKALTTT 134
AYV FK+ ++ E AL ++G I VD+++T T
Sbjct: 40 AYVTFKDPQAQETALLLSGATI------VDQSVTIT 69
>gnl|CDD|240867 cd12421, RRM1_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
RRM1 of the majority of family members that include
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. 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. The 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. In
addition, this family also includes RNA-binding motif
protein 20 (RBM20) that is an alternative splicing
regulator associated with dilated cardiomyopathy (DCM)
and contains only one RRM. .
Length = 74
Score = 26.4 bits (59), Expect = 4.6
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIR 172
+ + N+P + E +L G++ NV L+R
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLLR 33
>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 = 26.2 bits (58), Expect = 5.1
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 91 HEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRVDKA 130
+ R+ AYV+F + ES E+AL + I I + ++
Sbjct: 37 YRGRSTGEAYVQFASQESAERALGKHKEKIGHRYIEIFRS 76
>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 = 26.2 bits (58), Expect = 5.3
Identities = 20/91 (21%), Positives = 34/91 (37%), Gaps = 27/91 (29%)
Query: 44 TKSKNHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMN---AY 100
+KS + ++VT F YG + V+ R A+
Sbjct: 13 SKSDDELEAAVTEHFSKYGTLVFVKVL-----------------------RDWRQRPYAF 49
Query: 101 VRFKNLESVEKALEM-NGHVIDEHTIRVDKA 130
V+F N + + AL G ++D IR ++A
Sbjct: 50 VQFTNDDDAKNALAKGQGTILDGRHIRCERA 80
>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 = 26.1 bits (58), Expect = 5.4
Identities = 21/70 (30%), Positives = 27/70 (38%), Gaps = 28/70 (40%)
Query: 52 SSVTSM-------FKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFK 104
SS TS+ FK +G+V +V KVH + A V F+
Sbjct: 11 SSDTSLKDGLFHEFKKHGKVTSV---------------------KVHGTGSERYAIVFFR 49
Query: 105 NLESVEKALE 114
E EKALE
Sbjct: 50 KPEDAEKALE 59
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its C-terminal
RRM motif. .
Length = 72
Score = 25.8 bits (57), Expect = 5.5
Identities = 9/47 (19%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNF 187
+ + +P + L++ FE G++ + ++ + KG V+F
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDVKGI-FVKKLLS---KGIVIVSF 46
>gnl|CDD|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM1 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa,which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 74
Score = 25.9 bits (57), Expect = 5.7
Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 138 SHSIFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQ 174
S ++++GN+P +EL S G I+NVR++ ++
Sbjct: 1 SRTVYLGNLPPNTTVKELLSHVRS-GPIENVRILPEK 36
>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 = 26.0 bits (58), Expect = 5.8
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 89 KVHEKRTNMNAYVRFKNLESVEKALE-MNG 117
KV + YV+FK +E+ +K ++ +NG
Sbjct: 42 KVDKNSPEGVVYVKFKTVEAAQKCIQALNG 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 = 26.1 bits (58), Expect = 6.4
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVR 169
+++GN+ + EE L + F G + +V+
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVK 32
>gnl|CDD|218780 pfam05854, MC1, Non-histone chromosomal protein MC1. This family
consists of archaeal chromosomal protein MC1 sequences
which protect DNA against thermal denaturation.
Length = 93
Score = 26.0 bits (57), Expect = 6.6
Identities = 9/41 (21%), Positives = 16/41 (39%)
Query: 130 ALTTTKSNSHSIFIGNIPFEAEEEELRKAFESCGEIDNVRL 170
AL N +F G P +A + + + + +RL
Sbjct: 7 ALRDKDGNEIGVFSGKQPRQAALKAANRGESEEADRNRIRL 47
>gnl|CDD|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional.
Length = 243
Score = 27.5 bits (61), Expect = 6.7
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 188 KAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFKVSF 230
KA E+++ F CG I++V +IR YV FK ++
Sbjct: 16 KATEKDVYDFFSHCGAIEHVEIIRSGEYACT---AYVTFKDAY 55
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 25.8 bits (57), Expect = 7.1
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNV 168
I I NIP E+L + G + N
Sbjct: 3 IQISNIPPHVRWEDLDSLLSTYGTVKNC 30
>gnl|CDD|240955 cd12511, RRM2_RBM12_like, RNA recognition motif 2 in RNA-binding
protein RBM12, RBM12B and similar proteins. This
subfamily corresponds to the RRM2 of RBM12 and RBM12B.
