RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16419
(346 letters)
>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 = 98.5 bits (246), Expect = 4e-26
Identities = 35/65 (53%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGMMVDG 104
K+FVGNL D T + E+R LF YGTV ECD+V+NYGFVH++ D IK LNG G
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKNYGFVHMEEEEDAEDAIKALNGYEFMG 60
Query: 105 KPMKV 109
K + V
Sbjct: 61 KRINV 65
Score = 73.4 bits (181), Expect = 8e-17
Identities = 25/38 (65%), Positives = 30/38 (78%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
K+F+GN+ T+ E +R LFEKYG V ECDVVKNYGFV
Sbjct: 1 KLFVGNLPDATTSEELRALFEKYGTVTECDVVKNYGFV 38
Score = 36.1 bits (84), Expect = 0.002
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIE 32
HME +E+ AIK LNG K + +E
Sbjct: 39 HMEEEEDAEDAIKALNGYEFMGKRINVE 66
>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 = 75.3 bits (185), Expect = 2e-17
Identities = 28/65 (43%), Positives = 40/65 (61%), Gaps = 1/65 (1%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDS-PDINKCIKELNGMMVDG 104
K+FVGNL E+R LF YG V+ECDI++NYGFVH+D ++ I+ L+ + G
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYGFVHMDDKTAADEAIRNLHHYKLHG 61
Query: 105 KPMKV 109
+ V
Sbjct: 62 VAINV 66
Score = 64.9 bits (158), Expect = 1e-13
Identities = 23/38 (60%), Positives = 32/38 (84%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
K+F+GN+ P + + IR LFE+YGKV+ECD++KNYGFV
Sbjct: 2 KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYGFV 39
>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 = 69.9 bits (171), Expect = 2e-15
Identities = 28/66 (42%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHID-SPDINKCIKELNGMMVD 103
K+FVGN+S + E+R LF +G VVECD V++Y FVH++ + I+ LNG V
Sbjct: 1 WKIFVGNVSATCTSDELRGLFEEFGRVVECDKVKDYAFVHMEREEEALAAIEALNGKEVK 60
Query: 104 GKPMKV 109
G+ + V
Sbjct: 61 GRRINV 66
Score = 56.0 bits (135), Expect = 2e-10
Identities = 21/38 (55%), Positives = 30/38 (78%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
KIF+GNV+ + + +R LFE++G+VVECD VK+Y FV
Sbjct: 2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKDYAFV 39
Score = 33.7 bits (77), Expect = 0.012
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIE 32
HME +EE AI+ LNG+ V + + +E
Sbjct: 40 HMEREEEALAAIEALNGKEVKGRRINVE 67
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 68.8 bits (169), Expect = 5e-15
Identities = 28/73 (38%), Positives = 41/73 (56%), Gaps = 9/73 (12%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKE 96
+FVGNL +T E+RELF +G V +VR+ + FV +S D K ++
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60
Query: 97 LNGMMVDGKPMKV 109
LNG +DG+P+KV
Sbjct: 61 LNGKELDGRPLKV 73
Score = 47.2 bits (113), Expect = 2e-07
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+F+GN+ P T+ E +R LF K+GKV +V K + FV
Sbjct: 1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFV 46
Score = 26.0 bits (58), Expect = 7.1
Identities = 9/27 (33%), Positives = 19/27 (70%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKI 31
E++E+ A++ LNG+ ++ +PLK+
Sbjct: 47 EFESEEDAEKALEALNGKELDGRPLKV 73
>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 = 67.2 bits (164), Expect = 2e-14
Identities = 25/65 (38%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHI-DSPDINKCIKELNGMMVDG 104
K+FVGN+ ++T E+R LF YG V+ C ++R + FVH+ ++ I+ELNG + G
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQFAFVHLRGEAAADRAIEELNGRELHG 61
Query: 105 KPMKV 109
+ + V
Sbjct: 62 RKLVV 66
Score = 49.1 bits (117), Expect = 5e-08
Identities = 20/38 (52%), Positives = 27/38 (71%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
KIF+GNV+ TS E +R LFE YG V+ C V++ + FV
Sbjct: 2 KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQFAFV 39
Score = 28.2 bits (63), Expect = 1.0
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIE 32
H+ + AI+ELNG+ ++ + L +E
Sbjct: 40 HLRGEAAADRAIEELNGRELHGRKLVVE 67
>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 = 65.4 bits (160), Expect = 7e-14
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSP-DINKCIKELN 98
+FVGNL +T ++RELF +G + IVR+ + FV +SP D K ++ LN
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 99 GMMVDGKPMKV 109
G +DG+ +KV
Sbjct: 61 GKELDGRKLKV 71
Score = 45.0 bits (107), Expect = 1e-06
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 7/44 (15%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+F+GN+ P T+ E +R LF K+G++ +V K + FV
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFV 44
Score = 25.7 bits (57), Expect = 8.6
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIE 32
E+ E+ A++ LNG+ ++ + LK+
Sbjct: 45 EFESPEDAEKALEALNGKELDGRKLKVS 72
>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous
nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA
recognition motif 1 (hRBMY), testis-specific
heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T)
and similar proteins. This subfamily corresponds to the
RRM domain of hnRNP G, also termed glycoprotein p43 or
RBMX, an RNA-binding motif protein located on the X
chromosome. It is expressed ubiquitously and has been
implicated in the splicing control of several pre-mRNAs.
Moreover, hnRNP G may function as a regulator of
transcription for SREBP-1c and GnRH1. Research has shown
that hnRNP G may also act as a tumor-suppressor since it
upregulates the Txnip gene and promotes the fidelity of
DNA end-joining activity. In addition, hnRNP G appears
to play a critical role in proper neural development of
zebrafish and frog embryos. The family also includes
several paralogs of hnRNP G, such as hRBMY and hnRNP G-T
(also termed RNA-binding motif protein,
X-linked-like-2). Both, hRBMY and hnRNP G-T, are
exclusively expressed in testis and critical for male
fertility. Like hnRNP G, hRBMY and hnRNP G-T interact
with factors implicated in the regulation of pre-mRNA
splicing, such as hTra2-beta1 and T-STAR. Although
members in this family share a high conserved N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), they
appear to recognize different RNA targets. For instance,
hRBMY interacts specifically with a stem-loop structure
in which the loop is formed by the sequence CA/UCAA. In
contrast, hnRNP G associates with single stranded RNA
sequences containing a CCA/C motif. In addition to the
RRM, hnRNP G contains a nascent transcripts targeting
domain (NTD) in the middle region and a novel auxiliary
RNA-binding domain (RBD) in its C-terminal region. The
C-terminal RBD exhibits distinct RNA binding
specificity, and would play a critical role in the
regulation of alternative splicing by hnRNP G. .
