RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6353
(136 letters)
>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 = 177 bits (449), Expect = 9e-56
Identities = 73/86 (84%), Positives = 80/86 (93%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPK 90
T QSLGYGFVNY RPEDAEKA+N+LNGLRLQNKTIKVSYARPSS+SIKGANLYVSGLPK
Sbjct: 40 VTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPK 99
Query: 91 HMSQQELESLFSPYGRIITSRILCDN 116
M+Q ELES+FSP+G+IITSRIL DN
Sbjct: 100 TMTQHELESIFSPFGQIITSRILSDN 125
Score = 37.6 bits (87), Expect = 8e-04
Identities = 17/40 (42%), Positives = 26/40 (65%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+T Q GYGFV+ ++A AI +LNG L N+ ++VS+
Sbjct: 306 TTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSF 345
Score = 34.9 bits (80), Expect = 0.007
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT--IKVSYAR-PSSESIKG 80
T S G GF+ + + ++A++AI TLNG T I V +A PSS + KG
Sbjct: 127 TGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKG 178
Score = 33.4 bits (76), Expect = 0.024
Identities = 14/34 (41%), Positives = 24/34 (70%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ LP+ M+Q+E+ SLF+ G I + +++ D
Sbjct: 5 NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRD 38
>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 = 92.8 bits (230), Expect = 2e-23
Identities = 40/86 (46%), Positives = 59/86 (68%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKH 91
T S GY FV++ D+++AI LNG+ ++NK +KVSYARP ESIK NLYV+ LP+
Sbjct: 145 TGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT 204
Query: 92 MSQQELESLFSPYGRIITSRILCDNL 117
++ +L+++F YG+I+ IL D L
Sbjct: 205 ITDDQLDTIFGKYGQIVQKNILRDKL 230
Score = 33.8 bits (77), Expect = 0.017
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
G NL V+ LP+ M+ +EL +LF G I T RI+ D
Sbjct: 107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRD 142
>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 = 86.3 bits (214), Expect = 2e-23
Identities = 37/41 (90%), Positives = 37/41 (90%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T QSLGYGFVNY PEDAEKAINTLNGLRLQNKTIKVSYA
Sbjct: 38 VTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSYA 78
Score = 35.1 bits (81), Expect = 0.002
Identities = 15/34 (44%), Positives = 24/34 (70%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ LP++M+Q E+ SLFS G I + +++ D
Sbjct: 3 NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRD 36
>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 = 85.0 bits (211), Expect = 7e-23
Identities = 33/36 (91%), Positives = 35/36 (97%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
ANLYVSGLPK M+QQELE+LFSPYGRIITSRILCDN
Sbjct: 1 ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDN 36
Score = 31.9 bits (73), Expect = 0.024
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT--IKVSYA 71
T S G GF+ + + +AE+AI LNG T I V +A
Sbjct: 37 VTGLSRGVGFIRFDKRIEAERAIKALNGTIPPGATEPITVKFA 79
>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 = 78.2 bits (192), Expect = 4e-20
Identities = 39/44 (88%), Positives = 40/44 (90%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
T QSLGYGFVNY P+DAEKAINTLNGLRLQ KTIKVSYARPSS
Sbjct: 40 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSS 83
Score = 32.0 bits (72), Expect = 0.023
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
NL V+ LP++M+Q+E SLF G I + +++ D + ++ Y
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGY 46
>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 = 77.5 bits (190), Expect = 7e-20
Identities = 37/44 (84%), Positives = 39/44 (88%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
T QSLGYGFVNY P DA+KAINTLNGL+LQ KTIKVSYARPSS
Sbjct: 41 TGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYARPSS 84
Score = 31.2 bits (70), Expect = 0.037
Identities = 15/43 (34%), Positives = 28/43 (65%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
NL V+ LP++M+Q+E +SLF G I + +++ D + ++ Y
Sbjct: 5 NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGY 47
>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 = 75.9 bits (186), Expect = 3e-19
Identities = 37/42 (88%), Positives = 38/42 (90%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T QSLGYGFVNY P+DAEKAINTLNGLRLQ KTIKVSYARP
Sbjct: 42 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 83
Score = 33.2 bits (75), Expect = 0.007
Identities = 16/43 (37%), Positives = 29/43 (67%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
NL V+ LP++M+Q+EL+SLF G I + +++ D + ++ Y
Sbjct: 6 NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGY 48
>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 = 71.7 bits (175), Expect = 1e-17
Identities = 34/42 (80%), Positives = 37/42 (88%)
Query: 33 AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
SLGYGFVNY +DAE+AINTLNGLRLQ+KTIKVSYARPS
Sbjct: 40 GHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTIKVSYARPS 81
Score = 35.4 bits (81), Expect = 0.001
Identities = 17/43 (39%), Positives = 29/43 (67%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
NL V+ LP++M+Q EL SLFS G + +++++ D +A + Y
Sbjct: 3 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGY 45
>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 = 69.7 bits (171), Expect = 6e-17
Identities = 28/45 (62%), Positives = 34/45 (75%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
T S G+GFV+Y EDA++AI TLNGL+LQNK IKV+YARP
Sbjct: 37 RTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYARPGG 81
Score = 31.6 bits (72), Expect = 0.030
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL ++ LP+ ++ +E SLF G + +I+ D
Sbjct: 2 NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRD 35
>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 = 68.1 bits (167), Expect = 3e-16
Identities = 27/40 (67%), Positives = 32/40 (80%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T QSLGYGFV+Y DA+KAINTLNG ++NK +KVSYA
Sbjct: 38 TGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSYA 77
Score = 37.3 bits (87), Expect = 2e-04
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL V+ LP+ M+Q+EL SLF G I + +I+ D
Sbjct: 2 NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRD 35
>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 = 71.0 bits (174), Expect = 2e-15
Identities = 36/96 (37%), Positives = 53/96 (55%), Gaps = 6/96 (6%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV--SYARPSSESIKGANLYVSG 87
T +SLGYG+VN+ P DAE+A+ T+N RL K I++ S PS N++V
Sbjct: 36 SVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKN 95
Query: 88 LPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
L K + + L FS +G I++ ++ D ENGK
Sbjct: 96 LDKSVDNKALFDTFSKFGNILSCKVATD----ENGK 127
Score = 61.4 bits (149), Expect = 6e-12
Identities = 28/90 (31%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI-----KGANLYVS 86
+S GYGFV++ + E A+ AI +NG+ L +K + V E K NLYV
Sbjct: 125 NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVK 184
Query: 87 GLPKHMSQQELESLFSPYGRIITSRILCDN 116
L +++ +L LF+ +G I ++ ++ D
Sbjct: 185 NLDPSVNEDKLRELFAKFGEITSAAVMKDG 214
Score = 60.2 bits (146), Expect = 1e-11
Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 22/104 (21%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRL----QNKTIKVSYARPSSE------------- 76
+S G+ FVN+ + EDA KA+ +NG ++ + K + V A+ +E
Sbjct: 217 RSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQ 276
Query: 77 -----SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+G NLYV L ++ ++L LFS G I +++++ D
Sbjct: 277 QERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD 320
Score = 37.9 bits (88), Expect = 7e-04
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
V L S G+GFV + PE+A +A+ ++G L K + V+ A
Sbjct: 317 VMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA 361
>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 = 64.4 bits (156), Expect = 1e-14
Identities = 31/41 (75%), Positives = 35/41 (85%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
SI+ ANLYVSGLPK M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 2 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV 42
Score = 27.1 bits (59), Expect = 1.6
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT--IKVSYARPSSE 76
T S G GF+ + + +AE+AI LNG + T I V +A S+
Sbjct: 43 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPPGATEPITVKFANNPSQ 89
>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 = 62.3 bits (151), Expect = 5e-14
Identities = 29/37 (78%), Positives = 32/37 (86%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
ANLYVSGLPK MSQ+E+E LFS YGRIITSRIL D +
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQV 38
Score = 26.1 bits (57), Expect = 3.0
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG 58
T S G GF+ + + +AE+AI LNG
Sbjct: 39 TGISRGVGFIRFDKRIEAEEAIKGLNG 65
>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 = 61.3 bits (148), Expect = 2e-13
Identities = 29/39 (74%), Positives = 33/39 (84%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
+ ANLYVSGLPK M+Q+ELE LFS YGRIITSRIL D +
Sbjct: 1 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV 39
Score = 26.6 bits (58), Expect = 2.0
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT--IKVSYA 71
T S G GF+ + + +AE+AI LNG + I V +A
Sbjct: 40 TGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAAEPITVKFA 81
>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 = 60.7 bits (147), Expect = 2e-13
Identities = 30/37 (81%), Positives = 32/37 (86%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
ANLYVSGLPK M+Q+ELE LFS YGRIITSRIL D L
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQL 37
Score = 29.9 bits (67), Expect = 0.10
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG 58
T S G GF+ + + +AE+AI LNG
Sbjct: 38 TGVSRGVGFIRFDKRIEAEEAIKGLNG 64
>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 = 56.9 bits (137), Expect = 7e-12
Identities = 21/35 (60%), Positives = 30/35 (85%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
ANLY+SGLP+ M+Q+++E +FS +GRII SR+L D
Sbjct: 1 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVD 35
Score = 25.4 bits (55), Expect = 5.3
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNG 58
+T S G F+ + + +AE+AI + NG
Sbjct: 37 ATGLSRGVAFIRFDKRSEAEEAITSFNG 64
>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 = 55.0 bits (133), Expect = 4e-11
Identities = 20/41 (48%), Positives = 30/41 (73%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
NLY+S LP HM +Q+LE++ PYG++I++RIL D+ G
Sbjct: 2 NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRG 42
>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 = 50.9 bits (121), Expect = 2e-09
Identities = 21/52 (40%), Positives = 35/52 (67%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER 133
NLY+S LP M +QELE++ P+G++I++RIL D+ T G ++ + E+
Sbjct: 2 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEK 53
>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 = 50.2 bits (121), Expect = 2e-09
Identities = 19/41 (46%), Positives = 25/41 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T QS G+ FV +H EDAE+AI LNG N + V +A+
Sbjct: 37 TGQSRGFAFVTFHTREDAERAIEKLNGFGYDNLILSVEWAK 77
Score = 26.3 bits (59), Expect = 2.1
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 85 VSGLPKHMSQQELESLFSPYGRIITSRI 112
V+ L + + +L LF P+G I SR+
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPI--SRV 29
>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 = 50.4 bits (120), Expect = 3e-09
Identities = 22/52 (42%), Positives = 34/52 (65%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER 133
NLY+S LP M +QELES+ P+G++I++RIL D T G ++ + E+
Sbjct: 2 NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEK 53
>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 = 49.8 bits (120), Expect = 3e-09
Identities = 15/28 (53%), Positives = 22/28 (78%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLN 57
+ T +SLGY +VN+ P DAE+A++TLN
Sbjct: 35 LITRRSLGYAYVNFQNPADAERALDTLN 62
Score = 27.9 bits (63), Expect = 0.60
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLAT 119
LYV L +++ L +FSP G +++ R+ C +L T
Sbjct: 2 LYVGDLHPDVTEAMLYEIFSPAGPVLSIRV-CRDLIT 37
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 53.0 bits (126), Expect = 4e-09
Identities = 32/105 (30%), Positives = 48/105 (45%), Gaps = 24/105 (22%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI------------- 78
T +S G+ FV + E AEKAI LNG L+ + ++V A+P+S+
Sbjct: 153 TGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAK 212
Query: 79 -----------KGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
K NLYV LP +++EL LF G I+ + +
Sbjct: 213 KLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASL 257
Score = 36.1 bits (82), Expect = 0.003
Identities = 12/77 (15%), Positives = 25/77 (32%)
Query: 42 NYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLF 101
E + + S + L+V LP +++++L LF
Sbjct: 77 EREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELF 136
Query: 102 SPYGRIITSRILCDNLA 118
+G + R++ D
Sbjct: 137 KKFGPVKRVRLVRDRET 153
>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 = 49.1 bits (118), Expect = 6e-09
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
T +S G+ FV + EDAEKA+ LNG L + ++
Sbjct: 34 ETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRELR 70
Score = 41.8 bits (99), Expect = 4e-06
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
L+V LP ++++L+ LFS +G I + RI+ D G
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKG 40
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 49.1 bits (118), Expect = 6e-09
Identities = 17/37 (45%), Positives = 23/37 (62%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
T +S G+ FV + EDAEKA+ LNG L + +KV
Sbjct: 37 TGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
Score = 43.7 bits (104), Expect = 7e-07
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+V LP +++EL LFS +G++ + R++ D
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRD 34
>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 = 49.2 bits (118), Expect = 6e-09
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
T +S GYGF+ + EDA+KA+ LNG L + IKV
Sbjct: 36 TGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKVG 73
Score = 27.2 bits (61), Expect = 1.1
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
LYV L ++++ +L +F P+G I
Sbjct: 1 LYVGNLHFNITEDDLRGIFEPFGEI 25
>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 = 48.1 bits (115), Expect = 1e-08
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 24 EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
+ + +S G+ FV + PEDAEKA+ LNG L + +KVS
Sbjct: 27 SVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 72
Score = 40.8 bits (96), Expect = 8e-06
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
L+V LP ++++L LFS +G I + RI+ D G
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKG 40
>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 = 48.0 bits (115), Expect = 2e-08
Identities = 17/38 (44%), Positives = 24/38 (63%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
T QS +GFV+Y PE A+ AI +NG ++ K +KV
Sbjct: 36 TGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73
Score = 37.2 bits (87), Expect = 2e-04
Identities = 11/33 (33%), Positives = 22/33 (66%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L++ LP + Q+L LF+P+G +I++++ D
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVD 33
>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 = 47.2 bits (113), Expect = 4e-08
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
S GYGFV++ E A +AI +NG+ L +K + V
Sbjct: 41 GSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75
Score = 33.3 bits (77), Expect = 0.007
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
N+++ L K + + L FS +G I++ ++ D ENG
Sbjct: 3 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATD----ENGG 41
>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 = 47.2 bits (112), Expect = 4e-08
Identities = 18/38 (47%), Positives = 28/38 (73%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+ + YGFV YH+ DAE A+ TLNG +++N I+V++A
Sbjct: 37 KGVNYGFVEYHQSHDAEIALQTLNGRQIENNEIRVNWA 74
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to
the RRM domain of hnRNP G, also termed glycoprotein p43
or RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several
pre-mRNAs. Moreover, hnRNP G may function as a
regulator of transcription for SREBP-1c and GnRH1.
Research has shown that hnRNP G may also act as a
tumor-suppressor since it upregulates the Txnip gene
and promotes the fidelity of DNA end-joining activity.
In addition, hnRNP G appears to play a critical role in
proper neural development of zebrafish and frog
embryos. The family also includes several paralogs of
hnRNP G, such as hRBMY and hnRNP G-T (also termed
RNA-binding motif protein, X-linked-like-2). Both,
hRBMY and hnRNP G-T, are exclusively expressed in
testis and critical for male fertility. Like hnRNP G,
hRBMY and hnRNP G-T interact with factors implicated in
the regulation of pre-mRNA splicing, such as
hTra2-beta1 and T-STAR. Although members in this family
share a high conserved N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), they appear to recognize
different RNA targets. For instance, hRBMY interacts
specifically with a stem-loop structure in which the
loop is formed by the sequence CA/UCAA. In contrast,
hnRNP G associates with single stranded RNA sequences
containing a CCA/C motif. In addition to the RRM, hnRNP
G contains a nascent transcripts targeting domain (NTD)
in the middle region and a novel auxiliary RNA-binding
domain (RBD) in its C-terminal region. The C-terminal
RBD exhibits distinct RNA binding specificity, and
would play a critical role in the regulation of
alternative splicing by hnRNP G. .
Length = 80
Score = 46.8 bits (112), Expect = 4e-08
Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 27 VFLIS---TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
V L+ T +S G+GFV + EDA+ AI LNG L+ + IKV A+
Sbjct: 31 VLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKAK 79
Score = 42.6 bits (101), Expect = 2e-06
Identities = 15/36 (41%), Positives = 24/36 (66%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
G L+VSGL +++ELE+LFS +GR+ ++ D
Sbjct: 1 GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKD 36
>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 = 46.1 bits (110), Expect = 1e-07
Identities = 16/39 (41%), Positives = 22/39 (56%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
Q GY FV + E+AEKA+ +LNG K + V +A
Sbjct: 42 QPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWAH 80
>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 = 46.2 bits (109), Expect = 1e-07
Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYYSGLGGRER 133
NLY+S LP M +QELE++ P+G +I++RIL D G ++ + E+
Sbjct: 3 NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEK 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 = 45.7 bits (109), Expect = 1e-07
Identities = 13/34 (38%), Positives = 25/34 (73%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
N+Y+ GLP + + ++LE L P+G+II+++ + D
Sbjct: 2 NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILD 35
Score = 38.4 bits (90), Expect = 6e-05
Identities = 16/33 (48%), Positives = 20/33 (60%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN 63
T + GYGFV++ PE A KAI LNG +Q
Sbjct: 37 KTNKCKGYGFVDFDSPEAALKAIEGLNGRGVQA 69
>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 = 45.3 bits (108), Expect = 2e-07
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 39 GFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
GFV + + E A++AI LNG +Q +KVS AR
Sbjct: 41 GFVTFEKMESADRAIAELNGTTVQGVQLKVSLAR 74
Score = 29.5 bits (67), Expect = 0.14
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYGRII 108
KG LYV G ++++ L+ FSP+G II
Sbjct: 1 PRKGNTLYVHG--YGLTEEILKKAFSPFGNII 30
>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 = 45.0 bits (107), Expect = 2e-07
Identities = 17/41 (41%), Positives = 26/41 (63%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
++T + GYGFV E+A AI +LNG RL + ++VS+
Sbjct: 37 LTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQVSF 77
Score = 27.3 bits (61), Expect = 1.0
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
G ++V LP + L LFSP+G + +++ D L T K Y
Sbjct: 1 GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRD-LTTNKCKGY 45
>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 = 45.3 bits (108), Expect = 2e-07
Identities = 19/48 (39%), Positives = 25/48 (52%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
+ + Q G+ FV Y EDAE+A LNG LQ I+VS+ P
Sbjct: 35 LAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRVSFGNPG 82
>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 = 44.9 bits (107), Expect = 3e-07
Identities = 18/42 (42%), Positives = 24/42 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T +S G+GFV E+A AI LNG +T+ V+ ARP
Sbjct: 37 TGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEARP 78
Score = 38.0 bits (89), Expect = 1e-04
Identities = 12/34 (35%), Positives = 25/34 (73%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NLYV LP ++++++L+ LF +G + ++R++ D
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITD 34
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is an ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammalian,
such as ovary and testis. It may play an important role
in germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes the yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 44.5 bits (106), Expect = 3e-07
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
S G+GFVN+ E A+KA+ LNG + K + V A
Sbjct: 41 SKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYVGRA 77
Score = 36.4 bits (85), Expect = 5e-04
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 4/42 (9%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
N+YV L + M ++L+ LF YG+I +++++ D + GK
Sbjct: 3 NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD----DEGK 40
>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins.