RBM12, also termed SH3/WW domain anchor protein in the
nucleus (SWAN), is ubiquitously expressed. It contains
five distinct RNA binding motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two proline-rich regions, and several putative
transmembrane domains. RBM12B shows high sequence
semilarity with RBM12. It contains five distinct RRMs as
well. The biological roles of both RBM12 and RBM12B
remain unclear. .
Length = 73
Score = 25.5 bits (56), Expect = 7.3
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 89 KVHEKRTNMNAYVRFKNLESVEKALEMNGHVIDEHTIRV 127
K H R N NA V+F + ++AL+ + ++ I +
Sbjct: 32 KRHNGRNNGNAIVKFATFQDAKEALKRHRELMGSRYIEL 70
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch
site protein p14 (SF3B14) and similar proteins. This
subfamily corresponds to the RRM of SF3B14 (also termed
p14), a 14 kDa protein subunit of SF3B which is a
multiprotein complex that is an integral part of the U2
small nuclear ribonucleoprotein (snRNP) and the U11/U12
di-snRNP. SF3B is essential for the accurate excision of
introns from pre-messenger RNA and has been involved in
the recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B14 associates directly
with another SF3B subunit called SF3B155. It is also
present in both U2- and U12-dependent spliceosomes and
may contribute to branch site positioning in both the
major and minor spliceosome. Moreover, SF3B14 interacts
directly with the pre-mRNA branch adenosine early in
spliceosome assembly and within the fully assembled
spliceosome. SF3B14 contains one well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 25.7 bits (57), Expect = 7.5
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK 188
+++ N+PF+ EEL F G I +R+ + T +G +V ++
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYE 49
>gnl|CDD|241164 cd12720, RRM_SYNJ2, RNA recognition motif in synaptojanin-2 and
similar proteins. This subgroup corresponds to the RRM
of synaptojanin-2, also termed synaptic
inositol-1,4,5-trisphosphate 5-phosphatase 2, an
ubiquitously expressed central regulatory enzyme in the
phosphoinositide-signaling cascade. As a novel Rac1
effector regulating the early step of clathrin-mediated
endocytosis, synaptojanin-2 acts as a
polyphosphoinositide phosphatase directly and
specifically interacting with Rac1 in a GTP-dependent
manner. It mediates the inhibitory effect of Rac1 on
endocytosis and plays an important role in the
Rac1-mediated control of cell growth. Synaptojanin-2
shows high sequence homology to the N-terminal Sac1p
homology domain, the central inositol 5-phosphatase
domain, the putative RNA recognition motif (RRM) of
synaptojanin-1, but differs in the proline-rich region.
.
Length = 78
Score = 25.5 bits (56), Expect = 7.6
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 149 EAEEEELRKAFESCGEIDNVRLIRDQ 174
E EL + E G++ VR+ Q
Sbjct: 21 EDLRTELLQTLEGYGDVVLVRIAGGQ 46
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 26.5 bits (59), Expect = 8.1
Identities = 17/60 (28%), Positives = 22/60 (36%), Gaps = 13/60 (21%)
Query: 153 EELRKAFESCGEIDNVRLIRDQHTNIGKGFGYVNFK-------------AEEEELRKAFE 199
EL K S G + I I G V+F +EEELR+AF+
Sbjct: 40 NELGKILRSLGFNPSEAEINKLFEEIDAGNETVDFPEFLTVMSVKLKRGDKEEELREAFK 99
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 25.4 bits (56), Expect = 8.5
Identities = 14/60 (23%), Positives = 29/60 (48%), Gaps = 9/60 (15%)
Query: 141 IFIGNIPFEAEEEELRKAF-ESCGEIDNVRLIRDQHTNIGKGFGYVNFKAEEEELRKAFE 199
++IGN+ + E +LR+ F E + +V + + G+ +V+ ++ KA E
Sbjct: 1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVKK-------GGYAFVDC-PDQSWADKAIE 52
>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 = 25.3 bits (56), Expect = 8.7
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 141 IFIGNIPF-EAEEEELRKAFESCGEIDNVRLIRDQHTNIGKGF 182
+ + N+P E EL K E G++D+ + N K F
Sbjct: 3 VRLSNLPEGGYTEAELLKLAEPFGKVDHYIFLP----NRNKAF 41
>gnl|CDD|241163 cd12719, RRM_SYNJ1, RNA recognition motif in synaptojanin-1 and
similar proteins. This subgroup corresponds to the RRM