Length = 80
Score = 62.6 bits (153), Expect = 1e-12
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIK 95
K+FV LS T E+ LF +G V E ++ R +GFV +S D + I+
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61
Query: 96 ELNGMMVDGKPMKVVVA 112
+LNG ++G+ +KV A
Sbjct: 62 DLNGKELEGRVIKVEKA 78
Score = 39.9 bits (94), Expect = 1e-04
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+F+ ++ T+ + + LF K+G+V E ++K+ +GFV
Sbjct: 3 KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFV 48
Score = 34.1 bits (79), Expect = 0.013
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAAT 35
E+ E+ AI++LNG+ + + +K+E A
Sbjct: 50 FESVEDADAAIRDLNGKELEGRVIKVEKAK 79
>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 = 60.4 bits (146), Expect = 5e-12
Identities = 28/66 (42%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHID-SPDINKCIKELNGMMVD 103
TK+ VGN+S + E+R F YG V+ECDIV++Y FVH++ + D + I+ L+
Sbjct: 1 TKLHVGNISSSCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQ 60
Query: 104 GKPMKV 109
GK M V
Sbjct: 61 GKRMHV 66
Score = 50.0 bits (119), Expect = 2e-08
Identities = 17/38 (44%), Positives = 28/38 (73%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
K+ +GN++ + + +R FE+YG V+ECD+VK+Y FV
Sbjct: 2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKDYAFV 39
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 63.8 bits (154), Expect = 2e-11
Identities = 31/106 (29%), Positives = 48/106 (45%), Gaps = 9/106 (8%)
Query: 20 NGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-- 77
+ E E+ SR+ +FVGNL + ++RELF +G V +V
Sbjct: 91 TKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD 150
Query: 78 ------RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVAGFIS 116
R + FV +S K I+ELNG ++G+P++V A S
Sbjct: 151 RETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPAS 196
Score = 39.2 bits (90), Expect = 0.002
Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 23/91 (25%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTP--------------------- 43
E++E AI+ELNG+ + +PL+++ A P +
Sbjct: 163 EFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLL 222
Query: 44 --TTKVFVGNLSDNTRAPEVRELFVPYGTVV 72
+ ++VGNL T E+ +LF G +V
Sbjct: 223 EKSDNLYVGNLPLKTAEEELADLFKSRGDIV 253
Score = 36.1 bits (82), Expect = 0.019
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 294 IEARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGF 345
E+ S +F+GN+ + E +R LF+K+G V +V + + F
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAF 161
Query: 346 V 346
V
Sbjct: 162 V 162
>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 = 58.8 bits (143), Expect = 2e-11
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-DINKCIKELN 98
+FVGNL +T ++++LF +G + IV + + FV + D K ++ LN
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 99 GMMVDGKPMK 108
G + G+ ++
Sbjct: 61 GKELGGRELR 70
Score = 46.4 bits (111), Expect = 4e-07
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 7/44 (15%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+F+GN+ P T+ E ++ LF K+G + +V K + FV
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFV 44
>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 = 57.3 bits (139), Expect = 7e-11
Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDS-PDINKCIKELNGMMV 102
++FVGNL ++ E +ELF YG V E + + +GF+ +D+ + K EL+G+M
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFIRLDTRTNAEKAKAELDGIMR 62
Query: 103 DGKPMKV 109
G+ ++V
Sbjct: 63 KGRQLRV 69
Score = 38.4 bits (90), Expect = 3e-04
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
++F+GN+ + E + LF KYG+V E + K +GF+
Sbjct: 3 RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEKGFGFI 42
>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 = 55.7 bits (135), Expect = 3e-10
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 9/76 (11%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKE 96
++VGNL N ++++LF +G V ++ R +GFV +++ + N I++
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60
Query: 97 LNGMMVDGKPMKVVVA 112
LNG G+ + V A
Sbjct: 61 LNGTDFGGRTLTVNEA 76
Score = 30.3 bits (69), Expect = 0.28
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAA 34
ME EE AI++LNG + L + A
Sbjct: 48 METAEEANAAIEKLNGTDFGGRTLTVNEA 76
Score = 29.5 bits (67), Expect = 0.53
Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+++GN+ + E ++ LF ++G+V V+ + +GFV
Sbjct: 1 NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFV 46
>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 = 54.9 bits (133), Expect = 4e-10
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPD-INKCIKELNG 99
+V NL D+ +RE F P+GT+ ++ + +GFV SP+ K + E+NG
Sbjct: 5 YVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNG 64
Query: 100 MMVDGKPMKVVVA 112
++ GKP+ V +A
Sbjct: 65 RIIGGKPLYVALA 77
Score = 29.1 bits (66), Expect = 0.71
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 10 EEGRTAIKELNGQIVNEKPL 29
EE A+ E+NG+I+ KPL
Sbjct: 53 EEATKAVTEMNGRIIGGKPL 72
>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 = 54.9 bits (133), Expect = 4e-10
Identities = 24/67 (35%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDS-PDINKCIKELNGMMVDGK 105
++V NL +T ++RELF YG V +++Y FVH + D K ++E+NG ++G
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDYAFVHFEERDDAVKAMEEMNGKELEGS 63
Query: 106 PMKVVVA 112
P++V +A
Sbjct: 64 PIEVSLA 70
Score = 32.2 bits (74), Expect = 0.053
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
+++ N+ T+ E +R LF +YG+V +K+Y FV
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDYAFV 40
Score = 27.2 bits (61), Expect = 2.9
Identities = 8/30 (26%), Positives = 18/30 (60%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAA 34
H E ++ A++E+NG+ + P+++ A
Sbjct: 41 HFEERDDAVKAMEEMNGKELEGSPIEVSLA 70
>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 = 57.9 bits (140), Expect = 3e-09
Identities = 26/94 (27%), Positives = 47/94 (50%), Gaps = 13/94 (13%)
Query: 27 KPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------- 79
+ L+ E +G N ++V NL D ++RELF G + ++ +
Sbjct: 273 EELQQERKMKAQGVN-----LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRG 327
Query: 80 YGFVHIDSPD-INKCIKELNGMMVDGKPMKVVVA 112
+GFV +P+ N+ + E++G M+ GKP+ V +A
Sbjct: 328 FGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA 361
Score = 52.5 bits (126), Expect = 2e-07
Identities = 29/121 (23%), Positives = 57/121 (47%), Gaps = 14/121 (11%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIE---AATSRKGPNTPT-TKVFVGNLSDNTRAPE 60
H E +E + AI+++NG ++N+K + + R+ T ++V NL + +
Sbjct: 135 HFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDK 194
Query: 61 VRELFVPYGTVVECDI-------VRNYGFVHIDSP-DINKCIKELNGMMVDG--KPMKVV 110
+RELF +G + + R + FV+ + D K ++E+NG + + K+
Sbjct: 195 LRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY 254
Query: 111 V 111
V
Sbjct: 255 V 255
Score = 49.4 bits (118), Expect = 2e-06
Identities = 29/113 (25%), Positives = 56/113 (49%), Gaps = 15/113 (13%)
Query: 15 AIKELNGQIVNEKPLKIEAATSRKGPNTP---TTKVFVGNLSDNTRAPEVRELFVPYGTV 71
A++ +N + + KP++I S++ P+ +FV NL + + + F +G +
Sbjct: 58 ALETMNFKRLGGKPIRI--MWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNI 115
Query: 72 VECDIV-------RNYGFVHIDSPD-INKCIKELNGMMVDGKPMKVVVAGFIS 116
+ C + R YGFVH + + I+++NGM+++ K +V V FI
Sbjct: 116 LSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK--EVYVGRFIK 166
Score = 37.1 bits (86), Expect = 0.012
Identities = 18/72 (25%), Positives = 40/72 (55%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKEL 97
++VG+L + ++ +LF P+G V+ + R+ YG+V+ +P D + ++ +
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62
Query: 98 NGMMVDGKPMKV 109
N + GKP+++
Sbjct: 63 NFKRLGGKPIRI 74
Score = 32.5 bits (74), Expect = 0.31
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 8 NDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
N EE A+ E++G+++ KPL + A +
Sbjct: 335 NPEEANRAVTEMHGRMLGGKPLYVALAQRK 364
Score = 32.5 bits (74), Expect = 0.35
Identities = 10/44 (22%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+++ N++ + E +R LF + G++ V+ + +GFV
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFV 331
Score = 29.8 bits (67), Expect = 2.4
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 306 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
G IF+ N++ + + F K+G ++ C V + YGFV
Sbjct: 87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFV 134
Score = 28.2 bits (63), Expect = 7.4
Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 12/59 (20%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDV-------VKNYGFV 346
EA + F+++ ++ N++P + + +R LF K+G++ V + + FV
Sbjct: 171 EAAPLKKFTNL-----YVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFV 224
>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 = 51.4 bits (124), Expect = 8e-09
Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 8/73 (10%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSP-DINKCIKE 96
T V+V NL ++ +++ELF YG + ++++ +GFV+ ++ K ++E
Sbjct: 2 TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61
Query: 97 LNGMMVDGKPMKV 109
LNG V+GK + V
Sbjct: 62 LNGKEVNGKKLYV 74
Score = 30.6 bits (70), Expect = 0.21
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 7/44 (15%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+++ N+ E ++ LF KYGK+ V+ K +GFV
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFV 47
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 49.5 bits (119), Expect = 4e-08
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 7/67 (10%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHIDSP-DINKCIKELNG 99
++V NL + ++RE F PYG V +V R + FV SP D +K+LNG
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 100 MMVDGKP 106
+++DG+
Sbjct: 61 LVLDGRT 67
Score = 32.9 bits (76), Expect = 0.024
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN------YGFV 346
+++ N+ P + E +R F YGKV +V+N + FV
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFV 43
>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 = 49.1 bits (118), Expect = 4e-08
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 46 KVFVGNL-SDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGMMVD 103
+VFVGNL +D ++ E+F YG ++ + + YGFV D+ D + NG +
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDARAAVAGENGREIA 61
Query: 104 GKPMKV 109
G+ + +
Sbjct: 62 GQKLDI 67
Score = 44.9 bits (107), Expect = 2e-06
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 309 KIFIGNVNPG-TSVELIRPLFEKYGKVVECDVVKNYGFV 346
++F+GN+N S E + +F KYGK++ + K YGFV
Sbjct: 2 RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFV 40
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Although the
cellular function of RBM23 remains unclear, it shows
high sequence homology to RBM39 and contains two RRMs.