Length = 56
Score = 43.7 bits (104), Expect = 5e-07
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
G+ FV + E AEKA+ LNG+ + ++V Y+
Sbjct: 22 GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>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 = 46.8 bits (111), Expect = 6e-07
Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGAN 82
T +S G+GF+ +H E+A++A+ +NG L + IKV YA+ S+ + AN
Sbjct: 224 TGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAAN 274
Score = 39.1 bits (91), Expect = 3e-04
Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 13/94 (13%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV-----------SYARPSSESIKGA- 81
+S G +V ++ E KA+ L G L + I V A I
Sbjct: 129 RSKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFL 187
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
LYV L ++++QEL +F P+G I ++ D
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRD 221
>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 = 43.7 bits (104), Expect = 7e-07
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
T GYGFV + EDA+ AI +N ++L K I+V+
Sbjct: 36 TQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRVN 73
>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 = 43.4 bits (103), Expect = 8e-07
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 28 FLI---STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
FL+ ST +S GYGFV Y A KA N L+G ++ + ++V +A
Sbjct: 30 FLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKLQVDWA 76
Score = 30.3 bits (69), Expect = 0.070
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L V LP + ++ L SP+G +
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAV 26
>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 = 43.4 bits (103), Expect = 1e-06
Identities = 17/41 (41%), Positives = 24/41 (58%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T S G+ F++Y E ++ AI +NG L N+ I VSYA
Sbjct: 40 TGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYAF 80
Score = 34.2 bits (79), Expect = 0.003
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
GANL++ L + ++ L FS +G I+ + + + T N K +
Sbjct: 1 GANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGF 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 = 42.6 bits (101), Expect = 2e-06
Identities = 10/43 (23%), Positives = 22/43 (51%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ + G+G+V + EDA++A+ + + I V +A+
Sbjct: 36 GSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFAKK 78
Score = 29.1 bits (66), Expect = 0.19
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L+V LP + ++LE FS G I
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPI 26
>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 = 42.4 bits (100), Expect = 2e-06
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S G+G+V++ PEDA+KAI ++G L + I V ++
Sbjct: 37 TGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76
>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 = 42.5 bits (99), Expect = 3e-06
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
+ + NLY+ GLP + + Q+L L PYG+I++++ + D + Y
Sbjct: 3 DQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGY 51
Score = 30.9 bits (69), Expect = 0.062
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+T + GYGFV++ P A+KA++ L +Q + K P
Sbjct: 44 TTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDP 86
>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 = 42.2 bits (100), Expect = 3e-06
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
+T S GY F Y P ++AI LNG++L +K + V
Sbjct: 36 SATGLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLTV 74
Score = 25.7 bits (57), Expect = 4.3
Identities = 6/25 (24%), Positives = 18/25 (72%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+++ GLP ++S+ +++ L +G++
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKL 27
>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 = 44.7 bits (105), Expect = 3e-06
Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 15/90 (16%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS------------ESIK 79
T + G+ FV Y PE A+ A+ +NG L + IKV RPS+ E K
Sbjct: 145 TGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG--RPSNMPQAQPIIDMVQEEAK 202
Query: 80 GAN-LYVSGLPKHMSQQELESLFSPYGRII 108
N +YV+ + +S+ +++S+F +G I+
Sbjct: 203 KFNRIYVASVHPDLSETDIKSVFEAFGEIV 232
>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 = 41.7 bits (98), Expect = 5e-06
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 5 TLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNK 64
TL + SDA + ++ + + +S GYGFV++ +DAE AIN +NG L ++
Sbjct: 15 TLFAAFSAFP----SCSDARV-MWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSR 69
Query: 65 TIKVSY 70
I+ ++
Sbjct: 70 PIRCNW 75
>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM2 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated apoptosis.
TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 75
Score = 41.6 bits (98), Expect = 5e-06
Identities = 17/39 (43%), Positives = 27/39 (69%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
T +S GYGFV++ + EDAE AI ++NG L + I+ ++
Sbjct: 37 TGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAIRTNW 75
>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 = 41.1 bits (97), Expect = 7e-06
Identities = 16/40 (40%), Positives = 26/40 (65%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S G+GFV + EDA++A LNG+ + + I+V Y+
Sbjct: 37 TGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDYS 76
Score = 24.9 bits (55), Expect = 6.6
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
L V GL + ++++L +FS YG I +++ D
Sbjct: 2 LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQ 35
>gnl|CDD|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast
RNA-binding protein PIN4, fission yeast RNA-binding
post-transcriptional regulators cip1, cip2 and similar
proteins. This subfamily corresponds to the RRM in
PIN4, also termed psi inducibility protein 4 or
modifier of damage tolerance Mdt1, a novel
phosphothreonine (pThr)-containing protein that
specifically interacts with the pThr-binding site of
the Rad53 FHA1 domain. It is encoded by gene MDT1
(YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is
involved in normal G2/M cell cycle progression in the
absence of DNA damage and functions as a novel target
of checkpoint-dependent cell cycle arrest pathways. It
contains an N-terminal RRM, a nuclear localization
signal, a coiled coil, and a total of 15 SQ/TQ motifs.
cip1 (Csx1-interacting protein 1) and cip2
(Csx1-interacting protein 2) are novel cytoplasmic
RRM-containing proteins that counteract Csx1 function
during oxidative stress. They are not essential for
viability in fission yeast Schizosaccharomyces pombe.
Both cip1 and cip2 contain one RRM. Like PIN4, Cip2
also possesses an R3H motif that may function in
sequence-specific binding to single-stranded nucleic
acids. .
Length = 79
Score = 40.9 bits (96), Expect = 9e-06
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
G F N+ PE+A+ + LNG + + ++V Y R
Sbjct: 44 GLAFANFRSPEEAQTVVEALNGYEISGRRLRVEYKR 79
>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 = 41.0 bits (97), Expect = 1e-05
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T GY + Y ++A+ AI LNG L +TI V +A
Sbjct: 44 TGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVDWA 83
>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in
CELF/Bruno-like family of RNA binding proteins and plant
flowering time control protein FCA. This subfamily
corresponds to the RRM1 and RRM2 domains of the CUGBP1
and ETR-3-like factors (CELF) as well as plant flowering
time control protein FCA. CELF, also termed BRUNOL
(Bruno-like) proteins, is a family of structurally
related RNA-binding proteins involved in regulation of
pre-mRNA splicing in the nucleus, and control of mRNA
translation and deadenylation in the cytoplasm. The
family contains six members: CELF-1 (also known as
BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known
as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also
known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4
(BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6).
They all contain three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The low sequence
conservation of the linker region is highly suggestive
of a large variety in the co-factors that associate with
the various CELF family members. Based on both, sequence
similarity and function, the CELF family can be divided
into two subfamilies, the first containing CELFs 1 and
2, and the second containing CELFs 3, 4, 5, and 6. The
different CELF proteins may act through different sites
on at least some substrates. Furthermore, CELF proteins
may interact with each other in varying combinations to
influence alternative splicing in different contexts.
This subfamily also includes plant flowering time
control protein FCA that functions in the
posttranscriptional regulation of transcripts involved
in the flowering process. FCA contains two RRMs, and a
WW protein interaction domain. .
Length = 77
Score = 40.6 bits (96), Expect = 1e-05
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L+V LPK +++++ +LF YG I
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNI 26
Score = 32.1 bits (74), Expect = 0.016
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 27 VFLI---STAQSLGYGFVNYHRPEDAEKAINTLNG 58
V +I T QS G FV + E+A+KAI L+G
Sbjct: 29 VTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63
>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 = 40.6 bits (95), Expect = 1e-05
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T +S GYGFV + EDA++A+ L +L + +++ A
Sbjct: 37 TGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRLDIAER 78
>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 = 40.4 bits (95), Expect = 2e-05
Identities = 18/70 (25%), Positives = 29/70 (41%)
Query: 4 QTLLNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN 63
+ L L +E V + + F + LG + + PE AEK + LNG +N
Sbjct: 14 EDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKVVKDLNGKVFKN 73
Query: 64 KTIKVSYARP 73
+ + V P
Sbjct: 74 RKLFVKLHVP 83
>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 = 40.3 bits (95), Expect = 2e-05
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
G NLYV L + + L FSP+G I +++++ D E G+
Sbjct: 1 GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD----EKGR 40
Score = 37.6 bits (88), Expect = 1e-04
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+S G+GFV + PE+A KA+ +NG + K + V+ A
Sbjct: 40 RSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALA 77
>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 = 39.9 bits (94), Expect = 2e-05
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
+S G+G V + PEDA++AI NG L+ + ++V
Sbjct: 37 RSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71
Score = 29.2 bits (66), Expect = 0.18
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
++V LP ++ Q+L+ LF G ++ + + DN
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN 34
>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 = 40.3 bits (94), Expect = 2e-05
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
NLYV+ LP+ +++ EL +F YG I+ +L D
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKS 37
Score = 29.1 bits (65), Expect = 0.26
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKT--IKVSYA 71
ST G FV Y + E+A+ AI++LNG T + V YA
Sbjct: 37 STGLPRGVAFVRYDKREEAQAAISSLNGTIPPGSTMPLSVRYA 79
>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 = 39.9 bits (94), Expect = 2e-05
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
G+ FV + P DAE A+ L+G R+ ++V +R
Sbjct: 37 GFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELSRG 73
Score = 29.1 bits (66), Expect = 0.19
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIIT 109
+YV L +++ELE F YG + +
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRS 28
>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 = 39.8 bits (94), Expect = 2e-05
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
GY +V + PEDAEKAI ++G ++ + + V
Sbjct: 38 LPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73
>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 = 39.5 bits (93), Expect = 2e-05
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
G+ FV + DAEKAI +NG +++ + + V +A
Sbjct: 41 GFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVDWA 75
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich
splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or
SRp55). The second subgroup is composed of
serine/arginine-rich splicing factor 1 (SRSF1 or
ASF-1), serine/arginine-rich splicing factor 9 (SRSF9
or SRp30C) and plant pre-mRNA-splicing factor SF2
(SR1). These SR proteins are mainly involved in
regulating constitutive and alternative pre-mRNA
splicing. They also have been implicated in
transcription, genomic stability, mRNA export and
translation. All SR proteins in this family, except
SRSF5, undergo nucleocytoplasmic shuttling, suggesting
their widespread roles in gene expression. These SR
proteins share a common domain architecture comprising
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal
RS domains rich in serine-arginine dipeptides. Both
domains can directly contact with RNA. The RRMs appear
to determine the binding specificity and the SR domain
also mediates protein-protein interactions. In
addition, this subfamily includes the yeast nucleolar
protein 3 (Npl3p), also termed mitochondrial targeting
suppressor 1 protein, or nuclear polyadenylated
RNA-binding protein 1. It is a major yeast RNA-binding
protein that competes with 3'-end processing factors,
such as Rna15, for binding to the nascent RNA,
protecting the transcript from premature termination
and coordinating transcription termination and the
packaging of the fully processed transcript for export.
It specifically recognizes a class of G/U-rich RNAs.
Npl3p is a multi-domain protein with two RRMs,
separated by a short linker and a C-terminal domain
rich in glycine, arginine and serine residues. .
Length = 71
Score = 39.5 bits (93), Expect = 3e-05
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G G V + ED E+A+ L+G + + ++V
Sbjct: 38 GEGVVEFTSQEDMERALRKLDGTEFRGRRVRV 69
>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 = 39.3 bits (92), Expect = 3e-05
Identities = 17/39 (43%), Positives = 22/39 (56%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
GY FV+ A+KAI LNG LQ K I+V ++ P
Sbjct: 35 GYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSVPKK 73
>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 = 39.1 bits (92), Expect = 3e-05
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
+YV LP ++++EL+ FSP+G I R+
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRV 32
Score = 33.0 bits (76), Expect = 0.006
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
GY FV + E A AI +NG + +T+K S+ +
Sbjct: 37 GYAFVRFDTHEAAATAIVAVNGTSINGQTVKCSWGK 72
>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 = 38.7 bits (91), Expect = 5e-05
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
G+ FV + PEDA AI+ +N L +TI+V+
Sbjct: 41 GFAFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73
Score = 29.9 bits (68), Expect = 0.091
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
LYV GL + + ++ L + F P+G I
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIK 26
>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 = 38.7 bits (91), Expect = 6e-05
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
S+GYGFV + E A+KA+ L G L +++
Sbjct: 46 SMGYGFVEFKSKEAAQKALKRLQGTVLDGHALELKL 81
>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 = 38.4 bits (90), Expect = 6e-05
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + GYGF + E A AI LNG + ++V +A
Sbjct: 36 TGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDFA 75
Score = 24.9 bits (55), Expect = 7.5
Identities = 10/40 (25%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 84 YVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
+V +P ++++L +FS G +++ R++ D + GK
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDR---DTGK 38
>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 = 38.4 bits (90), Expect = 8e-05
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
Y FV++ +DA KA+ +NG L+ I+VS A+P
Sbjct: 37 YAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAKP 72
Score = 26.0 bits (58), Expect = 2.3
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
LYV LP ++++L LFS YG +
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEV 28
>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 = 37.8 bits (88), Expect = 1e-04
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+ F+ + E A+ AI TLNG + IKV
Sbjct: 38 PHAFITFENLEAAQLAIETLNGASVDGNCIKVQR 71
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 37.9 bits (89), Expect = 1e-04
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 19 GFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
+ E + + + G+ FV + PEDAE A+ LNGL L +T++
Sbjct: 21 PYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTLR 69
Score = 36.8 bits (86), Expect = 3e-04
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
LYV LP +++++L FSPYG++ R++ +
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN 33
>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 = 38.3 bits (89), Expect = 1e-04
Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 19/75 (25%)
Query: 10 LFTYEKVHL--GFSDAEIC-VFL-----IS--------TAQSLGYGFVNYHRPEDAEKAI 53
LF Y HL F DAE+ +FL IS T QS +GFV++ P A+ AI
Sbjct: 7 LFIY---HLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAI 63
Query: 54 NTLNGLRLQNKTIKV 68
+NG ++ K +KV
Sbjct: 64 QAMNGFQIGMKRLKV 78
Score = 37.9 bits (88), Expect = 1e-04
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
G NL++ LP+ EL +F P+G +I++++ D AT K
Sbjct: 4 GCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDR-ATNQSK 46
>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 = 37.9 bits (88), Expect = 1e-04
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
T +S G+GFV + P+DA+ A+ +NG + + I+V A S
Sbjct: 38 TQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQAGKS 80
Score = 29.8 bits (67), Expect = 0.14
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRI 107
L++ GL ++Q LE +FS YG+I
Sbjct: 1 GKLFIGGLSFDTNEQSLEQVFSKYGQI 27
>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 = 1e-04
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
S G+GFV + DA++A L+G ++ + I+V+ A
Sbjct: 39 SKGFGFVTFANSADADRAREKLHGTVVEGRKIEVNNA 75
Score = 29.3 bits (66), Expect = 0.20
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
L+VS +P +L +F +G I+ I+
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEII 33
>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 = 37.8 bits (87), Expect = 1e-04
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 21 SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
SDA + V ++T +S GYGFV++ DAE AI + G L + I+ ++A
Sbjct: 29 SDARV-VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 78
Score = 28.9 bits (64), Expect = 0.26
Identities = 13/44 (29%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
+++V L ++ ++++ F+P+GRI +R++ D +AT K Y
Sbjct: 3 HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKD-MATGKSKGY 45
>gnl|CDD|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF
family. This subfamily corresponds to the RRM of
Aly/REF family which includes THO complex subunit 4
(THOC4, also termed Aly/REF), S6K1 Aly/REF-like target
(SKAR, also termed PDIP3 or PDIP46) and similar
proteins. THOC4 is an mRNA transporter protein with a
well conserved RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It is involved in RNA transportation from the
nucleus, and was initially identified as a
transcription coactivator of LEF-1 and AML-1 for the
TCRalpha enhancer function. In addition, THOC4
specifically binds to rhesus (RH) promoter in
erythroid, and might be a novel transcription cofactor
for erythroid-specific genes. SKAR shows high sequence
homology with THOC4 and possesses one RRM as well. SKAR
is widely expressed and localizes to the nucleus. It
may be a critical player in the function of S6K1 in
cell and organism growth control by binding the
activated, hyperphosphorylated form of S6K1 but not
S6K2. Furthermore, SKAR functions as a protein partner
of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. .
Length = 75
Score = 37.6 bits (88), Expect = 1e-04
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
+ +S G V + + EDAE+AI NG+ L + ++V
Sbjct: 37 SGRSEGTADVVFEKREDAERAIKQFNGVLLDGQPMQVE 74
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed
in the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 37.8 bits (88), Expect = 1e-04
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
G +V Y A +A+ ++G ++ KTI V+ + P
Sbjct: 44 GLAYVEYENESSASQAVLKMDGTEIKEKTISVAISNP 80
Score = 33.9 bits (78), Expect = 0.004
Identities = 15/34 (44%), Positives = 24/34 (70%), Gaps = 5/34 (14%)
Query: 83 LYVSGLPKHMSQQELESLFSPYG-----RIITSR 111
L+VSGLP ++++ELE LF +G R++T+R
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR 38
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 39.9 bits (93), Expect = 2e-04
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 10/89 (11%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA----RPSSESIKGANLYV 85
I+T S GY F Y P + AI LNG + + V A ++ V
Sbjct: 331 IATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPV 390
Query: 86 SGLPKHMSQQELESLFSPYGRIITSRILC 114
+ L K +SQ S+ G+ ++++
Sbjct: 391 TLLAKALSQ----SILQIGGK--PTKVVQ 413
>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 = 37.5 bits (88), Expect = 2e-04
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLR---LQNKTIKVSYA 71
T S G+ FV + EDA + ++ LN L + + ++VSYA
Sbjct: 42 TGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 84
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine
kinase that is activated during Fas-mediated
apoptosis.TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both,
TIA-1 and TIAR, bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 37.3 bits (87), Expect = 2e-04
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
Y FV Y+ A A+ T+NG + + IKV++A
Sbjct: 39 YAFVEYYDHRSAAAALQTMNGRLILGQEIKVNWA 72
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 37.7 bits (87), Expect = 2e-04
Identities = 13/40 (32%), Positives = 26/40 (65%)
Query: 76 ESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
E +GANL++ LP+ Q+L +F P+G ++++++ D
Sbjct: 3 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 42
Score = 37.3 bits (86), Expect = 2e-04
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSES 77
+GFV+Y P A+ AI +NG ++ K +KV R ++S
Sbjct: 51 FGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKRSKNDS 90
>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 = 36.9 bits (86), Expect = 2e-04
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
T +S G+ FV++ PE A KA + L+G Q + + V
Sbjct: 36 ETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73
Score = 30.0 bits (68), Expect = 0.098
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
L+V LP +++EL LF +G I + D
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDK 35
>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 = 36.9 bits (86), Expect = 3e-04
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
V Y PE A++A+N LNG + +KVSY
Sbjct: 43 NVTYESPEQAQQAVNKLNGHEYEGSKLKVSY 73
Score = 31.5 bits (72), Expect = 0.029
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 85 VSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
+S +P H+ ++L+SL S YG + C+ + T++
Sbjct: 5 ISNIPPHVRWEDLDSLLSTYGTV----KNCEQVPTKSETA 40
>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 = 36.9 bits (86), Expect = 3e-04
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
G+GFV + P DA+ A+ LNG L + + V +AR
Sbjct: 34 GFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70
Score = 25.8 bits (57), Expect = 3.4
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+Y+ LP ++++E F YGRI
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRI 26
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit B (eIF-3B) and
similar proteins. This subfamily corresponds to the
RRM domain in eukaryotic translation initiation factor
3 (eIF-3), a large multisubunit complex that plays a
central role in the initiation of translation by
binding to the 40 S ribosomal subunit and promoting the
binding of methionyl-tRNAi and mRNA. eIF-3B, also
termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta,
eIF-3 p110, or eIF-3 p116, is the major scaffolding
subunit of eIF-3. It interacts with eIF-3 subunits A,
G, I, and J. eIF-3B contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
involved in the interaction with eIF-3J. The
interaction between eIF-3B and eIF-3J is crucial for
the eIF-3 recruitment to the 40 S ribosomal subunit.
eIF-3B also binds directly to domain III of the
internal ribosome-entry site (IRES) element of
hepatitis-C virus (HCV) RNA through its N-terminal RRM,
which may play a critical role in both cap-dependent
and cap-independent translation. Additional research
has shown that eIF-3B may function as an oncogene in
glioma cells and can be served as a potential
therapeutic target for anti-glioma therapy. This family
also includes the yeast homolog of eIF-3 subunit B
(eIF-3B, also termed PRT1 or eIF-3 p90) that interacts
with the yeast homologs of eIF-3 subunits A(TIF32),
G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast,
eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A
(TIF32) and eIF-3J (HCR1). In contrast to its human
homolog, yeast eIF-3B (PRT1) may have potential to bind
its total RNA through its RRM domain. .