of synaptojanin-1, also termed synaptojanin, or synaptic
inositol-1,4,5-trisphosphate 5-phosphatase 1, originally
identified as one of the major Grb2-binding proteins
that may participate in synaptic vesicle endocytosis. It
also acts as a Src homology 3 (SH3) domain-binding
brain-specific inositol 5-phosphatase with a putative
role in clathrin-mediated endocytosis. Synaptojanin-1
contains an N-terminal domain homologous to the
cytoplasmic portion of the yeast protein Sac1p, a
central inositol 5-phosphatase domain followed by a
putative RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal proline-rich region mediating the
binding of synaptojanin-1 to various SH3
domain-containing proteins including amphiphysin, SH3p4,
SH3p8, SH3p13, and Grb2. Synaptojanin-1 has two
tissue-specific alternative splicing isoforms,
synaptojanin-145 expressed in brain and synaptojanin-170
expressed in peripheral tissues. Synaptojanin-145 is
very abundant in nerve terminals and may play an
essential role in the clathrin-mediated endocytosis of
synaptic vesicles. In contrast to synaptojanin-145,
synaptojanin-170 contains three unique
asparagine-proline-phenylalanine (NPF) motifs in the
C-terminal region and may functions as a potential
binding partner for Eps15, a clathrin coat-associated
protein acting as a major substrate for the tyrosine
kinase activity of the epidermal growth factor receptor.
.
Length = 77
Score = 25.4 bits (56), Expect = 9.0
Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 25/80 (31%)
Query: 48 NHALSSVTSMFKPYGEVETVRFRSVPVADITLPRKACIKMNKVHEKRTNMNAYVRFKNLE 107
++ + ++ F +GEV +RF VAD KM +V F +
Sbjct: 20 DNLIDALLQQFASFGEVILIRF----VAD---------KM------------WVTFLEGQ 54
Query: 108 SVEKALEMNGHVIDEHTIRV 127
S AL +NG + TI +
Sbjct: 55 SALNALSLNGTEVLGKTITI 74
>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein
Vip1 and similar proteins. This subfamily corresponds
to Vip1, an RNA-binding protein encoded by gene vip1
from fission yeast Schizosaccharomyces pombe. Its
biological role remains unclear. Vip1 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 68
Score = 25.2 bits (55), Expect = 9.5
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 141 IFIGNIPFEAEEEELRKAFESCGEIDNVRLIRDQHT 176
+++ NI + E+++ F CG+I N+ L D +
Sbjct: 1 VYVSNISPKTTEKQISDFFSFCGKISNLDLTNDGES 36
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in yeast.
Yra2p belongs to the evolutionarily conserved REF (RNA
and export factor binding proteins) family of hnRNP-like
proteins. It is a major component of endogenous Yra1p
complexes. It interacts with Yra1p and functions as a
negative regulator of Yra1p. Yra2p consists of two
highly conserved N- and C-terminal boxes and a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 25.4 bits (56), Expect = 9.5
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 13/72 (18%)
Query: 67 VRFRSVP--VADITL-------PRKACIKMNKVHEKRTNMNAYVRFKNLESVEKALEM-N 116
+R ++P V+D T+ K + RT A F++ +EK +E N
Sbjct: 3 LRITNIPLDVSDYTIEDLIKEFGEPVYSKFYDHKDSRT---AVFEFEDPSILEKVVEKYN 59
Query: 117 GHVIDEHTIRVD 128
G ++ I V+
Sbjct: 60 GKELNGAKIEVE 71
>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 = 25.6 bits (57), Expect = 9.5
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 15/68 (22%)
Query: 143 IGNIPFEAEEEELRKAFESCGEIDN---------VRLIRD------QHTNIGKGFGYVNF 187
I N+P +E++L++ F V+++RD KG+G+V F
Sbjct: 5 IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64
Query: 188 KAEEEELR 195
E L+
Sbjct: 65 TNHEHALK 72
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
0.319 0.133 0.376
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,828,655
Number of extensions: 1095000
Number of successful extensions: 1969
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1894
Number of HSP's successfully gapped: 620
Length of query: 239
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 145
Effective length of database: 6,768,326
Effective search space: 981407270
Effective search space used: 981407270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.6 bits)