It may possibly function as a pre-mRNA splicing factor.
.
Length = 73
Score = 46.9 bits (112), Expect = 3e-07
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 9/71 (12%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCIKELN 98
+VGNL N ++R +F P+G + + R+ YGF+ D+ D K +++LN
Sbjct: 2 YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61
Query: 99 GMMVDGKPMKV 109
G + G+P+KV
Sbjct: 62 GFELAGRPIKV 72
>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM2 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is a
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence in
its 5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Unlike other PABPs, PABP-5 contains only
four RRMs, but lacks both the linker region and the CTD.
PABP-1-like and PABP-1-like 2 are the orthologs of
PABP-1. PABP-4-like is the ortholog of PABP-5. Their
cellular functions remain unclear. The family also
includes the yeast PABP, a conserved poly(A) binding
protein containing poly(A) tails that can be attached to
the 3'-ends of mRNAs. The yeast PABP and its homologs
may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 77
Score = 46.8 bits (112), Expect = 3e-07
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 10/74 (13%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSPD-INKCIKELN 98
+F+ NL + + + F +G ++ C + + YGFVH ++ + + I+++N
Sbjct: 5 IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64
Query: 99 GMMVDGKPMKVVVA 112
GM+++ K KV V
Sbjct: 65 GMLLNDK--KVFVG 76
Score = 29.4 bits (67), Expect = 0.59
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 18/47 (38%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGN 51
H E +E AI+++NG ++N+K KVFVG
Sbjct: 49 HFETEEAAVRAIEKVNGMLLNDK------------------KVFVGP 77
>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 = 45.9 bits (109), Expect = 6e-07
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGMMVDG 104
+++V +T +RE+F PYG V E ++ N+ FV +S + ++G +++
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISNFAFVEFESLESAIRAKDSVHGKVLNN 60
Query: 105 KPMKVV 110
P+ V
Sbjct: 61 NPLYVT 66
Score = 37.4 bits (87), Expect = 6e-04
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
++++ P TS IR +F YG V E ++ N+ FV
Sbjct: 1 RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISNFAFV 38
>gnl|CDD|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding
protein 19 (RBM19 or RBD-1) and similar proteins. This
subfamily corresponds to the RRM5 of RBM19 and RRM4 of
MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1),
is a nucleolar protein conserved in eukaryotes involved
in ribosome biogenesis by processing rRNA and is
essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 82
Score = 46.1 bits (110), Expect = 7e-07
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 14/74 (18%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------------YGFVHIDSPD-I 90
T +FV NL+ T +++ F G V I + YGFV S +
Sbjct: 1 TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60
Query: 91 NKCIKELNGMMVDG 104
K +K L G ++DG
Sbjct: 61 QKALKRLQGTVLDG 74
Score = 36.0 bits (84), Expect = 0.003
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 13/50 (26%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------------YGFV 346
+F+ N+N T+ E ++ FEK G V + K YGFV
Sbjct: 3 LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFV 52
>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 = 45.8 bits (109), Expect = 7e-07
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNG 99
+V++G L R +V F YG + E ++ +GFV + P D + + ELNG
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINLKNGFGFVEFEDPRDADDAVYELNG 55
Score = 32.7 bits (75), Expect = 0.037
Identities = 9/38 (23%), Positives = 20/38 (52%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
+++IG + + F+ YG++ E ++ +GFV
Sbjct: 1 RVYIGRLPYRARERDVERFFKGYGRIREINLKNGFGFV 38
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 45.9 bits (109), Expect = 8e-07
Identities = 26/77 (33%), Positives = 36/77 (46%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIK 95
T + V L N E+R LF G + C ++R+ YGFV+ P D K I
Sbjct: 2 TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61
Query: 96 ELNGMMVDGKPMKVVVA 112
LNG+ + K +KV A
Sbjct: 62 TLNGLRLQNKTIKVSYA 78
>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 = 45.8 bits (109), Expect = 8e-07
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 9/76 (11%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKE 96
+FVGNLS + ++ F +GTVV ++ R +G+V +SP D K I+
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60
Query: 97 LNGMMVDGKPMKVVVA 112
++G +DG+P+ V +
Sbjct: 61 MDGKELDGRPINVDFS 76
Score = 30.4 bits (69), Expect = 0.21
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+F+GN++ E ++ FEK+G VV V+ + +G+V
Sbjct: 1 TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYV 46
>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 = 45.7 bits (108), Expect = 8e-07
Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHI-DSPDINKCIKELNG 99
+V++G LS + R +++ F YG ++E D+ YGFV DS D + + ELNG
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLKNGYGFVEFEDSRDADDAVYELNG 55
Score = 29.9 bits (67), Expect = 0.37
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
+++IG ++ + I+ F YGK++E D+ YGFV
Sbjct: 1 RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLKNGYGFV 38
>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 = 45.4 bits (107), Expect = 1e-06
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGMMVDG 104
+V++G LS R +V F YG ++E D+ YGFV D D + + ELNG + G
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCG 60
Query: 105 KPMKVVV 111
+ +V+V
Sbjct: 61 E--RVIV 65
Score = 29.6 bits (66), Expect = 0.42
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
+++IG ++ + F+ YGK++E D+ YGFV
Sbjct: 1 RVYIGRLSYQARERDVERFFKGYGKILEVDLKNGYGFV 38
>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 = 45.2 bits (108), Expect = 1e-06
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKEL 97
+ VG L+ N ++E+F YGTV + D+ R Y +V +SP D K IK +
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60
Query: 98 NGMMVDGKPMKV 109
+G +DG+ + V
Sbjct: 61 DGGQIDGQEVTV 72
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 49.5 bits (118), Expect = 1e-06
Identities = 32/135 (23%), Positives = 62/135 (45%), Gaps = 20/135 (14%)
Query: 9 DEEGRTAIKELNGQIVNEKPLKI---EAATSRKGPNTPTT--------KVFVGNLSDNTR 57
D E L GQ++ +P+ + +A +R K++VGNL N
Sbjct: 140 DVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNIT 199
Query: 58 APEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKCIKELNGMMVDGKPMK 108
E+R++F P+G + + + R+ +GF+ D+ + + ++ +NG + G+P+K
Sbjct: 200 EQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIK 259
Query: 109 VVVAGFISSILSCLN 123
V A + +L N
Sbjct: 260 VGYAQDSTYLLDAAN 274
Score = 34.5 bits (79), Expect = 0.074
Identities = 27/118 (22%), Positives = 42/118 (35%), Gaps = 17/118 (14%)
Query: 9 DEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTT---------KVFVGNLSDNTRAP 59
GR+ + N R G NT VFV L+ R
Sbjct: 45 GRRGRSRSRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARER 104
Query: 60 EVRELFVPYGTVVECDIV------RNYGFVHIDSPDINKCIK--ELNGMMVDGKPMKV 109
++ E F G V + + R+ G +++ D+ IK L G M+ G+P+ V
Sbjct: 105 DLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIV 162
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMM 101
KV+VGNL E+ + F YG + + RN + FV + P D ++ L+G
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60
Query: 102 VDGKPMKV 109
+ G ++V
Sbjct: 61 ICGNRVRV 68
Score = 33.7 bits (78), Expect = 0.016
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---YGFV 346
K+++GN+ P + + FEKYG + V +N + FV
Sbjct: 1 KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFV 41
>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 = 44.7 bits (106), Expect = 2e-06
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 9/73 (12%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHIDSPD-INKCIKE 96
++FVGNL + E++E F +G V+E I + N+GFV D P+ + K +
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64