Length = 84
Score = 37.2 bits (87), Expect = 3e-04
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRL 61
++ GY FV + PE+A++A+ LNG +L
Sbjct: 48 KTKGYAFVEFATPEEAKEAVKALNGYKL 75
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 89
Score = 37.2 bits (87), Expect = 3e-04
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 34 QSLGYG--FVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
G G FV + EDA+KA L G + +T+ S
Sbjct: 52 DVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVVAS 89
>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 = 37.0 bits (85), Expect = 3e-04
Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 21 SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
SDA + V ++T +S GYGFV+++ DAE AI + G L + I+ ++A
Sbjct: 29 SDARV-VKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWA 78
Score = 26.6 bits (58), Expect = 2.2
Identities = 13/44 (29%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
+++V L ++ ++++S F+P+G+I +R++ D +AT K Y
Sbjct: 3 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKD-MATGKSKGY 45
>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 = 36.7 bits (84), Expect = 3e-04
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NLY+ GLP + Q+L L PYG+I++++ + D
Sbjct: 6 NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILD 39
Score = 30.9 bits (69), Expect = 0.051
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
+T Q GYGFV++ P A+KA+ +L +Q + K
Sbjct: 41 NTNQCKGYGFVDFDSPAAAQKAVASLKANGVQAQMAK 77
>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 = 36.8 bits (86), Expect = 4e-04
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
T +S GYGFV++ P D KA+ +NG + N+ IK+
Sbjct: 43 RTGKSKGYGFVSFSDPNDYLKAMKEMNGKYVGNRPIKLR 81
>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 = 36.5 bits (84), Expect = 4e-04
Identities = 11/37 (29%), Positives = 23/37 (62%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+G NL++ LP+ + +L F P+G +I++++ D
Sbjct: 3 EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFID 39
Score = 33.4 bits (76), Expect = 0.006
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
T S +GFV+Y P+ A+ AI +NG ++ K +KV
Sbjct: 42 TNLSKCFGFVSYDNPDSAQAAIQAMNGFQIGTKRLKV 78
>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 = 36.1 bits (84), Expect = 4e-04
Identities = 16/31 (51%), Positives = 17/31 (54%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
YGFV+ EDAE AI LNG K I V
Sbjct: 35 YGFVHMEEEEDAEDAIKALNGYEFMGKRINV 65
Score = 30.3 bits (69), Expect = 0.056
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+V LP + +EL +LF YG + CD
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTE----CD 30
>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold
attachment factor (SAFB) family. This subfamily
corresponds to the RRM domain of the SAFB family,
including scaffold attachment factor B1 (SAFB1),
scaffold attachment factor B2 (SAFB2), SAFB-like
transcriptional modulator (SLTM), and similar proteins,
which are ubiquitously expressed. SAFB1, SAFB2 and SLTM
have been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. They share high sequence
similarities and all contain a scaffold attachment
factor-box (SAF-box, also known as SAP domain)
DNA-binding motif, an RNA recognition motif (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region rich in
glutamine and arginine residues. SAFB1 is a nuclear
protein with a distribution similar to that of SLTM, but
unlike that of SAFB2, which is also found in the
cytoplasm. To a large extent, SAFB1 and SLTM might share
similar functions, such as the inhibition of an
oestrogen reporter gene. The additional cytoplasmic
localization of SAFB2 implies that it could play
additional roles in the cytoplasmic compartment which
are distinct from the nuclear functions shared with
SAFB1 and SLTM. .
Length = 74
Score = 36.2 bits (84), Expect = 5e-04
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
NL+VSGL +L+ LFS YG+++ ++I+ N + + +
Sbjct: 1 NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIV-TNARSPGARCF 43
Score = 28.5 bits (64), Expect = 0.32
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 29 LISTAQSLG---YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
+++ A+S G +GFV E+A K I L+ L + I V
Sbjct: 31 IVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVISV 73
>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 = 36.1 bits (83), Expect = 5e-04
Identities = 14/36 (38%), Positives = 23/36 (63%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
G+GFV + P DA+ A+ L+G L N+ + + +AR
Sbjct: 34 GFGFVEFDDPRDADDAVYELDGKELCNERVTIEHAR 69
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the
RRM of SRSF2 and SRSF8. SRSF2, also termed protein
PR264, or splicing component, 35 kDa (splicing factor
SC35 or SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of
pre-mRNA. It is also involved in transcription
elongation by directly or indirectly mediating the
recruitment of elongation factors to the C-terminal
domain of polymerase II. SRSF2 is exclusively localized
in the nucleus and is restricted to nuclear processes.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory
elements on the pre-mRNA. The RS domain modulates SRSF2
activity through phosphorylation, directly contacts
RNA, and promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 35.7 bits (83), Expect = 6e-04
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
T +S G+ FV ++ DAE A++ ++G L + ++V
Sbjct: 36 TRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 72
>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 = 36.1 bits (84), Expect = 6e-04
Identities = 13/40 (32%), Positives = 26/40 (65%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S GYGFV + ++ ++A+ +NG+ ++ ++VS A
Sbjct: 40 TGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPMRVSPA 79
>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 = 35.8 bits (82), Expect = 8e-04
Identities = 17/40 (42%), Positives = 26/40 (65%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+T + G+GFV E+A AI +LNG RL +K ++VS+
Sbjct: 38 NTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQVSF 77
>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 = 35.6 bits (82), Expect = 9e-04
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
S+G+GFV + E A+ A+ ++G L T+ V ++
Sbjct: 46 SMGFGFVGFKTKEQAQAALKAMDGFVLDGHTLVVKFSH 83
>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 = 35.2 bits (82), Expect = 0.001
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G+ FV Y+ EDAE A+ LNG +L ++ I+V
Sbjct: 41 GFCFVEYYTREDAENAVKYLNGTKLDDRIIRV 72
Score = 25.2 bits (56), Expect = 6.2
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
LYV L + +++++ LFS G I
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDI 25
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM3 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 86
Score = 35.3 bits (82), Expect = 0.001
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 36 LGYGFVNYHRPEDAEKAINTLNGLRLQN----KTIKVSYAR 72
+GY F+N+ PE AEK NG + +N K ++YAR
Sbjct: 43 VGYAFINFVNPEYAEKFYKAFNGKKWKNFKSKKVCDITYAR 83
>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 = 35.2 bits (81), Expect = 0.001
Identities = 12/25 (48%), Positives = 19/25 (76%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L+V L K +++E+E +FSPYGR+
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRV 26
Score = 34.1 bits (78), Expect = 0.003
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 7 LNKLFTYEKVHLGFSD----AEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGL--- 59
LNK T ++V FS +I + QS G FV Y E A+ AI LNG+
Sbjct: 7 LNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALNGVYTM 66
Query: 60 RLQNKTIKVSYARP 73
R ++ + V +A P
Sbjct: 67 RGCDQPLIVRFADP 80
>gnl|CDD|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM3 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 35.0 bits (80), Expect = 0.001
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
Y FV++ EDA A+N LNG L+ I+V+ A+P
Sbjct: 39 YAFVHFTSREDAVHAMNNLNGTELEGSCIEVTLAKP 74
>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 = 34.7 bits (80), Expect = 0.001
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+ FV + E A +A ++++G L N + V+Y
Sbjct: 34 NFAFVEFESLESAIRAKDSVHGKVLNNNPLYVTY 67
Score = 33.2 bits (76), Expect = 0.006
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
LYV P S+ + +FSPYG +
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAV 26
>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 = 35.0 bits (81), Expect = 0.001
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
G GFV + AE AI L G + I++S+
Sbjct: 38 GCGFVQFVHRAAAEAAIQQLQGTIIGGSRIRLSW 71
Score = 31.9 bits (73), Expect = 0.021
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
++V GL +++ EL SLF P+G I+ +I
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKI 33
>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 = 34.9 bits (80), Expect = 0.001
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
+S G G V + PE AE+A +NG +L + I V R
Sbjct: 37 KSKGCGVVRFESPEVAERACRMMNGYKLNGREIDVRIDR 75
>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 = 34.8 bits (80), Expect = 0.002
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
T S YGF+ + PE A A ++N L K ++V
Sbjct: 37 TGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQVHV 75
Score = 27.8 bits (62), Expect = 0.73
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
+Y+ LP ++EL+ FS +G + R + + T N K+Y
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVR-VARSKKTGNSKHY 43
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to the
RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which
belong to the CUGBP1 and ETR-3-like factors (CELF) or
BRUNOL (Bruno-like) family of RNA-binding proteins that
display dual nuclear and cytoplasmic localizations and
have been implicated in the regulation of pre-mRNA
splicing and in the control of mRNA translation and
deadenylation. CELF-3, expressed in brain and testis
only, is also known as bruno-like protein 1 (BRUNOL-1),
or CAG repeat protein 4, or CUG-BP- and ETR-3-like
factor 3, or embryonic lethal abnormal vision
(ELAV)-type RNA-binding protein 1 (ETR-1), or expanded
repeat domain protein CAG/CTG 4, or trinucleotide
repeat-containing gene 4 protein (TNRC4). It plays an
important role in the pathogenesis of tauopathies.
CELF-3 contains three highly conserved RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains): two consecutive
RRMs (RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein.The effect of
CELF-3 on tau splicing is mediated mainly by the
RNA-binding activity of RRM2. The divergent linker
region might mediate the interaction of CELF-3 with
other proteins regulating its activity or involved in
target recognition. CELF-4, highly expressed throughout
the brain and in glandular tissues, moderately expressed
in heart, skeletal muscle, and liver, is also known as
bruno-like protein 4 (BRUNOL-4), or CUG-BP- and
ETR-3-like factor 4. Like CELF-3, CELF-4 also contain
three highly conserved RRMs. The splicing activation or
repression activity of CELF-4 on some specific
substrates is mediated by its RRM1/RRM2. On the other
hand, both RRM1 and RRM2 of CELF-4 can activate cardiac
troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in
brain, is also known as bruno-like protein 5 (BRUNOL-5),
or CUG-BP- and ETR-3-like factor 5. Although its
biological role remains unclear, CELF-5 shares same
domain architecture with CELF-3. CELF-6, strongly
expressed in kidney, brain, and testis, is also known as
bruno-like protein 6 (BRUNOL-6), or CUG-BP- and
ETR-3-like factor 6. It activates exon inclusion of a
cardiac troponin T minigene in transient transfection
assays in an muscle-specific splicing enhancer
(MSE)-dependent manner and can activate inclusion via
multiple copies of a single element, MSE2. CELF-6 also
promotes skipping of exon 11 of insulin receptor, a
known target of CELF activity that is expressed in
kidney. In additiona to three highly conserved RRMs,
CELF-6 also possesses numerous potential phosphorylation
sites, a potential nuclear localization signal (NLS) at
the C terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 35.1 bits (81), Expect = 0.002
Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 75 SESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
++IK L+V +P+++ +++L LF +G+I +L D
Sbjct: 3 DDAIK---LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKY 42
>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1
complementation factor (ACF). This subgroup
corresponds to the RRM3 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. ACF
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which display high
affinity for an 11 nucleotide AU-rich mooring sequence
3' of the edited cytidine in apoB mRNA. All three RRMs
may be required for complementation of editing activity
in living cells. RRM2/3 are implicated in ACF
interaction with APOBEC-1. .
Length = 83
Score = 35.0 bits (80), Expect = 0.002
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
Y FV++ EDA A+N LNG + I+V+ A+P
Sbjct: 46 YAFVHFSNREDAVDAMNALNGKVIDGSPIEVTLAKP 81
>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 = 34.9 bits (81), Expect = 0.002
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 84 YVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
+V G+P +++EL FS +G + +I+ D G
Sbjct: 6 FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKG 44
Score = 29.5 bits (67), Expect = 0.16
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
S GYGFV + EDAEK + N L + K + + A
Sbjct: 39 AGVSKGYGFVTFETQEDAEKILAMGN-LNFRGKKLNIGPA 77
>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 = 34.6 bits (79), Expect = 0.002
Identities = 14/40 (35%), Positives = 26/40 (65%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S G+ FV + R +D+++A+ NG+ L + I+V Y+
Sbjct: 37 TGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVDYS 76
>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT
transcription complex subunit 4 (NOT4) and similar
proteins. This subfamily corresponds to the RRM of
NOT4, also termed CCR4-associated factor 4, or E3
ubiquitin-protein ligase CNOT4, or potential
transcriptional repressor NOT4Hp, a component of the
CCR4-NOT complex, a global negative regulator of RNA
polymerase II transcription. NOT4 functions as an
ubiquitin-protein ligase (E3). It contains an
N-terminal C4C4 type RING finger motif, followed by a
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RING fingers may interact with a subset of
ubiquitin-conjugating enzymes (E2s), including UbcH5B,
and mediate protein-protein interactions. T.
Length = 98
Score = 34.8 bits (81), Expect = 0.002
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+V Y R EDA + I ++G L + +K S+
Sbjct: 57 YVTYSRKEDALRCIQAVDGFYLDGRLLKASFG 88
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 35.8 bits (82), Expect = 0.002
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA--RPSSESIKGANLYVSG 87
T +S G+GFVN++ A AI+ ++G L + I+V+ A RPS+ G SG
Sbjct: 72 TGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSG 129
>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 = 34.2 bits (79), Expect = 0.002
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
G +V +DA +A+ L ++L K IKV++A
Sbjct: 39 GCAYVCMETRQDAHRALQKLRNVKLAGKKIKVAWAP 74
Score = 26.5 bits (59), Expect = 1.9
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
L++ L K +++++L++LF YG I
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQ 30
>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 = 34.2 bits (79), Expect = 0.003
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI 78
T SL Y F+ + ED E+A ++ + + ++ I V + S+S+
Sbjct: 41 TGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHVDF----SQSV 83
>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 = 35.7 bits (82), Expect = 0.004
Identities = 21/67 (31%), Positives = 32/67 (47%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQEL 97
Y FV++ EDA KA++ LNG L+ I+V+ A+P + +G Q
Sbjct: 271 YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAAR 330
Query: 98 ESLFSPY 104
+SL Y
Sbjct: 331 QSLGQVY 337
Score = 30.7 bits (69), Expect = 0.22
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQN-KTIKVSYARPSSESIKGANLYVSGLPKHM 92
Q+ GY FV + E+A++A+ LN ++ + + V S+ L+V G+PK+
Sbjct: 97 QNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI------SVDNCRLFVGGIPKNK 150
Query: 93 SQQELESLFS 102
++E+ FS
Sbjct: 151 KREEILEEFS 160
Score = 25.7 bits (56), Expect = 9.2
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+G ++V +P+ + + EL LF G I R++ D
Sbjct: 57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD 93
>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 = 33.9 bits (77), Expect = 0.004
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+T + G+GFV ++A AI +LNG RL ++ ++VS+
Sbjct: 40 NTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF 79
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the
RRM of TRMT2A, also known as HpaII tiny fragments locus
9c protein (HTF9C), a novel cell cycle regulated
protein. It is an independent biologic factor expressed
in tumors associated with clinical outcome in HER2
expressing breast cancer. The function of TRMT2A
remains unclear although by sequence homology it has a
RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
related to RNA methyltransferases. .
Length = 79
Score = 33.8 bits (78), Expect = 0.004
Identities = 9/36 (25%), Positives = 20/36 (55%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+ FV + E+ +KA+ L+G + + + + A+P
Sbjct: 44 FAFVTFRSEEERQKALEILDGFKWKGRVLSARLAKP 79
>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 = 33.4 bits (77), Expect = 0.004
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L+V LP ++++E + LFS YG +
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEV 28
Score = 29.6 bits (67), Expect = 0.13
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G+GF+ +AEKA L+G+ + + ++V
Sbjct: 38 GFGFIRLDTRTNAEKAKAELDGIMRKGRQLRV 69
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM2 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 79
Score = 33.5 bits (77), Expect = 0.005
Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 12/66 (18%)
Query: 7 LNKLFT----YEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ 62
L KLF+ +VH+ + +S G+ +V + PEDA KA L+G Q
Sbjct: 19 LEKLFSKFGELSEVHVAIDKK--------SGKSKGFAYVLFLDPEDAVKAYKELDGKVFQ 70
Query: 63 NKTIKV 68
+ I +
Sbjct: 71 GRLIHI 76
Score = 29.7 bits (67), Expect = 0.13
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L+V LP + +LE LFS +G +
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGEL 29
>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 = 33.3 bits (76), Expect = 0.005
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
L+V LP ++QE+ SLF YG+++ I+
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDII 33
Score = 25.6 bits (56), Expect = 3.6
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
YGFV+ A++AI L+ +L I V
Sbjct: 36 YGFVHMDDKTAADEAIRNLHHYKLHGVAINV 66
>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 = 33.9 bits (77), Expect = 0.005
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+T + G+GFV ++A AI +LNG RL ++ ++VS+
Sbjct: 40 NTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF 79
>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 = 33.3 bits (77), Expect = 0.005
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+GFV + EDA++A+ N + I V A
Sbjct: 43 FGFVGFKSEEDAQQAVKYFNKTFIDTSKISVELA 76
>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 = 33.6 bits (77), Expect = 0.005
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T S GYGFV + D ++A+ + G+ + +++S A
Sbjct: 40 TGVSRGYGFVRFSDENDQQRALIEMQGVYCGGRPMRISTA 79
>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 = 33.5 bits (76), Expect = 0.006
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 11 FTYEKVHLGFSDAEICVFL---ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
T++K+ FS +F + +S G G V + PE AEKA +NG+++ + I
Sbjct: 11 LTWQKLKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACRLMNGIKINGREID 70
Query: 68 VSYAR 72
V R
Sbjct: 71 VRLDR 75
Score = 25.0 bits (54), Expect = 6.0
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
++V LP ++ Q+L+ FS G ++ + I ENGK
Sbjct: 2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEI-----KMENGK 37
>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM2 of Nop4p (also known as
Nop77p), encoded by YPL043W from Saccharomyces
cerevisiae. It is an essential nucleolar protein
involved in processing and maturation of 27S pre-rRNA
and biogenesis of 60S ribosomal subunits. Nop4p has
four RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 83
Score = 33.7 bits (77), Expect = 0.006
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
G+ FV + ++AE A+ NGL + + + V +A
Sbjct: 43 GFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDWA 77
>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 = 33.3 bits (77), Expect = 0.006
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSR 111
+ L+V+ P Q ++ LF YG I++ R
Sbjct: 1 STLWVTNFPPSFDQSDIRDLFEQYGEILSIR 31
Score = 27.1 bits (61), Expect = 1.1
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
+V + PE A A+ LNG + + V + P
Sbjct: 45 YVQFTSPESAAAAVALLNGKLGEGYKLVVKISDP 78
>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 = 33.4 bits (77), Expect = 0.006
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S G F+ + EDA K + LN L +T+K S A
Sbjct: 39 TRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKCSIA 78
Score = 28.8 bits (65), Expect = 0.24
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+YVS LP ++ +L +FS YG+++ I+ D
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKD 36
>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM2 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 77
Score = 33.4 bits (76), Expect = 0.006
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 7/71 (9%)
Query: 7 LNKLFT---YEKVHLGFSDAEICVFLI---STAQSLGYGFVNYHRPEDAEKAINTLNGLR 60
L +T +E++ F + E C FL+ +T S GYGFV Y + + A +A + L G +
Sbjct: 7 LPPTYTQQQFEELVRPFGNLERC-FLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLGKQ 65
Query: 61 LQNKTIKVSYA 71
L ++T+ V +
Sbjct: 66 LGSRTLYVHWT 76
Score = 25.7 bits (56), Expect = 3.5
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L ++ LP +QQ+ E L P+G +
Sbjct: 2 LCIANLPPTYTQQQFEELVRPFGNL 26
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 33.1 bits (75), Expect = 0.006
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
C ++ TA + Y FV + A ++ +NG ++ K +KV++A
Sbjct: 29 CKMIMDTAGNDPYCFVEFFEHRHAAASLAAMNGRKIMGKEVKVNWA 74
>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in
fission yeast pre-mRNA-splicing factor Srp1p,
Arabidopsis thaliana arginine/serine-rich-splicing
factor RSp31 and similar proteins. This subfamily
corresponds to the RRM of Srp1p and RRM2 of plant SR
splicing factors. Srp1p is encoded by gene srp1 from
fission yeast Schizosaccharomyces pombe. It plays a
role in the pre-mRNA splicing process, but is not
essential for growth. Srp1p is closely related to the
SR protein family found in Metazoa. It contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a glycine hinge and a RS domain in the middle, and a
C-terminal domain. The family also includes a novel
group of arginine/serine (RS) or serine/arginine (SR)
splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RRMs at their N-terminus and an RS
domain at their C-terminus.
Length = 70
Score = 33.2 bits (76), Expect = 0.006
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
+ FV + EDA KA+ L+G R+ + V + +
Sbjct: 36 FAFVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70
Score = 28.2 bits (63), Expect = 0.36
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 83 LYVSGL-PKHMSQQELESLFSPYGRIITSRI 112
L+V G P ++++E LF P+G ++ I
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI 32
>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 = 33.5 bits (76), Expect = 0.007
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+T + G+GFV ++A AI +LNG RL ++ ++VS+
Sbjct: 38 TTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSF 77
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 33.0 bits (76), Expect = 0.008
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
G+ FV + AE A+ LNG L + I VS
Sbjct: 46 GFAFVTFKDASSAENALQ-LNGTELGGRKISVS 77
Score = 29.1 bits (66), Expect = 0.19
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
+YV L + + +L +FS +G + + RI
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRI 32
>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 = 33.2 bits (75), Expect = 0.008
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NLY+ GL + Q+L L PYG+I++++ + D
Sbjct: 2 TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILD 36
Score = 30.1 bits (67), Expect = 0.083
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
+T + GYGFV++ P A+KA+ L +Q + K
Sbjct: 38 TTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK 74
>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 = 33.0 bits (76), Expect = 0.008
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
GYGF+ Y P+ A+ AI ++N L + ++V A
Sbjct: 43 GYGFIEYENPQSAQDAIASMNLFDLGGQQLRVGKA 77
>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 = 32.5 bits (74), Expect = 0.011
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
Y FV+ R E+A AI LNG ++ + I V
Sbjct: 35 DYAFVHMEREEEALAAIEALNGKEVKGRRINV 66
Score = 25.2 bits (55), Expect = 4.8
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V + + EL LF +GR++ + D
Sbjct: 3 IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD 35
>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 = 32.6 bits (74), Expect = 0.011
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
T S G+GFV++ EDA+ A + + + + +A+P
Sbjct: 35 TGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAKP 76
>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 = 32.2 bits (74), Expect = 0.013
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
GYGFV + EDA A+ NG + + + ++
Sbjct: 36 GYGFVQFDNEEDARAAVAGENGREIAGQKLDIN 68
Score = 31.8 bits (73), Expect = 0.017
Identities = 10/27 (37%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 83 LYVSGLP-KHMSQQELESLFSPYGRII 108
++V L +S+++LE +FS YG+I+
Sbjct: 3 VFVGNLNTDKVSKEDLEEIFSKYGKIL 29
>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 = 32.3 bits (74), Expect = 0.013
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+ F+ + R + A +A+ + N L+NKT+ V Y
Sbjct: 45 FAFIKFEREQAAARAVESENHSMLKNKTMHVQY 77
>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 = 32.2 bits (74), Expect = 0.013
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
T +S GY FV + PE A+ T+N L + +K
Sbjct: 37 TGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLLKCK 74
>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway; it binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 75
Score = 32.3 bits (74), Expect = 0.013
Identities = 9/33 (27%), Positives = 24/33 (72%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V GLP ++++E + FS +G+++ ++++ D
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQD 34
Score = 26.9 bits (60), Expect = 1.1
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T +S G+GFV + E A + + + L L K ++V A
Sbjct: 36 DTGRSRGFGFVTFDS-ESAVERVFSAGMLELGGKQVEVKRA 75
>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 = 32.2 bits (73), Expect = 0.013
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
+GFV + E AI LNG+RL + IKV
Sbjct: 44 FGFVCFKHSESVPYAIALLNGIRLYGRPIKVH 75
>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold
attachment factor B1 (SAFB1), scaffold attachment factor
B2 (SAFB2), and similar proteins. This subgroup
corresponds to RRM of SAFB1, also termed scaffold
attachment factor B (SAF-B), heat-shock protein 27
estrogen response element ERE and TATA-box-binding
protein (HET), or heterogeneous nuclear
ribonucleoprotein hnRNP A1- associated protein (HAP), a
large multi-domain protein with well-described functions
in transcriptional repression, RNA splicing and
metabolism, and a proposed role in chromatin
organization. Based on the numerous functions, SAFB1 has
been implicated in many diverse cellular processes
including cell growth and transformation, stress
response, and apoptosis. SAFB1 specifically binds to
AT-rich scaffold or matrix attachment region DNA
elements (S/MAR DNA) by using its N-terminal scaffold
attachment factor-box (SAF-box, also known as SAP
domain), a homeodomain-like DNA binding motif. The
central region of SAFB1 is composed of an RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a nuclear
localization signal (NLS). The C-terminus of SAFB1
contains Glu/Arg- and Gly-rich regions that might be
involved in protein-protein interaction. Additional
studies indicate that the C-terminal region contains a
potent and transferable transcriptional repression
domain. Another family member is SAFB2, a homolog of
SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed
and share very high sequence similarity, suggesting that
they might function in a similar manner. However, unlike
SAFB1, exclusively existing in the nucleus, SAFB2 is
also present in the cytoplasm. The additional
cytoplasmic localization of SAFB2 implies that it could
play additional roles in the cytoplasmic compartment
which are distinct from the nuclear functions shared
with SAFB1.
Length = 76
Score = 32.4 bits (73), Expect = 0.014
Identities = 13/36 (36%), Positives = 25/36 (69%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
G NL+VSGL +L++LFS YG+++ ++++ +
Sbjct: 1 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTN 36
Score = 26.6 bits (58), Expect = 1.6
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 29 LISTAQSLG---YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
+++ A+S G YGFV E+A K IN L+ L + I V
Sbjct: 33 VVTNARSPGARCYGFVTMSTSEEATKCINHLHRTELHGRMISV 75
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. It interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20, and may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM11 is a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. It is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. Both, RBM7 and RBM11, contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 32.3 bits (74), Expect = 0.014
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
+ + FV + AI LNG+RL + +++
Sbjct: 40 KPKSFAFVTFKHEVSVPYAIQLLNGIRLFGRELRIK 75
>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 = 32.3 bits (73), Expect = 0.015
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
GYGFV + DA+ A+ LNG L + + V +AR
Sbjct: 34 GYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHAR 69
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 32.3 bits (73), Expect = 0.015
Identities = 13/36 (36%), Positives = 23/36 (63%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
Y FV++ EDA A++ +NG + +I+V+ A+P
Sbjct: 39 YAFVHFFNREDAVAAMSVMNGKCIDGASIEVTLAKP 74
>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 = 32.1 bits (73), Expect = 0.016
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
S GYGFV + EDA+K + N L ++K + + A
Sbjct: 42 SKGYGFVTFETQEDAQKILQEANRLCFRDKKLNIGQA 78
>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM4 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 = 68
Score = 31.9 bits (73), Expect = 0.016
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
YG+ Y E AE+AI TL+G + +KV
Sbjct: 37 YGYAKYADRESAERAITTLHGKEVNGVKLKV 67
>gnl|CDD|241074 cd12630, RRM2_IGF2BP3, RNA recognition motif 2 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 3
(IGF2BP3). This subgroup corresponds to the RRM2 of
IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also
termed KH domain-containing protein overexpressed in
cancer (KOC), or VICKZ family member 3, an RNA-binding
protein that plays an important role in the
differentiation process during early embryogenesis. It
is known to bind to and repress the translation of IGF2
leader 3 mRNA. IGF2BP3 also acts as a
Glioblastoma-specific proproliferative and proinvasive
marker acting through IGF2 resulting in the activation
of oncogenic phosphatidylinositol
3-kinase/mitogen-activated protein kinase (PI3K/MAPK)
pathways. IGF2BP3 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 76
Score = 31.9 bits (72), Expect = 0.019
Identities = 12/30 (40%), Positives = 21/30 (70%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
V Y + A +A++ LNG +L+N ++KV+Y
Sbjct: 44 VTYGNKDQARQALDKLNGFQLENYSLKVAY 73
>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 = 31.9 bits (73), Expect = 0.019
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+YV LPK+ + + L+++FS YG +
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTV 26
Score = 25.8 bits (57), Expect = 3.9
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLN 57
T G+ F+ + PE+A+KA LN
Sbjct: 36 HTGDIKGFAFIEFETPEEAQKACKHLN 62
>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 = 32.0 bits (73), Expect = 0.020
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G+ FV Y PE A+ A+ +NG+ L + IKV
Sbjct: 43 GFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74
>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 = 31.8 bits (73), Expect = 0.020
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIK 67
T +S GYGFV + E AE+A+ +LNG + N +
Sbjct: 36 QTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNTQQR 72
>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subfamily corresponds to the RRM1 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, which is an essential
splicing regulatory serine/arginine (SR) protein that
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.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal SR domains rich in
serine-arginine dipeptides. .
Length = 70
Score = 31.8 bits (72), Expect = 0.023
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
GYGFV + DA+ A+ LNG L + + V +AR
Sbjct: 34 GYGFVEFEDSRDADDAVYELNGKDLCGERVIVEHAR 69
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 32.1 bits (73), Expect = 0.023
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 83 LYVSGLPKHMSQQELESLFSPYG 105
LY+S LP +Q ELES F+ YG
Sbjct: 3 LYISNLPPDTTQLELESWFTQYG 25
>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 = 32.0 bits (73), Expect = 0.023
Identities = 11/41 (26%), Positives = 22/41 (53%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T + G+ +V + DAE A+ L+ R + I++ +A+
Sbjct: 38 TRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEIQFAQ 78
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2
protein homolog beta (TRA-2 beta) and similar proteins.
This subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 31.9 bits (72), Expect = 0.024
Identities = 14/50 (28%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 23 AEIC-VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
A++ V+ + +S G+ FV + +DA++A NG+ L + I+V ++
Sbjct: 37 ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 86
>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 = 31.8 bits (73), Expect = 0.024
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQN-KTIKVS 69
GY FV Y E A++A+ L+ ++ K + V
Sbjct: 43 GYAFVTYTNKEAAQRAVKQLHNYEIRPGKRLGVC 76
Score = 26.0 bits (58), Expect = 3.1
Identities = 12/46 (26%), Positives = 21/46 (45%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
G ++V +P+ + + EL LF G I R++ D G +
Sbjct: 1 GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAF 46
>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 = 31.9 bits (73), Expect = 0.025
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 27 VFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLR-LQNKTIKVSYARP 73
V L S GYGFV + + ++A+ + G L K I+VS A P
Sbjct: 34 VVLDQNGNSRGYGFVRFSDESEQKRALTEMQGASGLGGKPIRVSLAIP 81
>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 = 31.7 bits (73), Expect = 0.026
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIIT 109
N+YVSGLP ++ +E +FS G I
Sbjct: 3 NVYVSGLPLDITVEEFVEVFSKCGIIKE 30
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM1 of nucleolysin TIAR, also termed TIA-1-related
protein, and a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 81
Score = 31.6 bits (71), Expect = 0.029
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 26 CVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA-RPSSE 76
C + + Y FV ++ DA A+ +NG ++ K +KV++A PSS+
Sbjct: 29 CKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 80
>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant
pre-mRNA-splicing factor SF2 and similar proteins. This
subgroup corresponds to the RRM1 of SF2, also termed SR1
protein, a plant serine/arginine (SR)-rich
phosphoprotein similar to the mammalian splicing factor
SF2/ASF. It promotes splice site switching in mammalian
nuclear extracts. SF2 contains two N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a C-terminal domain rich in proline, serine and
lysine residues (PSK domain), a composition reminiscent
of histones. This PSK domain harbors a putative
phosphorylation site for the mitotic kinase
cyclin/p34cdc2. .
Length = 72
Score = 31.3 bits (71), Expect = 0.029
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
+YV LP + ++E+E LF YG I+
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIV 27
Score = 26.3 bits (58), Expect = 2.0
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
GY F+ + DAE AI +G + ++V
Sbjct: 39 GYAFIEFEDARDAEDAIRGRDGYDFDGQRLRV 70
>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment
factor (SAF)-like transcription modulator (SLTM) and
similar proteins. This subgroup corresponds to the RRM
domain of SLTM, also termed modulator of
estrogen-induced transcription, which shares high
sequence similarity with scaffold attachment factor B1
(SAFB1). It contains a scaffold attachment factor-box
(SAF-box, also known as SAP domain) DNA-binding motif,
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
region rich in glutamine and arginine residues. To a
large extent, SLTM co-localizes with SAFB1 in the
nucleus, which suggests that they share similar
functions, such as the inhibition of an oestrogen
reporter gene. However, rather than mediating a specific
inhibitory effect on oestrogen action, SLTM is shown to
exert a generalized inhibitory effect on gene expression
associated with induction of apoptosis in a wide range
of cell lines. .
Length = 74
Score = 31.2 bits (70), Expect = 0.033
Identities = 11/34 (32%), Positives = 25/34 (73%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
NL+VSGL + +L++LF YG++++++++ +
Sbjct: 1 NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTN 34
>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit
4 (THOC4) and similar proteins. This subgroup
corresponds to the RRM of THOC4, also termed
transcriptional coactivator Aly/REF, or ally of AML-1
and LEF-1, or bZIP-enhancing factor BEF, an mRNA
transporter protein with a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It is
involved in RNA transportation from the nucleus. THOC4
was initially identified as a transcription coactivator
of LEF-1 and AML-1 for the TCRalpha enhancer function.
In addition, THOC4 specifically binds to rhesus (RH)
promoter in erythroid. It might be a novel
transcription cofactor for erythroid-specific genes. .
Length = 75
Score = 31.1 bits (71), Expect = 0.034
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
SLG V + R DA KA+ NG+ L + +K+
Sbjct: 40 SLGTADVVFERRADALKAMKQYNGVPLDGRPMKI 73
>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 = 31.1 bits (71), Expect = 0.036
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L V LPK + + +L LF +G I
Sbjct: 3 LIVKNLPKGIKEDKLRKLFEAFGTI 27
Score = 26.5 bits (59), Expect = 1.9
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
+GFV Y E+A+KA+ N + I V
Sbjct: 42 KFGFVGYKTEEEAQKALKHFNNSFIDTSKITV 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 = 31.0 bits (70), Expect = 0.038
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
+ FV Y EDA KA+ + N ++ ++ I V YA
Sbjct: 36 FAFVQYETQEDATKALESTNMSKVLDRVISVEYA 69
Score = 24.8 bits (54), Expect = 7.9
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 89 PKHMSQQELESLFSPYGRIITSRI 112
P + ++LE F PYG+++ RI
Sbjct: 9 PINTRTRDLERHFEPYGKLVNVRI 32
>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 = 31.2 bits (71), Expect = 0.041
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
L+V LP +++ EL+ F +G ++ RI
Sbjct: 6 LFVGNLPHDITEDELKEFFKEFGNVLEVRI 35
>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 = 31.0 bits (71), Expect = 0.042
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
ST + +GF + PE A +A+ LNGL L K + V
Sbjct: 37 STGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLVK 75
>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM2 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind
to cytoplasmic proteins. Raver-2 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. Raver-2 binds to PTB through the
SLLGEPP motif only, and binds to RNA through its RRMs.
.
Length = 77
Score = 31.0 bits (70), Expect = 0.042
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 13 YEKVHLGFSDAEICVFLIS--TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+E++ + + E C + S T S GYGFV Y + + A KA L G +L T+ +
Sbjct: 16 FEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLGKQLGESTLFAQW 75
Query: 71 A 71
Sbjct: 76 M 76
>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 = 30.9 bits (70), Expect = 0.043
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+YV LP + +++LE LF YGRI
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRI 26
Score = 24.8 bits (54), Expect = 7.2
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+ FV + P DAE A+ NG ++V +
Sbjct: 40 FAFVRFEDPRDAEDAVFGRNGYDFGQCRLRVEF 72
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1),
serine/arginine-rich splicing factor 9 (SRSF9 or
SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1).
SRSF1 is a shuttling SR protein involved in constitutive
and alternative splicing, nonsense-mediated mRNA decay
(NMD), mRNA export and translation. It also functions as
a splicing-factor oncoprotein that regulates apoptosis
and proliferation to promote mammary epithelial cell
transformation. SRSF9 has been implicated in the
activity of many elements that control splice site
selection, the alternative splicing of the
glucocorticoid receptor beta in neutrophils and in the
gonadotropin-releasing hormone pre-mRNA. It can also
interact with other proteins implicated in alternative
splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4,
Nop30, and p32. Both, SRSF1 and SRSF9, contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal RS domains rich in
serine-arginine dipeptides. In contrast, SF2 contains
two N-terminal RRMs and a C-terminal PSK domain rich in
proline, serine and lysine residues. .
Length = 72
Score = 30.8 bits (70), Expect = 0.045
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+YV LP + ++++E LF YG I
Sbjct: 2 IYVGNLPGDIRERDIEDLFYKYGPI 26
Score = 24.7 bits (54), Expect = 8.1
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+ FV + P DAE A+ +G ++V +
Sbjct: 39 PFAFVEFEDPRDAEDAVRGRDGYDFDGYRLRVEF 72
>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 = 31.1 bits (71), Expect = 0.046
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 27 VFLISTAQ--SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
V L+ T S F+ Y E+A+KA + N + I V +A
Sbjct: 31 VKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNNTYINTSKISVEFA 77
Score = 24.5 bits (54), Expect = 8.2
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 83 LYVSGLPKHMSQQELESLFS-PYGRIITSRILCDNLATENGK 123
L V LP +++ EL+ FS G I ++ L TE+GK
Sbjct: 3 LIVKNLPASLTEAELKEHFSKHGGEITDVKL----LRTEDGK 40
>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 = 30.6 bits (70), Expect = 0.049
Identities = 10/33 (30%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
G+G+V + + A+ LNG++L+ + I+V
Sbjct: 42 GFGYVLFKTKDSVALALK-LNGIKLKGRKIRVK 73
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component
of the spliceosome complex, as well as a component of
the apobec-1 editosome. As an alternatively spliced
version of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two
well defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 30.7 bits (69), Expect = 0.049
Identities = 11/36 (30%), Positives = 23/36 (63%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
Y F+++ + A KA+ +NG L+ + I++ +A+P
Sbjct: 37 YAFIHFDERDGAVKAMEEMNGKELEGENIEIVFAKP 72
>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 = 30.9 bits (70), Expect = 0.052
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + GYGF Y E A A+ LNG L + ++V A
Sbjct: 36 TGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLRVDNA 75
>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM1 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 75
Score = 30.9 bits (70), Expect = 0.053
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
+L+V LP+++ ++ + F YGR+ + +IL
Sbjct: 1 HLWVGNLPENVREERISEHFKRYGRVESVKIL 32
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 30.8 bits (70), Expect = 0.053
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRL----QNKTIKVSYA 71
T GY FV + AE+ ++ LNG + K K++ A
Sbjct: 38 TGGPAGYCFVEFADEATAERCLHKLNGKPIPGSNPPKRFKLNRA 81
>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 = 30.9 bits (70), Expect = 0.053
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
L+V GL +Q+ L FS YG ++ I+ D
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDK 35
>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 = 30.7 bits (70), Expect = 0.055
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V GLP H + L FS +G I + ++ D
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITD 35
Score = 29.5 bits (67), Expect = 0.15
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 7/58 (12%)
Query: 3 YQTLLNKLFTYEKVHLGFSDAEICVFLIS---TAQSLGYGFVNYHRPEDAEKAINTLN 57
Y T + L Y F + E V +I+ T +S GYGFV + E AE+A N
Sbjct: 10 YHTTDDSLRKYFSQ---FGEIEEAV-VITDRQTGKSRGYGFVTFKDKESAERACKDPN 63
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM3 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). 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 polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Like PTB, PTBPH3
contains four RRMs.
Length = 71
Score = 30.2 bits (69), Expect = 0.063
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
G V P+ AE+AI LNG+ L + ++V++
Sbjct: 38 GTAMVQMGDPQAAERAIEYLNGVVLFGQKLEVNF 71
>gnl|CDD|241072 cd12628, RRM2_IGF2BP1, RNA recognition motif 2 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM2 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. It promotes mRNA
stabilization and functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD. It stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus
(HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and
enhancing HCV internal ribosome entry site
(IRES)-mediated translation initiation via the 3'-UTR.
IGF2BP1 contains four hnRNP K-homology (KH) domains,
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. It also
contains two putative nuclear export signals (NESs) and
a putative nuclear localization signal (NLS). .
Length = 76
Score = 30.4 bits (68), Expect = 0.066
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
V Y E +AI LNG +L+N +KVSY
Sbjct: 44 VTYGNREQTRQAIMKLNGHQLENHALKVSY 73
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in
yeast. Yra1p is associated with Pse1p and Kap123p, two
members of the beta-importin family, further mediating
transport of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission
yeast as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 30.5 bits (69), Expect = 0.068
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNK 64
+S G + + R DA KA + NG
Sbjct: 39 KSTGIANITFKRAGDATKAYDKFNGRIDDGN 69
>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 = 30.5 bits (69), Expect = 0.075
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD-NLA 118
N+Y+ LP+ S++EL +G I +I+ + N+A
Sbjct: 5 NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIA 42
>gnl|CDD|241070 cd12626, RRM1_IGF2BP2, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM1 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, which is a ubiquitously
expressed RNA-binding protein involved in the
stimulation of insulin action. It is predominantly
nuclear. SNPs in IGF2BP2 gene are implicated in
susceptibility to type 2 diabetes. IGF2BP2 plays an
important role in cellular motility; it regulates the
expression of PINCH-2, an important mediator of cell
adhesion and motility, and MURF-3, a
microtubule-stabilizing protein, through direct binding
to their mRNAs. IGF2BP2 may be involved in the
regulation of mRNA stability through the interaction
with the AU-rich element-binding factor AUF1. IGF2BP2
binds initially to nascent beta-actin transcripts and
facilitates the subsequent binding of the shuttling
IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 30.4 bits (68), Expect = 0.077
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARP 73
GY FV+Y A +AI TL+G + L K ++V Y+ P
Sbjct: 38 GYAFVDYPDQNWAIRAIETLSGKVELHGKVMEVDYSVP 75
>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 = 29.9 bits (67), Expect = 0.099
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
G ++V +P+ + + EL LF G I R++ D L+ +N Y
Sbjct: 1 GTEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGY 45
>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 = 29.9 bits (68), Expect = 0.100
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+T ++ G FV Y DA+ A + L+G + N+ + V Y
Sbjct: 36 NTKETRGTAFVVYEDIYDAKNACDHLSGFNVANRYLVVLY 75
Score = 29.1 bits (66), Expect = 0.18
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
LYV LP +S +EL LF YG I RI
Sbjct: 5 LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNT 37
>gnl|CDD|241091 cd12647, RRM_UHM_SPF45, RNA recognition motif in UHM domain of 45
kDa-splicing factor (SPF45) and similar proteins. This
subgroup corresponds to the RRM of SPF45, also termed
RNA-binding motif protein 17 (RBM17), an RNA-binding
protein consisting of an unstructured N-terminal
region, followed by a G-patch motif and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors a RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain)
and an Arg-Xaa-Phe sequence motif. SPF45 regulates
alternative splicing of the apoptosis regulatory gene
FAS (also known as CD95). It induces exon 6 skipping in
FAS pre-mRNA through the UHM domain that binds to
tryptophan-containing linear peptide motifs (UHM ligand
motifs, ULMs) present in the 3' splice site-recognizing
factors U2AF65, SF1 and SF3b155. .