Query: 97 LNGMMVDGKPMKV 109
+ V
Sbjct: 65 KPIYFRGDHRLNV 77
Score = 35.8 bits (83), Expect = 0.003
Identities = 11/46 (23%), Positives = 26/46 (56%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDV--------VKNYGFV 346
++F+GN+ + + ++ F+++G V+E + + N+GFV
Sbjct: 5 QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFV 50
>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 = 44.2 bits (105), Expect = 3e-06
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 7/71 (9%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPDINKCIKELN 98
++FVG + +T E+R+ F +G+V + I+ + YGFV ++ + + I +
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMG 63
Query: 99 GMMVDGKPMKV 109
+ GK + +
Sbjct: 64 NLNFRGKKLNI 74
Score = 35.3 bits (82), Expect = 0.004
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 7/45 (15%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+IF+G + P T+ E +R F ++G V + ++ K YGFV
Sbjct: 4 RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFV 48
>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 = 44.0 bits (104), Expect = 3e-06
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 47 VFVGNLSD-NTRAPEVRELFVPYGTVVECDIVRNYGFVHI-DSPDINKCIKELNGMMVDG 104
+FV TR ++ +LF P+G +V CDI + + FV DS D K ++ L+G +DG
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTFAFVEFEDSEDATKALEALHGSRIDG 61
Query: 105 KPMKV 109
+ V
Sbjct: 62 SVLTV 66
Score = 37.0 bits (86), Expect = 8e-04
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 310 IFIGNVNPG-TSVELIRPLFEKYGKVVECDVVKNYGFV 346
+F+ +PG T E I LFE +G +V CD+ K + FV
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTFAFV 39
>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 = 44.5 bits (105), Expect = 3e-06
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 9/77 (11%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINK-CIKE 96
K+F+G LS +T + ++F YG + E +V R +GFV ++PD K +
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61
Query: 97 LNGMMVDGKPMKVVVAG 113
+NG VDG+ ++V AG
Sbjct: 62 MNGKSVDGRQIRVDQAG 78
Score = 33.3 bits (76), Expect = 0.022
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ + + +F KYG++ E VVK+ +GFV
Sbjct: 2 KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFV 47
>gnl|CDD|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM3 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD complex.
SHARP recruits HDAC activity and binds to the steroid
receptor RNA coactivator SRA through four conserved
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), further suppressing SRA-potentiated steroid
receptor transcription activity. Thus, SHARP has the
capacity to modulate both liganded and nonliganded
nuclear receptors. SHARP also has been identified as a
component of transcriptional repression complexes in
Notch/RBP-Jkappa signaling pathways. In addition to the
N-terminal RRMs, SHARP possesses a C-terminal SPOC
domain (Spen paralog and ortholog C-terminal domain),
which is highly conserved among Spen proteins. .
Length = 74
Score = 43.9 bits (104), Expect = 4e-06
Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDI-----VRNYGFV-HIDSPDINKCIKEL 97
T +F+GNL T ++RE F +G +++ DI Y F+ + D + K ++++
Sbjct: 2 TRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKM 61
Query: 98 NGMMVDGKPMKV 109
+G + +K+
Sbjct: 62 DGEYLGNNRVKL 73
Score = 35.1 bits (81), Expect = 0.005
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 5/45 (11%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-----YGFV 346
T +FIGN+ T+ +R FE++G++++ D+ K Y F+
Sbjct: 2 TRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFI 46
>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like
family of RNA binding proteins CELF1, CELF2, CELF3,
CELF4, CELF5, CELF6 and similar proteins. This subgroup
corresponds to the RRM3 of the CUGBP1 and ETR-3-like
factors (CELF) or BRUNOL (Bruno-like) proteins, a family
of structurally related RNA-binding proteins involved in
the regulation of pre-mRNA splicing in the nucleus and
in the control of mRNA translation and deadenylation in
the cytoplasm. The family contains six members: CELF-1
(also termed BRUNOL-2, or CUG-BP1, or NAPOR, or
EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or
CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or
TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also
termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6
(also termed BRUNOL-6). They all contain three highly
conserved RNA recognition motifs (RRMs), also known as
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains): two consecutive RRMs (RRM1 and RRM2) situated
in the N-terminal region followed by a linker region and
the third RRM (RRM3) close to the C-terminus of the
protein. The low sequence conservation of the linker
region is highly suggestive of a large variety in the
co-factors that associate with the various CELF family
members. Based on both sequence similarity and function,
the CELF family can be divided into two subfamilies, the
first containing CELFs 1 and 2, and the second
containing CELFs 3, 4, 5, and 6. The different CELF
proteins may act through different sites on at least
some substrates. Furthermore, CELF proteins may interact
with each other in varying combinations to influence
alternative splicing in different contexts. .
Length = 73
Score = 43.8 bits (104), Expect = 4e-06
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 60 EVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKV 109
++ +LF P+G V+ + + +GFV D+P IK +NG V GK +KV
Sbjct: 14 DLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKV 72
Score = 26.4 bits (59), Expect = 5.6
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 7 ENDEEGRTAIKELNGQIVNEKPLKIE 32
+N E + AIK +NG V K LK++
Sbjct: 48 DNPESAQAAIKAMNGFQVGGKRLKVQ 73
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 43.8 bits (104), Expect = 4e-06
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 11/72 (15%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDS-PDINKCIKEL 97
VF LS T ++RE+F YG + + +V R +GFV+ +S D + + L
Sbjct: 4 VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61
Query: 98 NGMMVDGKPMKV 109
NGM +DG+ ++V
Sbjct: 62 NGMEIDGRRIRV 73
Score = 26.8 bits (60), Expect = 4.0
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 8/31 (25%)
Query: 324 IRPLFEKYGKVVECDVV--------KNYGFV 346
+R +F +YG + + VV + +GFV
Sbjct: 16 LREVFSRYGPIEKVQVVYDQKTGRSRGFGFV 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 = 43.8 bits (104), Expect = 4e-06
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKEL 97
+FV NL +T ++ E F G + C +V++ +G+V D + ++E
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61
Query: 98 NGMMVDGKPMKVVVA 112
G+ + V A
Sbjct: 62 KKTKFGGRKIHVEFA 76
Score = 28.7 bits (65), Expect = 0.96
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYG 344
+F+ N+ T+ E + F + G + C VVK+ G
Sbjct: 2 LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKG 36
>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 = 43.5 bits (103), Expect = 5e-06
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 9/71 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCIKEL 97
+FVG+LS +R F P+G + + +V++ YGFV + D I+ +
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61
Query: 98 NGMMVDGKPMK 108
NG + G+ ++
Sbjct: 62 NGQWLGGRAIR 72
Score = 38.9 bits (91), Expect = 2e-04
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
IF+G+++P E +R F +G++ + VVK+ YGFV
Sbjct: 2 IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFV 46
>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 = 43.6 bits (103), Expect = 5e-06
Identities = 19/74 (25%), Positives = 44/74 (59%), Gaps = 7/74 (9%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHIDSP-DINKCIKELN 98
++ V N+ R P++R++F +G +++ +I+ N +GFV + D ++ ++L+
Sbjct: 2 RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLH 61
Query: 99 GMMVDGKPMKVVVA 112
G +V+G+ ++V A
Sbjct: 62 GTVVEGRKIEVNNA 75
>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein A subfamily.