Length = 96
Score = 30.3 bits (69), Expect = 0.10
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
FV + R E A KA+ LNG +T+K S+
Sbjct: 55 FVEFERVESAIKAVVDLNGRFFGGRTVKASF 85
>gnl|CDD|241071 cd12627, RRM1_IGF2BP3, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 3
(IGF2BP3). This subgroup corresponds to the RRM1 of
IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also
termed KH domain-containing protein overexpressed in
cancer (KOC), or VICKZ family member 3, an RNA-binding
protein that plays an important role in the
differentiation process during early embryogenesis. It
is known to bind to and repress the translation of IGF2
leader 3 mRNA. IGF2BP3 also acts as a
Glioblastoma-specific proproliferative and proinvasive
marker acting through IGF2 resulting in the activation
of oncogenic phosphatidylinositol
3-kinase/mitogen-activated protein kinase (PI3K/MAPK)
pathways. IGF2BP3 contains four hnRNP K-homology (KH)
domains, two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. .
Length = 77
Score = 30.0 bits (67), Expect = 0.11
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 8/58 (13%)
Query: 20 FSDAEICV---FLISTAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSYARP 73
F D++I FL+ + GY FV+ A KAI+TL+G + L K I+V ++ P
Sbjct: 22 FKDSKIPFSGPFLVKS----GYAFVDCPDESWAMKAIDTLSGKVELHGKVIEVEHSVP 75
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 29.9 bits (68), Expect = 0.12
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRL----QNKTIKVSY 70
Y FV+Y EDA A + LNG L QNK + +SY
Sbjct: 41 YCFVSYSSIEDAAAAYDALNGKELELPQQNKPLYLSY 77
>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 = 29.7 bits (67), Expect = 0.12
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
T + G+ FV Y PE A KA L+G Q + + +
Sbjct: 40 TKKPKGFAFVTYMIPEHAVKAFAELDGTVFQGRLLHL 76
>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 = 29.9 bits (68), Expect = 0.13
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLN 57
+S GYGFV + E A KA+ LN
Sbjct: 53 KGKSKGYGFVEFTNHEHALKALRALN 78
>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 = 29.9 bits (67), Expect = 0.14
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG----LRLQNKTIKVSYAR 72
T Q+ G+ FV +A + + L L++ KTI V +A+
Sbjct: 42 TQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIGVDFAK 86
>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast
pre-mRNA-splicing factor Srp1p and similar proteins.
This subgroup corresponds to the RRM domain in Srp1p
encoded by gene srp1 from fission yeast
Schizosaccharomyces pombe. It plays a role in the
pre-mRNA splicing process, but not essential for growth.
Srp1p is closely related to the SR protein family found
in metazoa. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine hinge and a RS
domain in the middle, and a C-terminal domain. Some
family members also contain another RRM domain.
Length = 78
Score = 29.8 bits (67), Expect = 0.14
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
LYV+G ++L F YGR++
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLV 27
Score = 29.4 bits (66), Expect = 0.16
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNK--TIKVSYAR 72
T QS + FV Y DAE A ++G R + T+ V +A+
Sbjct: 36 TFQSRPFAFVEYESHRDAEDAYEEMHGRRFPDTGDTLHVQWAK 78
>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 = 29.5 bits (67), Expect = 0.15
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 39 GFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
GFV + DAE+A++ L+G + +K+ + +
Sbjct: 49 GFVAFMNRADAERALDELDGKDVMGYELKLGWGKA 83
Score = 27.2 bits (61), Expect = 1.0
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
NLYV L ++++ L F +G + + +I+
Sbjct: 2 TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIM 34
>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 = 29.3 bits (66), Expect = 0.15
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
G+G+V + E A+ A++ L G L + +++
Sbjct: 41 GFGYVEFSSQEAAQAALDALGGTDLLGRPVRL 72
>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 = 0.16
Identities = 11/34 (32%), Positives = 23/34 (67%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
GY FV + EDA++A+N+ N ++ ++I++ +
Sbjct: 39 GYAFVEFESAEDAKEALNSCNNTEIEGRSIRLEF 72
>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 = 29.5 bits (67), Expect = 0.16
Identities = 7/26 (26%), Positives = 15/26 (57%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
+YV G PK + +++ F +G++
Sbjct: 2 VYVKGFPKDATLDDIQEFFEKFGKVN 27
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site
of the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65
(also termed U2AF2). U2AF35 contains two N-terminal
zinc fingers, a central RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 30.0 bits (68), Expect = 0.17
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 40 FVNYHRPEDAEKAINTLN 57
+V + R EDAEKA+N LN
Sbjct: 72 YVKFRREEDAEKAVNDLN 89
>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 = 29.2 bits (66), Expect = 0.19
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 83 LYVSGLPKHMSQQELESLFSP 103
L+V G+PK +++E+ FS
Sbjct: 4 LFVGGIPKTKTKEEILEEFSK 24
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2, Smad3
and Smad4, and stimulates Smad-mediated transactivation.
Cpo may play an important role in regulating normal
function of the nervous system, whereas mutations in
Mec-8 affect mechanosensory and chemosensory neuronal
function. All members contain a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Some
uncharacterized family members contain two RRMs; this
subfamily includes their RRM1. Their RRM2 shows high
sequence homology to the RRM of yeast proteins scw1,
Whi3, and Whi4.
Length = 79
Score = 29.2 bits (66), Expect = 0.21
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 83 LYVSGLPKHMSQQELESLFSPY 104
L+VSGLP + ++EL LF P+
Sbjct: 3 LFVSGLPSDVKERELAHLFRPF 24
Score = 26.1 bits (58), Expect = 2.9
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKT 65
GFV++ + A A++ L G R T
Sbjct: 45 VGFVDFSSAQCAAAAMDALQGYRFDPDT 72
>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 = 29.1 bits (66), Expect = 0.21
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 6/44 (13%)
Query: 32 TAQSLGYGFVNYHRPEDAEK---AINTLNGLRLQNKTIKVSYAR 72
T +S G+ F+ Y ED A++ LNG++L +TI+V + R
Sbjct: 47 TGKSKGFAFLAY---EDQRSTILAVDNLNGIKLLGRTIRVDHVR 87
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46),
belonging to the Aly/REF family of RNA binding proteins
that have been implicated in coupling transcription
with pre-mRNA splicing and nucleo-cytoplasmic mRNA
transport. SKAR is widely expressed and localizes to
the nucleus. It may be a critical player in the
function of S6K1 in cell and organism growth control by
binding the activated, hyperphosphorylated form of S6K1
but not S6K2. Furthermore, SKAR functions as a protein
partner of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. SKAR contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain).
Length = 69
Score = 28.8 bits (65), Expect = 0.23
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
V Y R +DA AI+ N L + +K
Sbjct: 40 VVYVRKDDALTAIDKYNNRELDGQPMKCK 68
>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 = 29.0 bits (65), Expect = 0.24
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
++V +P+ S+++L LF YG + +L D
Sbjct: 4 MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRD 36
>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 = 29.0 bits (65), Expect = 0.25
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
G+ FV E A AI L G + + ++ + +
Sbjct: 37 GFAFVKLDTHEQAAMAIVQLQGFPVHGRPLRCGWGK 72
Score = 28.6 bits (64), Expect = 0.27
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 84 YVSGLPKHMSQQELESLFSPYGRIITSRI 112
YV +P + +Q +L LF +G I+ R
Sbjct: 4 YVGNIPPYTTQADLIPLFQNFGYILEFRH 32
>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM1 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two of which are followed by a glutamine-rich
stretch that may be involved in transcriptional
activity. In addition, NGR1 has an asparagine-rich
region near the carboxyl terminus which also harbors a
methionine-rich region. The subgroup also includes
NAM8, a putative RNA-binding protein that acts as a
suppressor of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 81
Score = 28.9 bits (65), Expect = 0.26
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKVSYA 71
++ + GY FV + P A+ A++ LNG + N +T K+++A
Sbjct: 37 NSGLNAGYCFVEFPSPHAAQNALS-LNGTPIPNSNRTFKLNWA 78
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM2 of Mei2-like
proteins from plant and fungi, terminal EAR1-like
proteins from plant, and other eukaryotic homologs.
Mei2-like proteins represent an ancient eukaryotic
RNA-binding proteins family whose corresponding
Mei2-like genes appear to have arisen early in
eukaryote evolution, been lost from some lineages such
as Saccharomyces cerevisiae and metazoans, and
diversified in the plant lineage. The plant Mei2-like
genes may function in cell fate specification during
development, rather than as stimulators of meiosis. In
the fission yeast Schizosaccharomyces pombe, the Mei2
protein is an essential component of the switch from
mitotic to meiotic growth. S. pombe Mei2 stimulates
meiosis in the nucleus upon binding a specific
non-coding RNA. The terminal EAR1-like protein 1 and 2
(TEL1 and TEL2) are mainly found in land plants. They
may play a role in the regulation of leaf initiation.
All members in this family are putative RNA-binding
proteins carrying three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). In addition to the RRMs,
the terminal EAR1-like proteins also contain TEL
characteristic motifs that allow sequence and putative
functional discrimination between them and Mei2-like
proteins. .
Length = 71
Score = 28.7 bits (65), Expect = 0.28
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
FV ++ AE A++ LNG +KV
Sbjct: 42 FVEFYDIRAAEAALDALNGRPFLGGRLKV 70
>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 = 28.4 bits (64), Expect = 0.31
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+V GL + +++++L FS YG + + I+ D
Sbjct: 2 LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTD 34
>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 = 28.8 bits (65), Expect = 0.31
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQN--KTIKV 68
T +S G +V + + A +A+ +NG L K +KV
Sbjct: 40 TKESKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPLKV 78
>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 = 28.7 bits (64), Expect = 0.33
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
+ FVN+ A+N LNG++L + + +
Sbjct: 44 FAFVNFKHEVSVPYAMNLLNGIKLYGRPLNI 74
>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV
Tat-specific factor 1 (Tat-SF1) and similar proteins.
This subfamily corresponds to the RRM2 of Tat-SF1 and
CUS2. Tat-SF1 is the cofactor for stimulation of
transcriptional elongation by human immunodeficiency
virus-type 1 (HIV-1) Tat. It is a substrate of an
associated cellular kinase. Tat-SF1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a highly acidic carboxyl-terminal half. The family
also includes CUS2, a yeast homolog of human Tat-SF1.
CUS2 interacts with U2 RNA in splicing extracts and
functions as a splicing factor that aids assembly of
the splicing-competent U2 snRNP in vivo. CUS2 also
associates with PRP11 that is a subunit of the
conserved splicing factor SF3a. Like Tat-SF1, CUS2
contains two RRMs as well. .
Length = 91
Score = 28.7 bits (65), Expect = 0.33
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
V + PE+A++ I LNG + ++
Sbjct: 55 VKFKEPEEADRCIEALNGRWFAGRQLEAER 84
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 28.2 bits (63), Expect = 0.34
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
++V + + SQ+EL +LF YG +++ ++
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVM 33
>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 = 28.7 bits (65), Expect = 0.35
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L+V GL +++ +LE FS +G +
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTV 26
Score = 27.1 bits (61), Expect = 1.2
Identities = 9/37 (24%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 37 GYGFVNYHRPEDA-EKAINTLNGLRLQNKTIKVSYAR 72
G+ +++ E +K +TLNG + + +K+ A+
Sbjct: 42 GFAYIDLRTSEAQLKKCKSTLNGTKWKGSVLKIEEAK 78
>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 = 28.4 bits (64), Expect = 0.37
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 91 HMSQQELESLFSPYGRIIT 109
S+ EL +FS YG +
Sbjct: 15 DYSEDELRKIFSKYGDVSD 33
>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 = 28.4 bits (64), Expect = 0.37
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
LYV GL + +++++L F +G I + ++
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVV 34
>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate
ribonucleoprotein PTB-binding 2 (raver-2). This
subgroup corresponds to the RRM3 of raver-2, a novel
member of the heterogeneous nuclear ribonucleoprotein
(hnRNP) family. It is present in vertebrates and shows
high sequence homology to raver-1, a ubiquitously
expressed co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. In contrast,
raver-2 exerts a distinct spatio-temporal expression
pattern during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind
to cytoplasmic proteins. Raver-2 contains three
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), two putative nuclear localization signals
(NLS) at the N- and C-termini, a central leucine-rich
region, and a C-terminal region harboring two
[SG][IL]LGxxP motifs. Raver-2 binds to PTB through the
SLLGEPP motif only, and binds to RNA through its RRMs.
.
Length = 98
Score = 28.7 bits (64), Expect = 0.38
Identities = 10/39 (25%), Positives = 20/39 (51%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSS 75
G+ V Y E AE+ ++G ++ I++S+ P +
Sbjct: 45 GFAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSFCAPGA 83
>gnl|CDD|241069 cd12625, RRM1_IGF2BP1, RNA recognition motif 1 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 1
(IGF2BP1). This subgroup corresponds to the RRM1 of
IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also
termed coding region determinant-binding protein
(CRD-BP), or VICKZ family member 1, or zipcode-binding
protein 1 (ZBP-1). IGF2BP1 is a multi-functional
regulator of RNA metabolism that has been implicated in
the control of aspects of localization, stability, and
translation for many mRNAs. It is predominantly located
in cytoplasm and was initially identified as a
trans-acting factor that interacts with the zipcode in
the 3'- untranslated region (UTR) of the beta-actin
mRNA, which is important for its localization and
translational regulation. It inhibits IGF-II mRNA
translation through binding to the 5'-UTR of the
transcript. IGF2BP1 also acts as human immunodeficiency
virus type 1 (HIV-1) Gag-binding factor that interacts
with HIV-1 Gag protein and blocks the formation of
infectious HIV-1 particles. IGF2BP1 promotes mRNA
stabilization; it functions as a coding region
determinant (CRD)-binding protein that binds to the
coding region of betaTrCP1 mRNA and prevents
miR-183-mediated degradation of betaTrCP1 mRNA. It also
promotes c-myc mRNA stability by associating with the
CRD and stabilizes CD44 mRNA via interaction with the
3'-UTR of the transcript. In addition, IGF2BP1
specifically interacts with both Hepatitis C virus
(HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and
enhancing HCV internal ribosome entry site
(IRES)-mediated translation initiation via the 3'-UTR.
IGF2BP1 contains four hnRNP K-homology (KH) domains,
two RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), and a RGG RNA-binding domain. It also
contains two putative nuclear export signals (NESs) and
a putative nuclear localization signal (NLS). .
Length = 77
Score = 28.5 bits (63), Expect = 0.38
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 7 LNKLFTYEKVHLGFSDAEICV---FLISTAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQ 62
LN+ T + F D +I FL+ + GY FV+ + A KAI T +G + L
Sbjct: 9 LNESVTPADLEKVFEDHKISYSGQFLVKS----GYAFVDCPDEQWAMKAIETFSGKVELH 64
Query: 63 NKTIKVSYARP 73
K +++ ++ P
Sbjct: 65 GKRLEIEHSVP 75
>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 = 28.4 bits (63), Expect = 0.38
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGK 123
L V LP+ +S + LE FS +G++ + ++ D+ GK
Sbjct: 2 LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGK 42
>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein R (hnRNP R).
This subgroup corresponds to the RRM3 of hnRNP R. a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. Upon binding of RNA, hnRNP R forms
oligomers, most probably dimers. hnRNP R has been
implicated in mRNA processing and mRNA transport, and
also acts as a regulator to modify binding to ribosomes
and RNA translation. hnRNP R is predominantly located
in axons of motor neurons and to a much lower degree in
sensory axons. In axons of motor neurons, it also
functions as a cytosolic protein and interacts with
wild type of survival motor neuron (SMN) proteins
directly, further providing a molecular link between
SMN and the spliceosome. Moreover, hnRNP R plays an
important role in neural differentiation and
development, as well as in retinal development and
light-elicited cellular activities. hnRNP R contains an
acidic auxiliary N-terminal region, followed by two
well-defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG
motif; hnRNP R binds RNA through its RRM domains. .
Length = 72
Score = 28.5 bits (63), Expect = 0.40
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
Y FV++ + A +A++ +NG ++ + I++ A+P
Sbjct: 37 YAFVHFEERDAAVRAMDEMNGKEIEGEEIEIVLAKP 72
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 28.4 bits (64), Expect = 0.41
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLR 60
YGFV Y DA +AI N
Sbjct: 43 YGFVTYRYACDAFRAIEHGNDDP 65
Score = 26.5 bits (59), Expect = 2.0
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRI 107
+YV +P ++ EL F P+G I
Sbjct: 4 VIYVGKIPIDTTRSELRQRFQPFGEI 29
>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif.
Length = 70
Score = 28.1 bits (63), Expect = 0.41
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 2/66 (3%)
Query: 4 QTLLNKLFTYEKVHLGFSDAEICVFLISTAQSL--GYGFVNYHRPEDAEKAINTLNGLRL 61
+ +L E+ ++ G ++ + R EDA +AI LNG
Sbjct: 3 EDFERELKEEEEYFGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYF 62
Query: 62 QNKTIK 67
+ +K
Sbjct: 63 DGRLVK 68
>gnl|CDD|240879 cd12433, RRM_Yme2p_like, RNA recognition motif in yeast
mitochondrial escape protein 2 (Yme2p) and similar
proteins. This subfamily corresponds to the RRM of
Yme2p, also termed protein RNA12, an inner mitochondrial
membrane protein that plays a critical role in
mitochondrial DNA transactions. It may serve as a
mediator of nucleoid structure and number in
mitochondria of the yeast Saccharomyces cerevisiae.
Yme2p contains an exonuclease domain, an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal domain. .