This subfamily corresponds to the RRM2 of hnRNP A0,
hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins.
hnRNP A0 is a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is
an abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A3 is also a RNA trafficking response
element-binding protein that participates in the
trafficking of A2RE-containing RNA. The hnRNP A
subfamily is characterized by two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 73
Score = 43.4 bits (103), Expect = 5e-06
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCI 94
K+FVG L ++ ++RE F YG V +IV R + FV D D ++K +
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58
Score = 31.8 bits (73), Expect = 0.071
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
K+F+G + + E +R F +YG V ++V + + FV
Sbjct: 1 KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFV 46
>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 = 43.5 bits (103), Expect = 6e-06
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKEL 97
K+FVG L + E +E F +G VV+ ++ R +GFV DS + +
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60
Query: 98 NGMMVDGKPMKV 109
+ + GK ++V
Sbjct: 61 GMLELGGKQVEV 72
Score = 32.7 bits (75), Expect = 0.031
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
KIF+G + P + E + F ++GKVV+ ++ + +GFV
Sbjct: 1 KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFV 46
>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 = 43.1 bits (102), Expect = 7e-06
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHIDSPD-INKCIKELNG 99
+FVG LS + E+ E F +G ++E +++ + F+ + + ++ N
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65
Query: 100 MMVDGKPMKV 109
M+ K M V
Sbjct: 66 SMLKNKTMHV 75
Score = 41.9 bits (99), Expect = 2e-05
Identities = 10/34 (29%), Positives = 23/34 (67%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK 341
+ IF+G ++P + E + F ++GK++E +++K
Sbjct: 4 YSIFVGQLSPDVTKEELNERFSRHGKILEVNLIK 37
>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein
Musashi homologs Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM2.in
Musashi-1 (also termed Msi1), a neural RNA-binding
protein putatively expressed in central nervous system
(CNS) stem cells and neural progenitor cells, and
associated with asymmetric divisions in neural
progenitor cells. It is evolutionarily conserved from
invertebrates to vertebrates. Musashi-1 is a homolog of
Drosophila Musashi and Xenopus laevis nervous
system-specific RNP protein-1 (Nrp-1). It has been
implicated in the maintenance of the stem-cell state,
differentiation, and tumorigenesis. It translationally
regulates the expression of a mammalian numb gene by
binding to the 3'-untranslated region of mRNA of Numb,
encoding a membrane-associated inhibitor of Notch
signaling, and further influences neural development.
Moreover, Musashi-1 represses translation by interacting
with the poly(A)-binding protein and competes for
binding of the eukaryotic initiation factor-4G (eIF-4G).
Musashi-2 (also termed Msi2) has been identified as a
regulator of the hematopoietic stem cell (HSC)
compartment and of leukemic stem cells after
transplantation of cells with loss and gain of function
of the gene. It influences proliferation and
differentiation of HSCs and myeloid progenitors, and
further modulates normal hematopoiesis and promotes
aggressive myeloid leukemia. Both, Musashi-1 and
Musashi-2, contain two conserved N-terminal tandem RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), along with
other domains of unknown function. .
Length = 74
Score = 42.8 bits (101), Expect = 8e-06
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDI--NKC-- 93
K+FVG LS NT +V++ F +G V + ++ R +GFV +S D+ C
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60
Query: 94 -IKELNGMMVDGK 105
E+N MV+ K
Sbjct: 61 HFHEINNKMVECK 73
Score = 35.5 bits (82), Expect = 0.004
Identities = 12/46 (26%), Positives = 26/46 (56%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
KIF+G ++ T+ + ++ F ++GKV + ++ + +GFV
Sbjct: 1 KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFV 46
>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 = 42.6 bits (100), Expect = 9e-06
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNG 99
+VF+G L+ R +V F YG + + D+ R +GFV D P D + + EL+G
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFDDPRDADDAVYELDG 55
Score = 34.5 bits (79), Expect = 0.007
Identities = 12/38 (31%), Positives = 24/38 (63%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
++FIG +NP + + F+ YG++ + D+ + +GFV
Sbjct: 1 RVFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFV 38
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 42.9 bits (102), Expect = 1e-05
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 10/73 (13%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD--INKCIKE 96
+FVG LS + ++ E F +GTV + +I+ R + ++ + + + + KC
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61
Query: 97 LNGMMVDGKPMKV 109
LNG G +K+
Sbjct: 62 LNGTKWKGSVLKI 74
Score = 30.6 bits (70), Expect = 0.23
Identities = 7/32 (21%), Positives = 19/32 (59%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVK 341
+F+G ++P + + F ++G V + +++K
Sbjct: 2 LFVGGLSPSVTESDLEERFSRFGTVSDVEIIK 33
>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 = 42.8 bits (100), Expect = 1e-05
Identities = 28/77 (36%), Positives = 36/77 (46%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCIK 95
T + V L N E R LF G + C +VR+ YGFV +ID D K I
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 96 ELNGMMVDGKPMKVVVA 112
LNG+ + K +KV A
Sbjct: 63 TLNGLRLQTKTIKVSYA 79
>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 = 41.4 bits (98), Expect = 2e-05
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 13/71 (18%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCIKE-- 96
F+G LS +T +RE F YG VV+C I+ R +GFV P ++K +
Sbjct: 2 FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61
Query: 97 --LNGMMVDGK 105
L+G +D K
Sbjct: 62 HVLDGREIDPK 72
Score = 36.0 bits (84), Expect = 0.002
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+FIG ++ T+ E +R F KYG+VV+C ++K+ +GFV
Sbjct: 1 LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFV 45
>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 = 41.6 bits (98), Expect = 3e-05
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 14/68 (20%)
Query: 49 VGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKCI----- 94
V LS T+A ++++LF YG VV IV N +GFV + + KCI
Sbjct: 4 VSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHLHR 63
Query: 95 KELNGMMV 102
EL+G ++
Sbjct: 64 TELHGRVI 71
Score = 29.6 bits (67), Expect = 0.39
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+++ ++ T ++ LF KYGKVV +V N +GFV
Sbjct: 2 LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFV 46
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 43.5 bits (102), Expect = 3e-05
Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 9/101 (8%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCI 94
+TK+F+G LS T +R+ F +G VV+ ++ R +GFV+ + I
Sbjct: 34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93
Query: 95 KELNGMMVDGKPMKVVVAGFISSILSCLNVIFFIRCGRGGH 135
E++G ++G+ ++V A S G GG+
Sbjct: 94 SEMDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGY 134
Score = 28.9 bits (64), Expect = 2.2
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 13/62 (20%)
Query: 298 NMPGFSSVGTF-----KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYG 344
N+P S +G+ K+FIG ++ GT +R F +G VV+ V+ + +G
Sbjct: 20 NVPVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFG 79
Query: 345 FV 346
FV
Sbjct: 80 FV 81
>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 = 45.3 bits (107), Expect = 3e-05
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 9/79 (11%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKC 93
T + V L E+R LF G + C +VR+ YGFV ++ D K
Sbjct: 2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61
Query: 94 IKELNGMMVDGKPMKVVVA 112
+ LNG+ + K +KV A
Sbjct: 62 VNSLNGLRLQNKTIKVSYA 80
Score = 37.2 bits (86), Expect = 0.008
Identities = 30/115 (26%), Positives = 48/115 (41%), Gaps = 18/115 (15%)
Query: 10 EEGRTAIKELNGQIVNEKPLKIEAA----TSRKGPNTPTTKVFVGNLSDNTRAPEVRELF 65
E+ A+ LNG + K +K+ A S KG N ++V L E+ +F
Sbjct: 56 EDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGAN-----LYVSGLPKTMTQHELESIF 110
Query: 66 VPYGTVVECDIV--------RNYGFVHIDSPD-INKCIKELNGMMVDGKPMKVVV 111
P+G ++ I+ + GF+ D D ++ IK LNG G + V
Sbjct: 111 SPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITV 165
Score = 34.9 bits (80), Expect = 0.048
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCIKEL 97
+FV NLS +T + +LF P+G V I+R+ YGFV + + D I L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 98 NGMMVDGKPMKVV 110
NG + + ++V
Sbjct: 332 NGYTLGNRVLQVS 344
Score = 30.7 bits (69), Expect = 1.1
Identities = 22/105 (20%), Positives = 35/105 (33%), Gaps = 15/105 (14%)
Query: 250 PMKFGLILIPRSQIESLDLCGHFKQTKTTIVWSPRYQSFGTVVVIEARNMPGFSSVGTFK 309
F +L + Q Q SP T + + G +
Sbjct: 219 AGDFTAVLAHQQQ------QHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAG-YC 271
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
IF+ N++P T ++ LF +G V ++ K YGFV
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFV 316
>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 = 41.6 bits (98), Expect = 3e-05
Identities = 21/65 (32%), Positives = 39/65 (60%), Gaps = 3/65 (4%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPD---INKCIKELNGMMVDG 104
++GNLS + ++R+LF + V +V+ G+ +D PD +K I++LNG ++ G
Sbjct: 2 YIGNLSSDVNESDLRQLFEEHKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKILQG 61
Query: 105 KPMKV 109
K ++V
Sbjct: 62 KVIEV 66
Score = 28.5 bits (64), Expect = 1.1
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 15 AIKELNGQIVNEKPLKIEAATSRK 38
AI++LNG+I+ K +++E + +K
Sbjct: 50 AIEKLNGKILQGKVIEVEHSVPKK 73
>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 = 41.5 bits (98), Expect = 3e-05
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 12/75 (16%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY---------GFVHIDSP-DINKCI 94
TK+ V NL +++ELF +G + + + +Y V + D K +
Sbjct: 1 TKLLVSNLDFGVSDDDIKELFAEFGALKKAAV--HYDRSGRSLGTADVVFERRADALKAM 58
Query: 95 KELNGMMVDGKPMKV 109
K+ NG+ +DG+PMK+
Sbjct: 59 KQYNGVPLDGRPMKI 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 = 41.1 bits (97), Expect = 4e-05
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDI-------VRNYGFVHIDS-PDINKCIKEL 97
++ V NL ++++LF P+G V E I + + FV S D K IK +
Sbjct: 1 RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60
Query: 98 NGMMVDGKPMKV 109
NG + G+P+ V
Sbjct: 61 NGKKIKGRPVAV 72
>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 = 40.6 bits (95), Expect = 4e-05
Identities = 17/37 (45%), Positives = 25/37 (67%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGF 345
++F+GN+ P + E +R LFEKYGK E + K+ GF
Sbjct: 3 RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGF 39
Score = 39.1 bits (91), Expect = 2e-04
Identities = 22/68 (32%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSPDINKCIK-ELNGMM 101
+++FVGNL + E+R+LF YG E I + +GF+ +++ + + K EL+ M
Sbjct: 2 SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDKGFGFIRLETRTLAEIAKAELDNMP 61
Query: 102 VDGKPMKV 109
+ GK ++V
Sbjct: 62 LRGKQLRV 69
>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 = 40.8 bits (96), Expect = 5e-05
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY-----GFVHID--SPDINKCIKELNG 99
+FVGNLS + ++ E F G VV+ I ++ GF H++ + + + E +G
Sbjct: 2 LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKSG 61
Query: 100 MMVDGKPMKVVVA 112
+ G+ ++V +A
Sbjct: 62 EELLGREIRVDLA 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 = 40.7 bits (96), Expect = 5e-05
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKEL 97
K+FVGNL + E++E F +G V C++ + YGFV S D + +
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60
Query: 98 NGMMVDGKPMKV 109
+++G ++V
Sbjct: 61 QKHILEGNKLQV 72
Score = 33.4 bits (77), Expect = 0.017
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
K+F+GN+ + ++ F ++GKV C+V K YGFV
Sbjct: 1 KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFV 46
>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 = 40.7 bits (96), Expect = 5e-05
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 9/69 (13%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKE 96
++FV NL T E+RELF +G + E + + + FV P K E
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60
Query: 97 LNGMMVDGK 105
L+G + G+
Sbjct: 61 LDGSIFQGR 69
Score = 33.8 bits (78), Expect = 0.015
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
++F+ N+ T+ E +R LFE +G++ E + K + FV
Sbjct: 1 RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFV 46
>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 = 41.0 bits (96), Expect = 6e-05
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 46 KVFVGNLSDNTRAPE-VRELFVPYGTVVECDIVRN-------YGFVHI-DSPDINKCIKE 96
K+ + NL + + P ++++F YG V E I R + FV + + ++
Sbjct: 2 KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALEN 61
Query: 97 LNGMMVDGKPMKV 109
NG+ +DG+P+ V
Sbjct: 62 TNGLEIDGRPVAV 74
>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 = 40.6 bits (95), Expect = 6e-05
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 79
K+FVG LS +VR +F P+G++ EC ++R+
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD 36
Score = 31.7 bits (72), Expect = 0.10
Identities = 9/34 (26%), Positives = 21/34 (61%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
K+F+G ++ + +R +F +G + EC V+++
Sbjct: 3 KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD 36
>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 = 40.3 bits (95), Expect = 6e-05
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR--NYGFVHIDSPD-INKCIKELNGMM 101
T V+VGNL E++ F P+G + E + + Y FV D+ + I +NG
Sbjct: 1 TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTS 60
Query: 102 VDGKPMKV 109
++G+ +K
Sbjct: 61 INGQTVKC 68
Score = 33.4 bits (77), Expect = 0.022
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+++GN+ G + E ++ F +G + E V K Y FV
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKGYAFV 41
>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 = 40.5 bits (95), Expect = 6e-05
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI----VRNYGFV-HIDSPDINKCIKELNGMM 101
V+ G + +V+ LF G V + + V+ + F+ + I+ LNG
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGAS 61
Query: 102 VDGKPMKV 109
VDG +KV
Sbjct: 62 VDGNCIKV 69
>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding
Raly-like protein (RALYL). This subgroup corresponds to
the RRM of RALYL, also termed heterogeneous nuclear
ribonucleoprotein C-like 3, or hnRNP core protein C-like
3, a putative RNA-binding protein that shows high
sequence homology with Raly, an RNA-binding protein
playing a critical role in embryonic development. The
biological role of RALYL remains unclear. Like Raly,
RALYL contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain. .
Length = 69
Score = 40.4 bits (94), Expect = 6e-05
Identities = 18/39 (46%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 309 KIFIGNVNPGTSVEL-IRPLFEKYGKVVECDVVKNYGFV 346
++FIGN+N + I +F KYGK+V C V K Y FV
Sbjct: 3 RVFIGNLNTAIVKKADIEAIFAKYGKIVGCSVHKGYAFV 41
Score = 36.5 bits (84), Expect = 0.001
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 45 TKVFVGNLSDN-TRAPEVRELFVPYGTVVECDIVRNYGFV-HIDSPDINKCIKELNGMMV 102
++VF+GNL+ + ++ +F YG +V C + + Y FV +I + N ++
Sbjct: 2 SRVFIGNLNTAIVKKADIEAIFAKYGKIVGCSVHKGYAFVQYISERHARAAVAGENARII 61
Query: 103 DGKPMKV 109
G+P+ +
Sbjct: 62 AGQPLDI 68
>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 = 40.5 bits (94), Expect = 8e-05
Identities = 26/77 (33%), Positives = 36/77 (46%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIK 95
T + V L N E + LF G + C +VR+ YGFV+ P D +K I
Sbjct: 4 TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63
Query: 96 ELNGMMVDGKPMKVVVA 112
LNG+ + K +KV A
Sbjct: 64 TLNGLKLQTKTIKVSYA 80
>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 = 39.4 bits (93), Expect = 9e-05
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 61 VRELFVPYGTVVECDIVR---NYGFVHIDSP-DINKCIKELNGMMVDGKPMKV 109
+ +LF P+G V + +++ + FV + K ++ LNG++ G+P++V
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53
Score = 27.5 bits (62), Expect = 1.6
Identities = 7/28 (25%), Positives = 15/28 (53%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIE 32
+E A++ LNG + +PL+++
Sbjct: 27 EFSTEEAAEKAVQYLNGVLFGGRPLRVD 54
Score = 26.7 bits (60), Expect = 3.2
Identities = 7/26 (26%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 324 IRPLFEKYGKVVECDVVK---NYGFV 346
+ LF +G V + ++K + FV
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFV 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 = 40.0 bits (94), Expect = 9e-05
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVH-IDSPDINKCIKELNGMM 101
T VFVG L E+R LF P+G +V I + GFV + I++L G +
Sbjct: 2 TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGTI 61
Query: 102 VDGKP 106
+ G
Sbjct: 62 IGGSR 66
Score = 26.9 bits (60), Expect = 3.3
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKV--VECDVVKNYGFV 346
+F+G ++P + + +R LF +G++ V+ K GFV
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFV 42
>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end)
protein family. This subfamily corresponds to the RRM2
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and component of the NXF1
pathway. It binds to NXF1 and serves as receptor for the
RNA export element RTE. It also possess mRNA export
activity and can facilitate the access of DEAD-box
protein DBP5 to mRNA at the nuclear pore complex (NPC).