Length = 86
Score = 28.4 bits (64), Expect = 0.42
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 17/49 (34%)
Query: 60 RLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYGRII 108
R + TI+V + P +SQ+EL SLF PYG+I
Sbjct: 1 RFPSTTIRVEFEGPE-----------------LSQEELYSLFRPYGKIK 32
Score = 26.1 bits (58), Expect = 2.8
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 2/37 (5%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNK--TIKVSYAR 72
Y V + R A A N L+G L + + Y
Sbjct: 45 YATVTFRRIRGAISAKNCLHGFELNEGKTRLHIQYEP 81
>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 = 28.2 bits (63), Expect = 0.42
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 28 FLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
F +S G G V + E +KA+ T+N L+ + + V
Sbjct: 33 FKDEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVV 73
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM1 of
heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL), and similar proteins. hnRNP-L is a higher
eukaryotic specific subunit of human KMT3a (also known
as HYPB or hSet2) complex required for histone H3 Lys-36
trimethylation activity. It plays both, nuclear and
cytoplasmic, roles in mRNA export of intronless genes,
IRES-mediated translation, mRNA stability, and splicing.
hnRNP-LL plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to hnRNP-L, which contains three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 28.5 bits (64), Expect = 0.43
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
++V GLP +++ +L S +G I
Sbjct: 5 VHVRGLPDGVTEADLVEALSEFGPI 29
>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 = 28.0 bits (63), Expect = 0.48
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
Y V + +PEDAEKA+ G I+V+
Sbjct: 43 YAIVFFRKPEDAEKALEVSKGKLFFGAEIEVT 74
>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 = 0.49
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+Y G+ +++Q + FSP+G+I+ R+ D
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD 35
Score = 28.1 bits (62), Expect = 0.51
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
GY FV ++ E A AI ++NG ++ +K + + +
Sbjct: 37 GYSFVRFNSHESAAHAIVSVNGTTIEGHVVKCYWGKET 74
>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 = 0.50
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
L++ + K ++ ++ +FSP+G+I RIL
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRIL 34
>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 = 28.0 bits (63), Expect = 0.51
Identities = 10/45 (22%), Positives = 21/45 (46%)
Query: 29 LISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
L + + G+ V+Y+ A +A L G L + + + ++ P
Sbjct: 31 LYTACKHRGFIMVSYYDIRAARRAKRALQGTELGGRKLDIHFSIP 75
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 28.1 bits (63), Expect = 0.54
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGL 59
T +S G+ +V Y P A A LNG
Sbjct: 36 YTGKSKGFAYVTYSNPASAIYAKEKLNGF 64
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM3 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 28.0 bits (63), Expect = 0.57
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
+ P+ A+ A+ LNG+RL K ++V+ ++
Sbjct: 42 IQMADPQQAQTALTHLNGIRLHGKKLRVTLSK 73
>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 = 27.9 bits (63), Expect = 0.58
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRL--QNKTIKVSYAR 72
Y ++ Y E A+ A L G L + ++V +A
Sbjct: 35 NYAYIEYESIEAAQAAKEALRGFPLGGPGRRLRVDFAD 72
Score = 24.5 bits (54), Expect = 8.6
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L+V GL S ELE F +G I
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAI 25
>gnl|CDD|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate
nucleolin. This subfamily corresponds to the RRM1 of
ubiquitously expressed protein nucleolin, also termed
protein C23. Nucleolin is a multifunctional major
nucleolar phosphoprotein that has been implicated in
various metabolic processes, such as ribosome
biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made
up of highly acidic regions separated from each other
by basic sequences, and contains multiple
phosphorylation sites. The central domain of nucleolin
contains four closely adjacent N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
which suggests that nucleolin is potentially able to
interact with multiple RNA targets. The C-terminal RGG
(or GAR) domain of nucleolin is rich in glycine,
arginine and phenylalanine residues, and contains high
levels of NG,NG-dimethylarginines. RRM1, together with
RRM2, binds specifically to RNA stem-loops containing
the sequence (U/G)CCCG(A/G) in the loop. .
Length = 75
Score = 27.8 bits (62), Expect = 0.58
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 20 FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
FS + V + S +G+V++ ED EKA+ L G +L IK+ A
Sbjct: 25 FSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKALE-LTGKKLLGNEIKLEKA 75
>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 = 28.0 bits (62), Expect = 0.58
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
L+V LP + + EL+ F YG ++ RI
Sbjct: 6 LFVGNLPHDVDKSELKEFFQQYGNVVELRI 35
>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 = 28.0 bits (63), Expect = 0.59
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
++V LP +++L+ LF +G I + R
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRF 32
>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 = 27.9 bits (62), Expect = 0.62
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 81 ANLYVSGLPKHMSQQELESLFSPYGR 106
+ L+V LP ++++E+ LF YG+
Sbjct: 2 SRLFVGNLPPDITEEEMRKLFEKYGK 27
>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 = 27.9 bits (62), Expect = 0.63
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNG----LRLQNKTIKVSYAR 72
T Q+ G+ FV +A + + L L++ KTI V +A+
Sbjct: 42 TQQNRGFAFVQLSSALEASQLLQILQALHPPLKIDGKTIGVDFAK 86
>gnl|CDD|222411 pfam13840, ACT_7, Family description. The ACT domain is a
structural motif of 70-90 amino acids that functions in
the control of metabolism, solute transport and signal
transduction. They are thus found in a variety of
different proteins in a variety of different
arrangements. In mammalian phenylalanine hydroxylase
the domain forms no contacts but promotes an allosteric
effect despite the apparent lack of ligand binding.
Length = 65
Score = 27.5 bits (62), Expect = 0.67
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 21 SDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTL 56
++A I +F IST + Y V ED EKA+N L
Sbjct: 32 AEAGISIFQISTYDT-DYILVPE---EDLEKAVNAL 63
>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 = 27.6 bits (62), Expect = 0.67
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
L V +P +++EL LFSP+G++ + R+
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRL 32
Score = 25.7 bits (57), Expect = 3.9
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
G+ FV + ++A+ A+ L L + + + YA
Sbjct: 42 GFAFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 76
>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein M (hnRNP M) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein M
(hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2
or MST156) and similar proteins. hnRNP M is pre-mRNA
binding protein that may play an important role in the
pre-mRNA processing. It also preferentially binds to
poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). MEF-2 is a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 shows high sequence homology with hnRNP M.
It also contains three RRMs, which may be responsible
for its ssDNA binding activity. .
Length = 74
Score = 27.7 bits (62), Expect = 0.69
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
S G G V + P +A +AI+ NG L ++ ++V
Sbjct: 38 SRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRV 71
>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 = 27.7 bits (62), Expect = 0.69
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINT 55
T QS G+GFV + ED K ++
Sbjct: 36 KTGQSKGFGFVRFADYEDQVKVLSQ 60
Score = 25.0 bits (55), Expect = 5.8
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+L V GLP ++Q+L+ FS +G ++ ++ D
Sbjct: 1 DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKD 34
>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 = 27.7 bits (62), Expect = 0.69
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 84 YVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA 118
+V G+ +S+ +L+ FS G + R+ D
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH 38
>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 = 27.4 bits (61), Expect = 0.80
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 15/61 (24%)
Query: 7 LNKLFTYEKVHLGFSDAEI------------CVFLI--STAQSLGYGFVNYHRPEDAEKA 52
L KLF ++L SD+ + CV ++ +T +S G+GF+ + ++A++A
Sbjct: 2 LCKLFV-GGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60
Query: 53 I 53
+
Sbjct: 61 M 61
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 27.5 bits (62), Expect = 0.80
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 40 FVNYHRPEDAEKAINTLNG 58
V + E AE A LNG
Sbjct: 43 LVQFDSVESAENAKKALNG 61
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5
(SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich
splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an
important role in both, constitutive and alternative,
splicing of many pre-mRNAs. It can shuttle between the
nucleus and cytoplasm. SRSF5 regulates both alternative
splicing and basal splicing. It is the only SR protein
efficiently selected from nuclear extracts (NE) by the
splicing enhancer (ESE) and is essential for enhancer
activation. SRSF6 preferentially interacts with a
number of purine-rich splicing enhancers (ESEs) to
activate splicing of the ESE-containing exon. It is the
only protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types
of RNA sites. Members in this family contain two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 27.3 bits (61), Expect = 0.83
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
Q G V + D ++AI L+G L + IK+
Sbjct: 35 QRPNEGVVEFATYSDMKRAIEKLDGTELNGRKIKLI 70
>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen
(La or SS-B or LARP3), La-related protein 7 (LARP7 or
PIP7S) and similar proteins. This subfamily
corresponds to the RRM2 of La and LARP7. La is a highly
abundant nuclear phosphoprotein and well conserved in
eukaryotes. It specifically binds the 3'-terminal
UUU-OH motif of nascent RNA polymerase III transcripts
and protects them from exonucleolytic degradation by 3'
exonucleases. In addition, La can directly facilitate
the translation and/or metabolism of many UUU-3'
OH-lacking cellular and viral mRNAs, through binding
internal RNA sequences within the untranslated regions
of target mRNAs. LARP7 is an oligopyrimidine-binding
protein that binds to the highly conserved 3'-terminal
U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable
component of the 7SK small nuclear ribonucleoprotein
(7SK snRNP), intimately associates with all the nuclear
7SK and is required for 7SK stability. LARP7 also acts
as a negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. LARP7 plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. Both La and LARP7 contain an N-terminal
La motif (LAM), followed by two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 27.3 bits (61), Expect = 0.83
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 39 GFVNYHRPEDAEKAIN--TLNGLRLQNKTIKVS 69
G++ + PE A+KA G L K IK+S
Sbjct: 40 GYIRFKTPEAAQKAREAFVEKGEGLLGKEIKLS 72
>gnl|CDD|202408 pfam02812, ELFV_dehydrog_N, Glu/Leu/Phe/Val dehydrogenase,
dimerisation domain.
Length = 131
Score = 28.2 bits (64), Expect = 0.84
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 11/48 (22%)
Query: 89 PKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY----SGLGGRE 132
PK +S ELE L +GR + S I G+ G G RE
Sbjct: 79 PKGLSDAELERLTRAFGRELESIIG-------PGRDIPAPDVGTGPRE 119
>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 = 0.84
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 83 LYVSGLPKHMSQQELESLFSPYG 105
++VSG + S+++L FS +G
Sbjct: 5 VFVSGFKRGTSEEQLMDYFSAFG 27
>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 = 27.6 bits (62), Expect = 0.87
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLN-----GLRLQNKTIKVSYA 71
T S G FV + E A+K + + GL L + + V+ A
Sbjct: 38 TGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRRLIVTLA 82
>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 = 27.4 bits (61), Expect = 0.89
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAI 53
T +S G+G+V +H+P A A+
Sbjct: 38 TGESKGFGYVKFHKPSQAAVAL 59
>gnl|CDD|241212 cd12768, RRM2_SRSF9, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM2 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C, 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 = 76
Score = 27.3 bits (60), Expect = 0.90
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSE 76
Q G G V + R ED E A+ L+ + ++ + SY R E
Sbjct: 33 QKDGMGVVEFLRKEDMEYALRKLDDTKFRSHEGETSYIRVMPE 75
>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 = 27.6 bits (61), Expect = 0.94
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
L+V LP + + EL+ F +G ++ RI
Sbjct: 8 LFVGNLPHDIDESELKEFFMSFGNVVELRI 37
>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 = 27.6 bits (62), Expect = 1.0
Identities = 9/42 (21%), Positives = 18/42 (42%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
T + GY F+ + D + A +G ++ + + V R
Sbjct: 38 KTGKPRGYAFIEFEHERDMKAAYKYADGKKIDGRRVLVDVER 79
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 27.2 bits (60), Expect = 1.2
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
G ++V +P+ + + EL +F GRI R++ D
Sbjct: 1 GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMD 36
>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 = 26.8 bits (60), Expect = 1.2
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAIN----TLNG 58
T +S G+GFV + P +K + L+G
Sbjct: 35 ITGRSRGFGFVTFADPSSVDKVLAAKPHVLDG 66
Score = 25.2 bits (56), Expect = 4.4
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNL 117
L++ GL +++ L FS YG ++ I+ D +
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPI 35
>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 = 27.2 bits (60), Expect = 1.2
Identities = 9/33 (27%), Positives = 21/33 (63%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+V +P+ +++QE+ +F +G ++ I+ D
Sbjct: 2 LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKD 34
Score = 25.7 bits (56), Expect = 4.2
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLR 60
T G FV Y ++A++AI L+ R
Sbjct: 37 TGHQQGCCFVKYSTRDEADRAIRALHNQR 65
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM1 of RBM40, also known
as RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of
the U12 small nuclear RNA (snRNA). The proline-rich
region might be involved in protein-protein
interactions. .
Length = 73
Score = 26.8 bits (60), Expect = 1.2
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
F + + A +A++ L+ L++ K + V YA
Sbjct: 42 FATFDNEQAASQALSRLHQLKILGKRLVVEYA 73
>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein
44 (RBM44) and similar proteins. This subgroup
corresponds to the RRM of RBM44, a novel germ cell
intercellular bridge protein that is localized in the
cytoplasm and intercellular bridges from pachytene to
secondary spermatocyte stages. RBM44 interacts with
itself and testis-expressed gene 14 (TEX14). Unlike
TEX14, RBM44 does not function in the formation of
stable intercellular bridges. It carries an RNA
recognition motif (RRM) that could potentially bind a
multitude of RNA sequences in the cytoplasm and help to
shuttle them through the intercellular bridge,
facilitating their dispersion into the interconnected
neighboring cells.
Length = 74
Score = 26.8 bits (59), Expect = 1.3
Identities = 14/55 (25%), Positives = 25/55 (45%)
Query: 20 FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPS 74
F ++ V + + Y +++ R DA A+ +NG L +IKV + S
Sbjct: 20 FQKYQVSVISLCKLSNYRYASLHFDRASDALLAVKKMNGGVLSGLSIKVRMVKAS 74
>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila
melanogaster RNA-binding protein cabeza and similar
proteins. This subgroup corresponds to the RRM in
cabeza, also termed P19, or sarcoma-associated
RNA-binding fly homolog (SARFH). It is a putative
homolog of human RNA-binding proteins FUS (also termed
TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1),
TAF15 (also termed hTAFII68 or TAF2N or RPB56), and
belongs to the of the FET (previously TET) (FUS/TLS,
EWS, TAF15) family of RNA- and DNA-binding proteins
whose expression is altered in cancer. It is a nuclear
RNA binding protein that may play an important role in
the regulation of RNA metabolism during fly development.
Cabeza contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 27.0 bits (60), Expect = 1.3
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
++VS LP + ++Q+L F G I
Sbjct: 1 VFVSNLPPNTTEQDLAEHFGSIGII 25
Score = 27.0 bits (60), Expect = 1.4
Identities = 15/40 (37%), Positives = 16/40 (40%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
T + G V Y P A AI N TIKVS A
Sbjct: 44 TGEPKGEATVTYDDPHAASAAIEWFNNKDFMGNTIKVSLA 83
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 79
Score = 27.1 bits (60), Expect = 1.3
Identities = 6/30 (20%), Positives = 20/30 (66%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
++VS LP ++++++ + + +G I+ ++
Sbjct: 10 IHVSNLPSDVTEEDVINHLAEHGVIVNVKV 39
>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 = 26.8 bits (60), Expect = 1.3
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 19 GFSDAEICVFLISTAQ--SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVS 69
G + ++ G +V + PEDA +A+ N ++ + I+V
Sbjct: 22 GLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNN-KMGGRYIEVF 73
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12
small nuclear ribonucleoprotein 35 kDa protein
(U11/U12-35K) and similar proteins. This subfamily
corresponds to the RRM of U11/U12-35K, also termed
protein HM-1, or U1 snRNP-binding protein homolog, and
is one of the components of the U11/U12 snRNP, which is
a subunit of the minor (U12-dependent) spliceosome
required for splicing U12-type nuclear pre-mRNA
introns. U11/U12-35K is highly conserved among
bilateria and plants, but lacks in some organisms, such
as Saccharomyces cerevisiae and Caenorhabditis elegans.
Moreover, U11/U12-35K shows significant sequence
homology to U1 snRNP-specific 70 kDa protein (U1-70K or
snRNP70). It contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5'
splice site recognition in the minor spliceosome and
play a role in exon bridging, interacting with
components of the major spliceosome bound to the
pyrimidine tract of an upstream U2-type intron. The
family corresponds to the RRM of U11/U12-35K that may
directly contact the U11 or U12 snRNA through the RRM
domain.
Length = 93
Score = 27.2 bits (61), Expect = 1.3
Identities = 15/43 (34%), Positives = 19/43 (44%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
I T S GY FV Y DA +A + L + I V + R
Sbjct: 39 IVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSEIFVDFER 81
Score = 26.1 bits (58), Expect = 3.8
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKYY 125
L+V L +++ L +FS YG I R++ D + T K Y
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRD-IVTGFSKGY 47
>gnl|CDD|238969 cd02011, TPP_PK, Thiamine pyrophosphate (TPP) family,
Phosphoketolase (PK) subfamily, TPP-binding module; PK
catalyzes the conversion of D-xylulose 5-phosphate and
phosphate to acetyl phosphate,
D-glyceraldehyde-3-phosphate and H2O. This enzyme
requires divalent magnesium ions and TPP for activity.
Length = 227
Score = 28.1 bits (63), Expect = 1.4
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 22/50 (44%)
Query: 56 LNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG 105
LNG ++ N TI AR +S +ELE+LF YG
Sbjct: 121 LNGYKISNPTI---LAR-------------------ISHEELEALFRGYG 148
>gnl|CDD|240709 cd12263, RRM_ABT1_like, RNA recognition motif found in activator of
basal transcription 1 (ABT1) and similar proteins. This
subfamily corresponds to the RRM of novel nuclear
proteins termed ABT1 and its homologous counterpart,
pre-rRNA-processing protein ESF2 (eighteen S factor 2),
from yeast. ABT1 associates with the TATA-binding
protein (TBP) and enhances basal transcription activity
of class II promoters. Meanwhile, ABT1 could be a
transcription cofactor that can bind to DNA in a
sequence-independent manner. The yeast ABT1 homolog,
ESF2, is a component of 90S preribosomes and 5'
ETS-based RNPs. It is previously identified as a
putative partner of the TATA-element binding protein.
However, it is primarily localized to the nucleolus and
physically associates with pre-rRNA processing factors.
ESF2 may play a role in ribosome biogenesis. It is
required for normal pre-rRNA processing, as well as for
SSU processome assembly and function. Both ABT1 and ESF2
contain an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 98
Score = 27.2 bits (61), Expect = 1.4
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 84 YVSGLPKHMSQQELESLFSPYGRI 107
Y+S +P M+ +L L S YG +
Sbjct: 4 YLSRIPPRMNPAKLRQLLSQYGEV 27
>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 = 27.0 bits (60), Expect = 1.4
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
L+V L K ++ ++ LF P+G I IL
Sbjct: 4 LFVGMLSKQQTEDDVRRLFEPFGTIEECTIL 34
Score = 25.5 bits (56), Expect = 4.1
Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 6 LLNKLFTYEKVH---LGFSDAEICVFLIST-AQSLGYGFVNYHRPEDAEKAINTLNGLR 60
+L+K T + V F E C L S G FV + +A+ AIN L+G +
Sbjct: 8 MLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQ 66
>gnl|CDD|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup
corresponds to the RRM2 of RBM4, a ubiquitously
expressed splicing factor that has two isoforms, RBM4A
(also known as Lark homolog) and RBM4B (also known as
RBM30), which are very similar in structure and
sequence. RBM4 may function as a translational
regulator of stress-associated mRNAs and also plays a
role in micro-RNA-mediated gene regulation. RBM4
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region,
are responsible for the splicing function of RBM4. .
Length = 67
Score = 26.5 bits (58), Expect = 1.6
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
Y FV+ R EDA +AI L+ Q K + V
Sbjct: 36 YAFVHMERAEDAVEAIRGLDNTEFQGKRMHV 66
>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 = 26.6 bits (59), Expect = 1.6
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 85 VSGLPKHMSQQELESLFSPYGRIITSRIL 113
V P + +EL LF P+G++ +R+L
Sbjct: 5 VKNFPYGTTAEELRDLFEPHGKL--TRVL 31
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed
U2 snRNP B") a unique protein that comprises the U2
snRNP. It was initially identified as binding to
stem-loop IV (SLIV) at the 3' end of U2 snRNA.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B"
does not require an auxiliary protein for binding to
RNA. In addition, the nuclear transport of U2B" is
independent of U2 snRNA binding. U2B" contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It also contains a nuclear localization signal (NLS) in
the central domain. However, nuclear import of U2B''
does not depend on this NLS. The N-terminal RRM is
sufficient to direct U2B" to the nucleus. .
Length = 91
Score = 26.9 bits (59), Expect = 1.6
Identities = 12/49 (24%), Positives = 22/49 (44%)
Query: 30 ISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARPSSESI 78
+ T + G FV + A A+ L G K +++ YA+ S+ +
Sbjct: 38 LKTMKMRGQAFVIFKELSSATNALRQLQGFPFYGKPMRIQYAKTDSDIV 86
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM2 of RBM40 and the RRM
of RBM41. RBM40, also known as RNA-binding
region-containing protein 3 (RNPC3) or U11/U12 small
nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K
protein). It serves as a bridging factor between the
U11 and U12 snRNPs. It contains two RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), connected by a
linker that includes a proline-rich region. It binds to
the U11-associated 59K protein via its RRM1 and employs
the RRM2 to bind hairpin III of the U12 small nuclear
RNA (snRNA). The proline-rich region might be involved
in protein-protein interactions. RBM41 contains only
one RRM. Its biological function remains unclear. .