RNA-binding protein 15B (RBM15B), also termed one
twenty-two 3 (OTT3), is a paralog of RBM15 and therefore
has post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. Members in this family belong to the Spen
(split end) protein family, which share a domain
architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 79
Score = 40.1 bits (94), Expect = 1e-04
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR-------NYGFVHIDSPDI-NKCIK 95
T +FVGNL E+R F YG V + DI R Y FV + D+ ++
Sbjct: 2 TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKV 61
Query: 96 ELNGMMVDGKPMKV 109
++G + +K+
Sbjct: 62 AMSGQYIGRNQIKI 75
Score = 37.8 bits (88), Expect = 6e-04
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 7/47 (14%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK-------NYGFV 346
T +F+GN+ + E +R FE+YG V + D+ + Y FV
Sbjct: 2 TRTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFV 48
>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 = 39.6 bits (93), Expect = 1e-04
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-DINKCIKELN 98
+FV NL + ++++LF G V+ D+ + +G V +SP D + I+ N
Sbjct: 1 IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60
Query: 99 GMMVDGKPMKV 109
G ++G+ ++V
Sbjct: 61 GYDLEGRELEV 71
>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 = 39.7 bits (92), Expect = 1e-04
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKEL 97
++V LS NT+A +++ LF YG V+ +V N YG V + S ++ +CI L
Sbjct: 2 LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61
Query: 98 NGMMVDGKPMKV 109
+ + G+ + V
Sbjct: 62 HRTELHGQQISV 73
>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 = 39.7 bits (93), Expect = 1e-04
Identities = 17/33 (51%), Positives = 22/33 (66%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR 78
K+FVG LS +VR LF P+GT+ EC I+R
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILR 35
Score = 31.6 bits (72), Expect = 0.092
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK 341
K+F+G ++ + + +R LFE +G + EC +++
Sbjct: 3 KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILR 35
>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM1 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads and is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 83
Score = 39.7 bits (92), Expect = 2e-04
Identities = 27/77 (35%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCIK 95
T + V L N E++ LF G + C +VR+ YGFV +ID D K I
Sbjct: 5 TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64
Query: 96 ELNGMMVDGKPMKVVVA 112
LNG+ + K +KV A
Sbjct: 65 TLNGLRLQTKTIKVSYA 81
>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 = 39.3 bits (91), Expect = 2e-04
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDS-PDINKCIKEL 97
++V LS TRA +++ LF YG VV +V N YGFV + + + KCI L
Sbjct: 4 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63
Query: 98 NGMMVDGKPMKV 109
+ + G+ + V
Sbjct: 64 HRTELHGRMISV 75
Score = 28.2 bits (62), Expect = 1.4
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+++ ++ T ++ LF KYGKVV VV N YGFV
Sbjct: 4 LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFV 48
>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 = 39.3 bits (92), Expect = 2e-04
Identities = 23/62 (37%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 60 EVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVV 110
E+R LF G + C IVR+ YGFV D K I LNG + K +KV
Sbjct: 16 ELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVS 75
Query: 111 VA 112
A
Sbjct: 76 YA 77
>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 = 39.1 bits (91), Expect = 2e-04
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--YGFVHIDSPDINKCIK-ELNGMMV 102
++FVGNL + + ++LF YG E I R+ +GF+ ++S + + K EL+G ++
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 62
Query: 103 DGKPMKV 109
+P+++
Sbjct: 63 KNRPLRI 69
Score = 28.7 bits (64), Expect = 0.90
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGF 345
++F+GN+ + E + LFEKYG+ E + ++ GF
Sbjct: 3 RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDRGF 39
>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 = 39.1 bits (92), Expect = 2e-04
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 10/77 (12%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI-DSPDINKCIK 95
TK+FVG L +T +R+ F +G + E ++ R YGFV D + K
Sbjct: 1 TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Query: 96 ELNGMMVDGKPMKVVVA 112
+ N ++ DG+ V +A
Sbjct: 61 DPNPII-DGRKANVNLA 76
Score = 37.6 bits (88), Expect = 6e-04
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
KIF+G + T+ + +R F ++G++ E V+ + YGFV
Sbjct: 2 KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFV 47
>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in
granule-associated RNA binding proteins p40-TIA-1 and
TIAR. This subfamily corresponds to the RRM1 of
nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and
nucleolysin TIA-1-related protein (TIAR), both of which
are granule-associated RNA binding proteins involved in
inducing apoptosis in cytotoxic lymphocyte (CTL) target
cells. TIA-1 and TIAR share high sequence similarity.
They are expressed in a wide variety of cell types.
TIA-1 can be phosphorylated by a serine/threonine kinase
that is activated during Fas-mediated apoptosis.TIAR is
mainly localized in the nucleus of hematopoietic and
nonhematopoietic cells. It is translocated from the
nucleus to the cytoplasm in response to exogenous
triggers of apoptosis. Both, TIA-1 and TIAR, bind
specifically to poly(A) but not to poly(C) homopolymers.
They are composed of three N-terminal highly homologous
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glutamine-rich C-terminal auxiliary domain
containing a lysosome-targeting motif. TIA-1 and TIAR
interact with RNAs containing short stretches of
uridylates and their RRM2 can mediate the specific
binding to uridylate-rich RNAs. The C-terminal auxiliary
domain may be responsible for interacting with other
proteins. In addition, TIA-1 and TIAR share a potential
serine protease-cleavage site (Phe-Val-Arg) localized at
the junction between their RNA binding domains and their
C-terminal auxiliary domains.
Length = 72
Score = 38.8 bits (91), Expect = 2e-04
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 6/69 (8%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVR-----NYGFVHI-DSPDINKCIKELNGM 100
++VGNL + ELF G + C ++R Y FV D ++ +NG
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60
Query: 101 MVDGKPMKV 109
++ G+ +KV
Sbjct: 61 LILGQEIKV 69
Score = 26.9 bits (60), Expect = 3.6
Identities = 10/42 (23%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVK-----NYGFV 346
+++GN++ + +L+ LF + G + C +++ Y FV
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFV 42
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B
subunit 4 (SF3B4) and similar proteins. This subfamily
corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor 3b
(SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B
is essential for the accurate excision of introns from
pre-messenger RNA, and is involved in the recognition of
the pre-mRNA's branch site within the major and minor
spliceosomes. SF3B4 functions to tether U2 snRNP with
pre-mRNA at the branch site during spliceosome assembly.
It is an evolutionarily highly conserved protein with
orthologs across diverse species. SF3B4 contains two
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It binds directly to
pre-mRNA and also interacts directly and highly
specifically with another SF3B subunit called SAP 145. .