Length = 82
Score = 26.8 bits (60), Expect = 1.7
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
G FV + E A KA+N +NG L+ K + + +
Sbjct: 48 GQAFVTFPSEEIATKALNLVNGYVLKGKPMVIQFG 82
Score = 25.2 bits (56), Expect = 6.4
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 83 LYVSGLPKHMSQQELESLFSPY 104
LYV L K +++++L +F +
Sbjct: 4 LYVKNLSKRVTEEDLVYIFGRF 25
>gnl|CDD|239167 cd02766, MopB_3, The MopB_3 CD includes a group of related
uncharacterized bacterial and archaeal
molybdopterin-binding oxidoreductase-like domains with a
putative N-terminal iron-sulfur [4Fe-4S] cluster binding
site and molybdopterin cofactor binding site. These
members belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 501
Score = 28.0 bits (63), Expect = 1.8
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 18 LGFSDAE--ICVFLISTAQSLGYGFVNYHRPEDAEKA 52
LG S+ IC AQ +G + PED A
Sbjct: 122 LGASELRGTICSGAGIEAQKYDFGASLGNDPEDMVNA 158
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM1
of U1A/U2B"/SNF protein family which contains Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs), connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. Moreover,
U2B" does not require an auxiliary protein for binding
to RNA, and its nuclear transport is independent of U2
snRNA binding. .
Length = 78
Score = 26.3 bits (59), Expect = 1.8
Identities = 9/30 (30%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 83 LYVSGLPKHMSQQE----LESLFSPYGRII 108
LY++ L + + + E L +LFS +G ++
Sbjct: 2 LYINNLNEKIKKDELKRSLYALFSQFGPVL 31
Score = 26.3 bits (59), Expect = 2.4
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
G FV + E A A+ L G +K +++ YA+
Sbjct: 43 GQAFVVFKDVESATNALRALQGFPFYDKPMRIQYAK 78
>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 7 (SRSF7). This
subgroup corresponds to the RRM of SRSF7, also termed
splicing factor 9G8, is a splicing regulatory
serine/arginine (SR) protein that plays a crucial role
in both constitutive splicing and alternative splicing
of many pre-mRNAs. Its localization and functions are
tightly regulated by phosphorylation. SRSF7 is
predominantly present in the nuclear and can shuttle
between nucleus and cytoplasm. It cooperates with the
export protein, Tap/NXF1, helps mRNA export to the
cytoplasm, and enhances the expression of unspliced
mRNA. SRSF7 inhibits tau E10 inclusion through directly
interacting with the proximal downstream intron of E10,
a clustering region for frontotemporal dementia with
Parkinsonism (FTDP) mutations. SRSF7 contains a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
followed by a CCHC-type zinc knuckle motif in its
median region, and a C-terminal RS domain rich in
serine-arginine dipeptides. The RRM domain is involved
in RNA binding, and the RS domain has been implicated
in protein shuttling and protein-protein interactions.
.
Length = 77
Score = 26.5 bits (58), Expect = 1.9
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 37 GYGFVNYHRPEDAEKAINTLNG 58
G+ FV + P DAE A+ L+G
Sbjct: 37 GFAFVEFEDPRDAEDAVRGLDG 58
>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 = 26.6 bits (59), Expect = 1.9
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 85 VSGLPKHMSQQELESLFSPYGRIITSRI 112
V +P + +EL LFS +G + T R+
Sbjct: 5 VRNIPFEATVKELRELFSTFGELKTVRL 32
>gnl|CDD|201032 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding proteins,
NifH/frxC family.
Length = 272
Score = 27.7 bits (62), Expect = 2.0
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 89 PKHMSQQELESLFSPYG 105
PK ++ ELE L +G
Sbjct: 253 PKPLTMDELEELLMDFG 269
>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 = 26.4 bits (58), Expect = 2.0
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 79 KGANLYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
+G +Y+ L MS EL+ F +G I ++L
Sbjct: 1 EGRVIYIRNLSSSMSSTELKKRFEVFGEIEECKVL 35
>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 = 26.4 bits (58), Expect = 2.0
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 82 NLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLA 118
++YV + + +ELE+ FS G I ILCD +
Sbjct: 1 SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFS 37
>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 = 26.3 bits (58), Expect = 2.0
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
G+ FV + ++A A+N L L + + + YA
Sbjct: 42 GFAFVEFSTAKEALNAMNALKDTHLLGRRLVLQYA 76
Score = 24.8 bits (54), Expect = 6.9
Identities = 9/30 (30%), Positives = 20/30 (66%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRI 112
+ V LP +++++ +LFS YG++ + R+
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVRV 32
>gnl|CDD|235379 PRK05261, PRK05261, putative phosphoketolase; Provisional.
Length = 785
Score = 27.8 bits (63), Expect = 2.1
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 22/50 (44%)
Query: 56 LNGLRLQNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPYG 105
LNG ++ N TI AR +S +ELE+LF YG
Sbjct: 201 LNGYKIANPTI---LAR-------------------ISDEELEALFRGYG 228
>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 = 26.3 bits (58), Expect = 2.1
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDN 116
L+V L K ++ ++ +F+P+G I +L D
Sbjct: 4 LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ 37
>gnl|CDD|163695 cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in eIF3f.
Eukaryotic translation initiation factor 3 (eIF3)
subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic
translation initiation factor 3, subunit 5 epsilon,
47kDa; Mov34/MPN/PAD-1 family protein) is an
evolutionarily non-conserved subunit of the functional
core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f,
and eIF3h, and contains the MPN domain. However, it
lacks the canonical JAMM motif, and therefore does not
show catalytic isopeptidase activity. It has been shown
that eIF3f mRNA expression is significantly decreased
in many human tumors including pancreatic cancer and
melanoma. EIF3f is a potent inhibitor of HIV-1
replication; it mediates restriction of HIV-1
expression through several factors including the
serine/arginine-rich (SR) protein 9G8, and
cyclin-dependent kinase 11 (CDK11). EIF3f
phosphorylation by CDK11 is important in regulating its
function in translation and apoptosis. It enhances its
association with the core eIF3 subunits during
apoptosis, suggesting that eIF3f may inhibit
translation by increasing the binding to the eIF3
complex during apoptosis. Thus, eIF3f may be an
important negative regulator of cell growth and
proliferation.
Length = 265
Score = 27.6 bits (62), Expect = 2.1
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 43 YHRPEDAEKAINTLNGLRLQNK-TIKVSYARPSSES 77
R E E+ I TL G R + + I +A P +ES
Sbjct: 16 ERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNES 51
>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing
Sarcoma Protein (EWS). This subgroup corresponds to
the RRM of EWS, also termed Ewing sarcoma breakpoint
region 1 protein, a member of the FET (previously TET)
(FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding
proteins whose expression is altered in cancer. It is a
multifunctional protein and may play roles in
transcription and RNA processing. EWS is involved in
transcriptional regulation by interacting with the
preinitiation complex TFIID and the RNA polymerase II
(RNAPII) complexes. It is also associated with splicing
factors, such as the U1 snRNP protein U1C, suggesting
its implication in pre-mRNA splicing. Additionally, EWS
has been shown to regulate DNA damage-induced
alternative splicing (AS). Like other members in the
FET family, EWS contains an N-terminal Ser, Gly, Gln
and Tyr-rich region composed of multiple copies of a
degenerate hexapeptide repeat motif. The C-terminal
region consists of a conserved nuclear import and
retention signal (C-NLS), a C2/C2 zinc-finger motif, a
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and at least 1 arginine-glycine-glycine (RGG)-repeat
region. EWS specifically binds to poly G and poly U
RNA. It also binds to the proximal-element DNA of the
macrophage-specific promoter of the CSF-1 receptor
gene. .
Length = 84
Score = 26.4 bits (58), Expect = 2.1
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 7 LNKLFTYEKVHLGFSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTI 66
+NK V++ ++D E T + G V+Y P A+ A+ +G Q +
Sbjct: 29 INKRTGQPMVNI-YTDKE-------TGKPKGDATVSYEDPPSAKAAVEWFDGKDFQGSKL 80
Query: 67 KVS 69
KVS
Sbjct: 81 KVS 83
>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast
Schizosaccharomyces pombe SET domain-containing protein
1 (spSet1p) and similar proteins. This subfamily
corresponds to the RRM of spSet1p, also termed H3
lysine-4 specific histone-lysine N-methyltransferase,
or COMPASS component SET1, or lysine
N-methyltransferase 2, or Set1 complex component, is
encoded by SET1 from the fission yeast S. pombe. It is
essential for the H3 lysine-4 methylation. in vivo, and
plays an important role in telomere maintenance and DNA
repair in an ATM kinase Rad3-dependent pathway. spSet1p
is the homology counterpart of Saccharomyces cerevisiae
Set1p (scSet1p). However, it is more closely related to
Set1 found in mammalian. Moreover, unlike scSet1p,
spSet1p is not required for heterochromatin assembly in
fission yeast. spSet1p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), followed by
a conserved SET domain that may play a role in DNA
repair and telomere function. .
Length = 86
Score = 26.6 bits (59), Expect = 2.3
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 32 TAQSLGYGFVNY-HRP-------EDAEKAINTLNGLRLQNKTIKV 68
T QSLG V + P E A+ A++ LNG R+ K ++V
Sbjct: 36 TGQSLGICRVTFRGDPLRPSAAHEAAKAAVDGLNGRRIGGKRVRV 80
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing (RBP-MS).
This subfamily corresponds to the RRM of RBP-MS, also
termed heart and RRM expressed sequence (hermes), an
RNA-binding proteins found in various vertebrate
species. It contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). RBP-MS physically interacts
with Smad2, Smad3 and Smad4 and plays a role in
regulation of Smad-mediated transcriptional activity.
In addition, RBP-MS may be involved in regulation of
mRNA translation and localization during Xenopus laevis
development. .
Length = 76
Score = 26.2 bits (57), Expect = 2.5
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 29 LISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL 61
LI GFV++ +AE A N LNG+R
Sbjct: 32 LIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRF 64
Score = 25.4 bits (55), Expect = 5.4
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 83 LYVSGLPKHMSQQELESLFSPY 104
L+VSGLP + +EL LF P+
Sbjct: 4 LFVSGLPLDIKPRELYLLFRPF 25
>gnl|CDD|240974 cd12530, RRM3_EAR1_like, RNA recognition motif 3 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM3 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 = 101
Score = 26.7 bits (59), Expect = 2.5
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 36 LGYGFVNYHRPEDAEKAINTLNGLRLQ----NKTIKVSYAR 72
LGY FVN+ PE + + + + K +++YAR
Sbjct: 58 LGYAFVNFTSPEATWRFYKAFHNQQWEEFNSRKICQITYAR 98
>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 = 26.3 bits (58), Expect = 2.5
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 12 TYEKVHLGFSDA-EICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
T +++ F DA +I + S G ++ + +AEKA+ G + ++I V Y
Sbjct: 16 TVDELKEVFEDAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQGAEVDGRSIVVDY 75
>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 = 26.1 bits (58), Expect = 2.5
Identities = 9/37 (24%), Positives = 14/37 (37%)
Query: 34 QSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
+S G+ +V + A L G K V+Y
Sbjct: 40 KSKGFAYVEFASEAAAAAVKEKLEGREFNGKKCVVTY 76
>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 = 26.2 bits (58), Expect = 2.6
Identities = 10/33 (30%), Positives = 23/33 (69%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
+YVS + + +++++L +LFS G+++ R+ D
Sbjct: 5 VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD 37
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and
similar proteins. This subfamily corresponds to the
RRM of Acinus, a caspase-3-activated nuclear factor
that induces apoptotic chromatin condensation after
cleavage by caspase-3 without inducing DNA
fragmentation. It is essential for apoptotic chromatin
condensation and may also participate in nuclear
structural changes occurring in normal cells. Acinus
contains a P-loop motif and an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which indicates Acinus
might have ATPase and DNA/RNA-binding activity. .
Length = 90
Score = 26.4 bits (59), Expect = 2.6
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 40 FVNYHRPEDAEKAINTLNGLR--LQN-KTIKVSYARP 73
+V Y E+A L+GL+ N K +KV +
Sbjct: 43 YVTYSTVEEAVATREALHGLQWPSSNPKRLKVDFVPQ 79
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM2 of Mei2-like proteins that represent an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and is highly conserved between
plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 25.9 bits (57), Expect = 2.7
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
F+ ++ AE A+ LN + K IK+
Sbjct: 42 FIEFYDVRSAEAALKALNRSEIAGKRIKL 70
>gnl|CDD|241073 cd12629, RRM2_IGF2BP2, RNA recognition motif 2 in vertebrate
insulin-like growth factor 2 mRNA-binding protein 2
(IGF2BP2). This subgroup corresponds to the RRM2 of
IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also
termed hepatocellular carcinoma autoantigen p62, or
VICKZ family member 2, a ubiquitously expressed
RNA-binding protein involved in the stimulation of
insulin action. It is predominantly nuclear. SNPs in
IGF2BP2 gene are implicated in susceptibility to type 2
diabetes. IGF2BP2 plays an important role in cellular
motility; it regulates the expression of PINCH-2, an
important mediator of cell adhesion and motility, and
MURF-3, a microtubule-stabilizing protein, through
direct binding to their mRNAs. IGF2BP2 may be involved
in the regulation of mRNA stability through the
interaction with the AU-rich element-binding factor
AUF1. In addition, IGF2BP2 binds initially to nascent
beta-actin transcripts and facilitates the subsequent
binding of the shuttling IGF2BP1. IGF2BP2 contains four
hnRNP K-homology (KH) domains, two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a RGG
RNA-binding domain. .
Length = 76
Score = 26.2 bits (57), Expect = 2.7
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
V Y E+A+ A+ L+G + ++ + KVSY
Sbjct: 44 VTYATKEEAKVAVEKLSGHQFEDYSFKVSY 73
>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 = 26.4 bits (58), Expect = 2.8
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+Y+ +P M++ EL+ FS +G I
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEI 29
Score = 24.8 bits (54), Expect = 8.0
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 20 FSDAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNGLRL 61
F + E C + + YGFV Y E+A AI + LR
Sbjct: 26 FGEIEECTIHFRS-EGDNYGFVTYRYTEEAFAAIENGHKLRR 66
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM3 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 73
Score = 26.1 bits (57), Expect = 2.9
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYAR 72
GY F+ + E A AI ++NG ++ +K + +
Sbjct: 37 GYSFIRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK 72
Score = 25.4 bits (55), Expect = 4.4
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
+Y G+ +++Q + FSP+G+I+ R+
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEIRVF 33
>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 = 25.9 bits (57), Expect = 2.9
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENG 122
++V G+ M + E+ S F+ YG + +I+ D G
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKG 47
>gnl|CDD|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing 2 (RBP-MS2).
This subfamily corresponds to the RRM of RBP-MS2,
encoded by RBPMS2 gene, a paralog of RNA-binding protein
with multiple splicing (RBP-MS). The biological function
of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 76
Score = 26.2 bits (57), Expect = 3.0
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 83 LYVSGLPKHMSQQELESLFSPY 104
L+VSGLP + +EL LF P+
Sbjct: 4 LFVSGLPVDIKPRELYLLFRPF 25
>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM1 of RBM46, also termed
cancer/testis antigen 68 (CT68), a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 26.0 bits (57), Expect = 3.0
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLN 57
+ ++ GY FV Y E+A+ AI LN
Sbjct: 38 SGENRGYAFVMYTTKEEAQLAIRILN 63
Score = 25.2 bits (55), Expect = 5.7
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCDNLATENGKY 124
G ++V +P+ M + EL LF G+I R++ + + EN Y
Sbjct: 1 GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGY 44
>gnl|CDD|240702 cd12256, RRM2_LKAP, RNA recognition motif 2 in Limkain-b1 (LKAP)
and similar proteins. This subfamily corresponds to
the RRM2 of LKAP, a novel peroxisomal autoantigen that
co-localizes with a subset of cytoplasmic microbodies
marked by ABCD3 (ATP-binding cassette subfamily D
member 3, known previously as PMP-70) and/or PXF
(peroxisomal farnesylated protein, known previously as
PEX19). It associates with LIM kinase 2 (LIMK2) and may
serve as a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. LKAP contains two RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). However, whether
those RRMs are bona fide RNA binding sites remains
unclear. Moreover, there is no evidence of LAKP
localization in the nucleus. Therefore, if the RRMs are
functional, their interaction with RNA species would be
restricted to the cytoplasm and peroxisomes.
Length = 89
Score = 26.1 bits (58), Expect = 3.0
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 47 EDAEKAINTLNGLRLQNKTIKVSYARPSS 75
+DA+ AI+ L+ ++ +K I VSYA+ SS
Sbjct: 58 QDAQYAISQLHRRKIGSKRILVSYAQGSS 86
Score = 25.8 bits (57), Expect = 4.2
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 79 KGANLYVSGLPKHMS----QQELESLFSPYGRI 107
G +L VS L +S QQ L + F +G++
Sbjct: 3 TGVDLQVSNLDYRLSRKELQQTLTNQFKRHGKV 35
>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 = 26.0 bits (58), Expect = 3.0
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
L++ LP +++ +L +L SP+G++ +L
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLL 32
>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate
APOBEC-1 complementation factor (ACF). This subgroup
corresponds to the RRM1 of ACF, also termed
APOBEC-1-stimulating protein, an RNA-binding subunit of
a core complex that interacts with apoB mRNA to
facilitate C to U RNA editing. It may also act as an
apoB mRNA recognition factor and chaperone, and play a
key role in cell growth and differentiation. ACF
shuttles between the cytoplasm and nucleus. It contains
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), which display high affinity for an 11
nucleotide AU-rich mooring sequence 3' of the edited
cytidine in apoB mRNA. All three RRMs may be required
for complementation of editing activity in living
cells. RRM2/3 are implicated in ACF interaction with
APOBEC-1. .
Length = 78
Score = 26.1 bits (57), Expect = 3.0
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQN 63
GY FV + ++A+ AI LN ++N
Sbjct: 43 GYAFVTFSNKQEAKNAIKQLNNYEIRN 69
Score = 24.9 bits (54), Expect = 8.3
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
G +++ LP+ + + EL L G+I R++ D
Sbjct: 1 GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD 36
>gnl|CDD|240698 cd12252, RRM_DbpA, RNA recognition motif in the DbpA subfamily of
prokaryotic DEAD-box rRNA helicases. This subfamily
corresponds to the C-terminal RRM homology domain of
dbpA proteins implicated in ribosome biogenesis. They
bind with high affinity and specificity to RNA
substrates containing hairpin 92 of 23S rRNA (HP92),
which is part of the ribosomal A-site. The majority of
dbpA proteins contain two N-terminal ATPase catalytic
domains and a C-terminal RNA binding domain, an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain). The catalytic domains bind to nearby regions
of RNA to stimulate ATP hydrolysis and disrupt RNA
structures. The C-terminal domain is responsible for
the high-affinity RNA binding. Several members of this
family lack specificity for 23S rRNA. These proteins
can generally be distinguished by a basic region that
extends beyond the C-terminal domain.
Length = 71
Score = 25.6 bits (57), Expect = 3.1
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 47 EDAEKAINTLNGLRLQNKTIKVS 69
E AEK I LNG +++ K ++V
Sbjct: 49 EVAEKVIEALNGKKIKGKKVRVE 71
>gnl|CDD|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant
proteins related to the La autoantigen. This subfamily
corresponds to the RRM of plant La-like proteins
related to the La autoantigen. A variety of La-related
proteins (LARPs or La ribonucleoproteins), with
differing domain architecture, appear to function as
RNA-binding proteins in eukaryotic cellular processes.
Members in this family contain an LAM domain followed
by an RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 93
Score = 26.3 bits (58), Expect = 3.2
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 7/30 (23%)
Query: 40 FVNYHRPEDAEKAINTL-------NGLRLQ 62
V Y E AEKA+ L +GLR++
Sbjct: 61 LVEYETVEAAEKAVTELSDEGNWRSGLRVR 90
>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 = 26.0 bits (57), Expect = 3.3
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 78 IKGANLYVSGLPKHMSQQELESLFSPYGRIIT 109
+ L+ G+ +M + +L S F +G + +
Sbjct: 1 VYSRTLFPGGVTFNMIEYDLRSGFGRFGEVQS 32
>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small
nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa
subunit (U2AF35) and similar proteins. This subfamily
corresponds to the RRM in U2 small nuclear
ribonucleoprotein (snRNP) auxiliary factor (U2AF) which
has been implicated in the recruitment of U2 snRNP to
pre-mRNAs. It is a highly conserved heterodimer
composed of large and small subunits; this family
includes the small subunit of U2AF (U2AF35 or U2AF1)
and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35
directly binds to the 3' splice site of the conserved
AG dinucleotide and performs multiple functions in the
splicing process in a substrate-specific manner. It
promotes U2 snRNP binding to the branch-point sequences
of introns through association with the large subunit
of U2AF (U2AF65 or U2AF2). Although the biological role
of U2AF35B remains unclear, it shows high sequence
homolgy to U2AF35, which contains two N-terminal zinc
fingers, a central RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR) -rich segment interrupted by
glycines. In contrast to U2AF35, U2AF35B has a
plant-specific conserved C-terminal region containing
SERE motif(s), which may have an important function
specific to higher plants. .
Length = 102
Score = 26.1 bits (58), Expect = 3.4
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 40 FVNYHRPEDAEKAINTLNG 58
+V + EDAE A+ LNG
Sbjct: 70 YVKFETEEDAEAALQALNG 88
>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 = 25.7 bits (57), Expect = 3.5
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+Y+SGLP +++ L LF G I
Sbjct: 1 IYISGLPDDVTEDSLAELFGGIGII 25
>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 = 25.7 bits (57), Expect = 3.7
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 35 SLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
S G+G V + E A+KA+ +G L + I+V A
Sbjct: 39 SKGFGHVEFATEEGAQKALE-KSGEELLGREIRVDLATE 76
>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear
polyadenylated RNA-binding protein 3 (Nab3p) and
similar proteins. This subfamily corresponds to the
RRM of Nab3p, an acidic nuclear polyadenylated
RNA-binding protein encoded by Saccharomyces cerevisiae
NAB3 gene that is essential for cell viability. Nab3p
is predominantly localized within the nucleoplasm and
essential for growth in yeast. It may play an important
role in packaging pre-mRNAs into ribonucleoprotein
structures amenable to efficient nuclear RNA
processing. Nab3p contains an N-terminal
aspartic/glutamic acid-rich region, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal region rich in glutamine and proline
residues. .
Length = 71
Score = 25.5 bits (56), Expect = 3.7
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
YGFV + PE AIN G ++ + + + ++P
Sbjct: 36 YGFVQFDSPESCANAINCEQGKMIRGRKLHLEVSKP 71
>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 = 25.6 bits (57), Expect = 3.8
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRIL 113
+ V LP +++EL LF +G + R+L
Sbjct: 3 ILVKNLPFGTTEEELRELFEKFGSL--GRLL 31
>gnl|CDD|240997 cd12553, RRM1_RBM15, RNA recognition motif 1 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM1 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 contains 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 = 78
Score = 25.7 bits (56), Expect = 4.0
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 39 GFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
FVN+ RPEDA A + L L ++ +K+
Sbjct: 45 AFVNFRRPEDARAAKHARGRLVLYDRPLKI 74
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52
motif-containing protein 1 (RDM1) and similar proteins.
This subfamily corresponds to the RRM of RDM1, also
termed RAD52 homolog B, a novel factor involved in the
cellular response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 25.4 bits (56), Expect = 4.2
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 38 YGFVNYHRPEDAEKAINTLNGLRL-QNKTIKV 68
Y FV ++ A +A NG L Q +KV
Sbjct: 48 YAFVKFYSARAASRAQKACNGKWLFQGSPLKV 79
>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 = 25.3 bits (56), Expect = 4.4
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 85 VSGLPKHMSQQELESLFSPYGRII 108
V LPK ++ ++ F G I
Sbjct: 5 VKNLPKDTTENKIRQFFKDCGEIR 28
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT
motif responsible for docking many substrates to
calcineurin, and an unrecognized C-terminal TxxP motif
of unknown function. .
Length = 75
Score = 25.2 bits (56), Expect = 4.5
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNKTIKVSYA 71
V + PE+A A L+G + ++V +
Sbjct: 44 VVFSSPEEAALARIELHGTVFEGSVLRVYFG 74
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 26.6 bits (58), Expect = 4.6
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSY 70
STA G ++ Y EDA + I ++G L + +K +Y
Sbjct: 161 STASHAGV-YITYSTKEDAARCIAEVDGSLLDGRVLKATY 199
>gnl|CDD|233881 TIGR02470, sucr_synth, sucrose synthase. This model represents
sucrose synthase, an enzyme that, despite its name,
generally uses rather produces sucrose. Sucrose plus UDP
(or ADP) becomes D-fructose plus UDP-glucose (or
ADP-glucose), which is then available for cell wall (or
starch) biosynthesis. The enzyme is homologous to
sucrose phosphate synthase, which catalyzes the
penultimate step in sucrose synthesis. Sucrose synthase
is found, so far, exclusively in plants and
cyanobacteria [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 784
Score = 26.6 bits (59), Expect = 4.6
Identities = 19/89 (21%), Positives = 32/89 (35%), Gaps = 13/89 (14%)
Query: 30 ISTAQSLGYG--FVN-------YHRPEDAEKAINTLNGLRLQNKTIKVSYARPS----SE 76
S ++S+G G F+N + PE E +N L + ++ S
Sbjct: 126 PSDSKSIGNGVQFLNRHLSSKLFQDPESMEPLLNFLRVHNYNGIQLMINDRIQSVSHLQS 185
Query: 77 SIKGANLYVSGLPKHMSQQELESLFSPYG 105
++ A ++S LP E E G
Sbjct: 186 QLRKAEEFLSALPPDTPYSEFEFELQELG 214
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP),
an RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 25.3 bits (56), Expect = 4.9
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 40 FVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
V + P DA KA +LNG + KTIK+
Sbjct: 41 LVEFESPSDAGKASLSLNGSQFGGKTIKI 69
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important
role in the pre-mRNA processing. It also preferentially
binds to poly(G) and poly(U) RNA homopolymers. hnRNP M
is able to interact with early spliceosomes, further
influencing splicing patterns of specific pre-mRNAs. It
functions as the receptor of carcinoembryonic antigen
(CEA) that contains the penta-peptide sequence PELPK
signaling motif. In addition, hnRNP M and another
splicing factor Nova-1 work together as dopamine D2
receptor (D2R) pre-mRNA-binding proteins. They regulate
alternative splicing of D2R pre-mRNA in an antagonistic
manner. hnRNP M contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 25.4 bits (55), Expect = 4.9
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 33 AQSLGYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
+S G G V + +P +A +AI+ NG L ++ + V
Sbjct: 38 GKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHV 73
>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182
family proteins. This subfamily corresponds to the RRM
of the GW182 family which includes three paralogs of
TNRC6 (GW182-related) proteins comprising GW182/TNGW1,
TNRC6B (containing three isoforms) and TNRC6C in
mammal, a single Drosophila ortholog (dGW182, also
called Gawky) and two Caenorhabditis elegans orthologs
AIN-1 and AIN-2, which contain multiple miRNA-binding
sites and have important functions in miRNA-mediated
translational repression, as well as mRNA degradation
in Metazoa. The GW182 family proteins directly interact
with Argonaute (Ago) proteins, and thus function as
downstream effectors in the miRNA pathway, responsible
for inhibition of translation and acceleration of mRNA
decay. Members in this family are characterized by an
abnormally high content of glycine/tryptophan (G/W)
repeats, one or more glutamine (Q)-rich motifs, and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The only exception is the worm protein that does not
contain a recognizable RRM domain. The GW182 family
proteins are recruited to miRNA targets through an
interaction between their N-terminal domain and an
Argonaute protein. Then they promote translational
repression and/or degradation of miRNA targets through
their C-terminal silencing domain. .
Length = 71
Score = 25.4 bits (56), Expect = 5.0
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTI 66
G + Y E+A KA + LN L N T+
Sbjct: 38 GNALIRYSSKEEAAKAQSALNNCVLGNTTL 67
>gnl|CDD|241092 cd12648, RRM3_UHM_PUF60, RNA recognition motif 3 in UHM domain of
poly(U)-binding-splicing factor PUF60 and similar
proteins. This subgroup corresponds to the RRM3 of
PUF60, also termed FUSE-binding protein-interacting
repressor (FBP-interacting repressor or FIR), or
Ro-binding protein 1 (RoBP1), or Siah-binding protein 1
(Siah-BP1), an essential splicing factor that functions
as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
U2AF (U2 auxiliary factor) homology motifs (UHM) that
harbors another RRM and binds to tryptophan-containing
linear peptide motifs (UHM ligand motifs, ULMs) in
several nuclear proteins. The research indicates that
PUF60 binds FUSE as a dimer, and only the first two RRM
domains participate in the single-stranded DNA
recognition. .
Length = 98
Score = 25.8 bits (57), Expect = 5.1
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 10/37 (27%)
Query: 22 DAEICVFLISTAQSLGYGFVNYHRPEDAEKAINTLNG 58
DAEI V + FV + P +AEKAI LNG
Sbjct: 48 DAEIIVKI----------FVEFSLPSEAEKAIQALNG 74
>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 = 25.3 bits (56), Expect = 5.2
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+V LP + +EL+ FS +G++ + + D
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFD 34
>gnl|CDD|236674 PRK10364, PRK10364, sensor protein ZraS; Provisional.
Length = 457
Score = 26.7 bits (59), Expect = 5.3
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 62 QNKTIKVSYARPSSESIKGANLYVSGLPKHMSQQELESLFSPY 104
Q+ I V+ +SES G + V+ K ++ +LE++F+PY
Sbjct: 366 QHGVISVT----ASESGAGVKISVTDSGKGIAADQLEAIFTPY 404
>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 = 25.1 bits (55), Expect = 5.3
Identities = 8/31 (25%), Positives = 13/31 (41%)
Query: 32 TAQSLGYGFVNYHRPEDAEKAINTLNGLRLQ 62
+ + G+ + Y A AI TL+ L
Sbjct: 38 SGLNRGFAYAKYSDRRGASAAIATLHNYELP 68
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs) connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 25.2 bits (56), Expect = 5.8
Identities = 7/22 (31%), Positives = 15/22 (68%)
Query: 83 LYVSGLPKHMSQQELESLFSPY 104
L++ LP+ +++ LE LF+ +
Sbjct: 5 LFLQNLPEETTKEMLEMLFNQF 26
Score = 24.8 bits (55), Expect = 7.0
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRL-QNKTIKVS 69
G FV + E A A+ L G ++ +K+S
Sbjct: 39 GIAFVEFETEEQATVALQALQGFKITPGHAMKIS 72
>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the RRM1
of SRSF1, also termed alternative-splicing factor 1
(ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit.
SRSF1 is a splicing regulatory serine/arginine (SR)
protein involved in constitutive and alternative
splicing, nonsense-mediated mRNA decay (NMD), mRNA
export and translation. It also functions as a
splicing-factor oncoprotein that regulates apoptosis and
proliferation to promote mammary epithelial cell
transformation. SRSF1 is a shuttling SR protein and
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), separated by a long
glycine-rich spacer, and a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 25.1 bits (55), Expect = 5.8
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
+YV LP + +++E LF YG I
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAI 26
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show significant
sequence similarity to polypyrimidine tract binding
protein (PTB) that is an important negative regulator of
alternative splicing in mammalian cells and also
functions at several other aspects of mRNA metabolism,
including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 81
Score = 25.3 bits (55), Expect = 5.8
Identities = 9/29 (31%), Positives = 19/29 (65%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSR 111
L++ LP +++EL L P+G+I+ ++
Sbjct: 5 LHLRNLPWECTEEELIELCKPFGKIVNTK 33
>gnl|CDD|184587 PRK14241, PRK14241, phosphate transporter ATP-binding protein;
Provisional.
Length = 258
Score = 26.2 bits (58), Expect = 5.9
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 54 NTLNGLRLQNKTIKVSYARPSSESIKGANLY 84
N + GL+L K +S++GANL+
Sbjct: 105 NVVAGLKLNGVRNKKDLDELVEKSLRGANLW 135
>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 = 24.9 bits (54), Expect = 6.0
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 83 LYVSGLPKHMSQQELESLFSPYG 105
L+V LP +++++ + LF YG
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYG 26
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 26.3 bits (58), Expect = 6.0
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKV 68
+ P A+ A+ LNG++L K ++V
Sbjct: 314 ETALIEMADPYQAQLALTHLNGVKLFGKPLRV 345
>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 = 25.3 bits (56), Expect = 6.1
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 83 LYVSGLP-KHMSQQELESLFSPYGRIITSRIL 113
+ LP + + + + LFS G I RIL
Sbjct: 3 VVAVNLPEEESTIESVLELFSTCGVIALIRIL 34
>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate
ribonucleoprotein PTB-binding 1 (raver-1). This
subgroup corresponds to the RRM3 of raver-1, a
ubiquitously expressed heterogeneous nuclear
ribonucleoprotein (hnRNP) that serves as a co-repressor
of the nucleoplasmic splicing repressor polypyrimidine
tract-binding protein (PTB)-directed splicing of select
mRNAs. It shuttles between the cytoplasm and the
nucleus and can accumulate in the perinucleolar
compartment, a dynamic nuclear substructure that
harbors PTB. Raver-1 also modulates focal adhesion
assembly by binding to the cytoskeletal proteins,
including alpha-actinin, vinculin, and metavinculin (an
alternatively spliced isoform of vinculin) at adhesion
complexes, particularly in differentiated muscle
tissue. Raver-1 contains three N-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
two putative nuclear localization signals (NLS) at the
N- and C-termini, a central leucine-rich region, and a
C-terminal region harboring two PTB-binding
[SG][IL]LGxxP motifs. Raver1 binds to PTB through the
PTB-binding motifs at its C-terminal half, and binds to
other partners, such as RNA having the sequence
UCAUGCAGUCUG, through its N-terminal RRMs.
Interestingly, the 12-nucleotide RNA having the
sequence UCAUGCAGUCUG with micromolar affinity is found
in vinculin mRNA. Additional research indicates that
the RRM1 of raver-1 directs its interaction with the
tail domain of activated vinculin. Then the
raver1/vinculin tail (Vt) complex binds to vinculin
mRNA, which is permissive for vinculin binding to
F-actin. .
Length = 92
Score = 25.2 bits (55), Expect = 6.1
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTIKVSYARP 73
G+ + Y E AE +GL L I+VS+ P
Sbjct: 45 GFAVLEYESAEMAEMVQQQADGLSLAGSHIRVSFCAP 81
>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 = 25.7 bits (56), Expect = 6.1
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRIITSRILCD 115
L+V LP +++ L FS +G + + + D
Sbjct: 1 DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVID 36
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also
stimulate translation initiation. It contains a five
stranded beta sheet which forms an atypical RNA
recognition motif.
Length = 102
Score = 25.4 bits (56), Expect = 6.3
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 39 GFVNYHRPEDAEKAINTLNGLRLQNK 64
G+V + PE A+KA+ +L+ K
Sbjct: 40 GYVRFKTPEAAKKALEKATEAKLKIK 65
>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 = 25.1 bits (55), Expect = 6.4
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRIITSR 111
++V GLP++ +++ + +F G II R
Sbjct: 9 VFVGGLPENATEEIIREVFEQCGEIIAIR 37
>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 = 25.0 bits (55), Expect = 6.5
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 31 STAQSLGYGFVNYHRPEDAEKAINTLNG-LRLQNKTIKVSY 70
+T S G+ FV + E+A + + G L+LQ+ I + Y
Sbjct: 40 TTGASRGFAFVEFMSLEEATRWMELNQGKLQLQDYKITLHY 80
>gnl|CDD|236283 PRK08540, PRK08540, adenylosuccinate lyase; Reviewed.
Length = 449
Score = 26.1 bits (58), Expect = 6.5
Identities = 9/37 (24%), Positives = 21/37 (56%)
Query: 90 KHMSQQELESLFSPYGRIITSRILCDNLATENGKYYS 126
K+++++ELE L P I T+ + +N+ + ++
Sbjct: 413 KYLTEEELEELLDPETYIGTAPEIVENVIEKLKEWEK 449
>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 = 24.9 bits (55), Expect = 6.5
Identities = 7/26 (26%), Positives = 16/26 (61%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
++V L + M++++L FS +G +
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGEVT 28
>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 = 25.0 bits (55), Expect = 6.9
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRI 107
L V+G+PK +S L+ +F G +
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDV 28
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 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). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 24.9 bits (55), Expect = 7.1
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 80 GANLYVSGLPKHMSQQELESLFSPYGRI 107
G L+ SG+ + S+++L+ F +G +
Sbjct: 1 GCVLHFSGVGEQTSREDLKEAFEEFGEV 28
>gnl|CDD|240975 cd12531, RRM3_MEI2_like, RNA recognition motif 3 in plant
Mei2-like proteins. This subgroup corresponds to the
RRM3 of Mei2-like proteins, representing an ancient
eukaryotic RNA-binding proteins family. Their
corresponding Mei2-like genes appear to have arisen
early in eukaryote evolution, been lost from some
lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. Members in this family contain
three RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The C-terminal RRM (RRM3) is unique to
Mei2-like proteins and is highly conserved between
plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 86
Score = 25.0 bits (55), Expect = 7.1
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 36 LGYGFVNYHRPEDAEKAINTLNGLRLQN----KTIKVSYAR 72
+GY F+N PE NG + + K ++YAR
Sbjct: 42 VGYAFINMISPELIVPFYKAFNGKKWEKFNSEKVCSLAYAR 82
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human
c-myc gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 24.9 bits (55), Expect = 7.4
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 40 FVNYHRPEDAEKAINTLNG 58
FV + ++A KA+ LNG
Sbjct: 53 FVEFSDADEAIKAVRALNG 71
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 24.7 bits (54), Expect = 7.7
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
L++ L K + +L F +G II
Sbjct: 5 LFIGNLEKTTTYSDLREAFERFGEII 30
>gnl|CDD|166325 PLN02684, PLN02684, Probable galactinol--sucrose
galactosyltransferase.
Length = 750
Score = 26.1 bits (57), Expect = 7.9
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 74 SSESIKGANLYVSGLPKHMSQQELESLFSPYGRIITSRI 112
S+ +I G LYVS P + + L+ L P G I+ +R+
Sbjct: 495 SARAISGGPLYVSDAPGKHNFELLKKLVLPDGSILRARL 533
>gnl|CDD|241230 cd12786, RRM2_hnRPLL, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). The subgroup corresponds to the RRM2 of
hnRNP-LL which plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 96
Score = 25.0 bits (54), Expect = 7.9
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 41 VNYHRPEDAEKAINTLNGLRLQNK--TIKVSYARPS 74
V + A+KA LNG + T+K+ YARP+
Sbjct: 46 VEFESVHCAQKAKAALNGADIYAGCCTLKIEYARPT 81
>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the RRM
of SHARP, also termed Msx2-interacting protein (MINT),
or SPEN homolog, is an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 77
Score = 24.9 bits (55), Expect = 8.1
Identities = 8/26 (30%), Positives = 17/26 (65%)
Query: 83 LYVSGLPKHMSQQELESLFSPYGRII 108
+++ GL + +++Q L FS YG ++
Sbjct: 10 VWLDGLDESVTEQYLTRHFSRYGPVV 35
>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM1 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 = 70
Score = 24.4 bits (53), Expect = 8.8
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 85 VSGLPKHMSQQELESLFSPYG 105
+ LP +++QE+ L S Y
Sbjct: 4 IRNLPADVTKQEVHDLLSDYQ 24
>gnl|CDD|223228 COG0150, PurM, Phosphoribosylaminoimidazole (AIR) synthetase
[Nucleotide transport and metabolism].
Length = 345
Score = 25.6 bits (57), Expect = 8.8
Identities = 13/46 (28%), Positives = 16/46 (34%), Gaps = 1/46 (2%)
Query: 37 GYGFVNYHRPEDAEKAINTLNGLRLQNKTI-KVSYARPSSESIKGA 81
G G V EDAEKA+ L I +V +K
Sbjct: 300 GVGMVLIVPEEDAEKALALLKEQGETAYVIGRVEAGEGEVVGVKLN 345
>gnl|CDD|240984 cd12540, RRM_U2AFBPL, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL) and similar
proteins. This subgroup corresponds to the RRM of
U2AFBPL, a human homolog of the imprinted mouse gene
U2afbp-rs, which encodes a U2 small nuclear
ribonucleoprotein auxiliary factor 35 kDa
subunit-related protein 1 (U2AFBPL), also termed CCCH
type zinc finger, RNA-binding motif and serine/arginine
rich protein 1 (U2AF1RS1), or U2 small nuclear RNA
auxiliary factor 1-like 1 (U2AF1L1). Although the
biological role of U2AFBPL remains unclear, it shows
high sequence homology to splicing factor U2AF 35 kDa
subunit (U2AF35 or U2AF1) that directly binds to the 3'
splice site of the conserved AG dinucleotide and
performs multiple functions in the splicing process in
a substrate-specific manner. Like U2AF35, U2AFBPL
contains two N-terminal zinc fingers, a central RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal arginine/serine (SR)-rich domain. .
Length = 105
Score = 24.9 bits (55), Expect = 9.2
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 40 FVNYHRPEDAEKAINTLNG 58
+V Y E+A A NG
Sbjct: 73 YVQYQSEEEALAAFKMFNG 91
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
0.318 0.136 0.387
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,787,683
Number of extensions: 576808
Number of successful extensions: 1224
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1219
Number of HSP's successfully gapped: 488
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.7 bits)