Length = 74
Score = 38.7 bits (91), Expect = 2e-04
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVR--------NYGFVHIDSP-DINKCIKEL 97
V+VGNL + + ELF+ G VV I + YGFV S D + IK +
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 98 NGMMVDGKPMKV 109
N + + GKP++V
Sbjct: 61 NMIKLYGKPIRV 72
>gnl|CDD|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subfamily corresponds to the
RRM3 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. PUB1 is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA); however, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 74
Score = 38.6 bits (90), Expect = 2e-04
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSPD-INKCIKELNGMM 101
T V+VGN+ T ++ LF +G ++E R + FV +D+ + I +L G
Sbjct: 1 TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFVKLDTHEQAAMAIVQLQGFP 60
Query: 102 VDGKPMK 108
V G+P++
Sbjct: 61 VHGRPLR 67
Score = 26.3 bits (58), Expect = 6.3
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+++GN+ P T+ + PLF+ +G ++E + + FV
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDRGFAFV 41
>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 = 38.6 bits (90), Expect = 2e-04
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 46 KVFVGNL-SDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGMMVD 103
++F+GNL + ++ +F YG + + + YGFV DSP I G M+
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNAYGFVQFDSPESCANAINCEQGKMIR 60
Query: 104 GKPMKVVVA 112
G+ + + V+
Sbjct: 61 GRKLHLEVS 69
Score = 26.6 bits (59), Expect = 4.6
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 309 KIFIGNV-NPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
++FIGN+ S E + +F YG++ + + YGFV
Sbjct: 1 RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNAYGFV 39
>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 = 38.5 bits (90), Expect = 3e-04
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-----YGFVHIDSP-DINKCIKELNG 99
+++VGNL + R ++ +LF YG + D+ + FV + P D ++ +G
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60
Query: 100 MMVDGKPMKV 109
DG ++V
Sbjct: 61 YDFDGYRLRV 70
Score = 28.9 bits (65), Expect = 0.86
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDV 339
+I++GN+ I LF KYG + D+
Sbjct: 1 RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL 31
>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 = 38.5 bits (90), Expect = 3e-04
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 60 EVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVV 110
E R LF+ G V C IVR+ +GFV S D + I+ LNG+ + K +KV
Sbjct: 16 EFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVA 75
Query: 111 VA 112
A
Sbjct: 76 YA 77
>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 2 (Musashi-2) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 79
Score = 38.5 bits (89), Expect = 3e-04
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 13/77 (16%)
Query: 42 TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKC 93
T T K+FVG LS NT +V++ F +G V + ++ R +GFV ++ D+ +
Sbjct: 1 TRTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK 60
Query: 94 I-----KELNGMMVDGK 105
+ E+N MV+ K
Sbjct: 61 VCEIHFHEINNKMVECK 77
Score = 32.7 bits (74), Expect = 0.038
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKV 334
T KIF+G ++ T VE ++ FE++GKV
Sbjct: 3 TKKIFVGGLSANTVVEDVKQYFEQFGKV 30
>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen
R (HuR). This subgroup corresponds to the RRM1 of HuR,
also termed ELAV-like protein 1 (ELAV-1), a ubiquitously
expressed Hu family member. It has a variety of
biological functions mostly related to the regulation of
cellular response to DNA damage and other types of
stress. HuR has an anti-apoptotic function during early
cell stress response; it binds to mRNAs and enhances the
expression of several anti-apoptotic proteins, such as
p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also
has pro-apoptotic function by promoting apoptosis when
cell death is unavoidable. Furthermore, HuR may be
important in muscle differentiation, adipogenesis,
suppression of inflammatory response and modulation of
gene expression in response to chronic ethanol exposure
and amino acid starvation. Like other Hu proteins, HuR
contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 38.1 bits (88), Expect = 5e-04
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCIK 95
T + V L N E+R LF G V ++R+ YGFV ++++ D + I
Sbjct: 2 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61
Query: 96 ELNGMMVDGKPMKVVVA 112
LNG+ + K +KV A
Sbjct: 62 TLNGLRLQSKTIKVSYA 78
>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 = 37.6 bits (88), Expect = 6e-04
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 62 RELFVPYGTVVEC--DIVRNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVVVA 112
++ F P+G ++ + +N GFV + + ++ I ELNG V G +KV +A
Sbjct: 20 KKAFSPFGNIINISMEKEKNCGFVTFEKMESADRAIAELNGTTVQGVQLKVSLA 73
>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 = 37.7 bits (87), Expect = 6e-04
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDIN-KCIKELNGMMVDGK 105
+FV NL+ + + F +G + +++Y FVH + D + + E+NG ++G+
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFEERDAAVRAMDEMNGKEIEGE 63
Query: 106 PMKVVVA 112
+++V+A
Sbjct: 64 EIEIVLA 70
>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 = 37.9 bits (88), Expect = 6e-04
Identities = 23/63 (36%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVV-------ECDIVRNYGFVHIDSPDINK-CIKEL 97
K+FVG L+ EV E+F PYG V E R FV S ++ + IK L
Sbjct: 1 KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60
Query: 98 NGM 100
NG+
Sbjct: 61 NGV 63
>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 = 37.4 bits (87), Expect = 6e-04
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 6/69 (8%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI---VRNYGFVHI---DSPDINKCIKELNGM 100
V+VGNL + R EV +LF YG +V+ D+ R G+ I D+ D I+ +G
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDGY 61
Query: 101 MVDGKPMKV 109
DG+ ++V
Sbjct: 62 DFDGQRLRV 70
>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in
azoospermia-associated protein 1 (DAZAP1) and similar
proteins. This subfamily corresponds to the RRM2 of
DAZAP1 or DAZ-associated protein 1, also termed
proline-rich RNA binding protein (Prrp), a
multi-functional ubiquitous RNA-binding protein
expressed most abundantly in the testis and essential
for normal cell growth, development, and
spermatogenesis. DAZAP1 is a shuttling protein whose
acetylated is predominantly nuclear and the
nonacetylated form is in cytoplasm. DAZAP1 also
functions as a translational regulator that activates
translation in an mRNA-specific manner. DAZAP1 was
initially identified as a binding partner of Deleted in
Azoospermia (DAZ). It also interacts with numerous
hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1,
hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate
and cooperate with hnRNP particles to regulate
adenylate-uridylate-rich elements (AU-rich element or
ARE)-containing mRNAs. DAZAP1 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal proline-rich domain. .
Length = 80
Score = 37.7 bits (88), Expect = 7e-04
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 13/75 (17%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDI----- 90
T K+FVG L N ++R+ F +GTV E ++ R +GF+ +S D
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV 61
Query: 91 NKCIKELNGMMVDGK 105
N+ ++NG V+ K
Sbjct: 62 NEHFHDINGKKVEVK 76
Score = 28.1 bits (63), Expect = 1.7
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 306 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVE 336
T KIF+G + P + +R F ++G V E
Sbjct: 1 RTKKIFVGGLPPNVTETDLRKYFSQFGTVTE 31
>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 = 37.6 bits (88), Expect = 7e-04
Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD 89
VGNL + REL P+G V C +V + YGFV S
Sbjct: 3 CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKA 52
Score = 33.8 bits (78), Expect = 0.017
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ +GN+ + E R L +G V C +V K YGFV
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFV 46
>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 = 37.6 bits (87), Expect = 7e-04
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 5/49 (10%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDI-----VRNYGFVHIDSPD 89
++FVGNL + E++E F YG VVE I + N+GFV D +
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGKLPNFGFVVFDDSE 53
Score = 28.7 bits (64), Expect = 1.1
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDV-----VKNYGFV 346
++F+GN+ ++ F++YG VVE + + N+GFV
Sbjct: 5 QLFVGNLPHDVDKSELKEFFQQYGNVVELRINSGGKLPNFGFV 47
>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate
heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP
C1/C2). This subgroup corresponds to the RRM of
heterogeneous nuclear ribonucleoprotein C (hnRNP)
proteins C1 and C2, produced by a single coding
sequence. They are the major constituents of the
heterogeneous nuclear RNA (hnRNA) ribonucleoprotein
(hnRNP) complex in vertebrates. They bind hnRNA tightly,
suggesting a central role in the formation of the
ubiquitous hnRNP complex. They are involved in the
packaging of hnRNA in the nucleus and in processing of
pre-mRNA such as splicing and 3'-end formation. hnRNP C
proteins contain two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes the variable
region, the basic region and the KSG box rich in
repeated Lys-Ser-Gly sequences, the leucine zipper, and
the acidic region. The RRM is capable of binding
poly(U). The KSG box may bind to RNA. The leucine zipper
may be involved in dimer formation. The acidic and
hydrophilic C-teminus harbors a putative nucleoside
triphosphate (NTP)-binding fold and a protein kinase
phosphorylation site. .
Length = 71
Score = 37.3 bits (86), Expect = 7e-04
Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 7/42 (16%)
Query: 309 KIFIGNVN----PGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
++FIGN+N + VE I F KYGK+V C V K + FV
Sbjct: 3 RVFIGNLNTLVVKKSDVEAI---FSKYGKIVGCSVHKGFAFV 41
Score = 32.7 bits (74), Expect = 0.034
Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 45 TKVFVGNLSDNT---RAPEVRELFVPYGTVVECDIVRNYGFVHI-DSPDINKCIKELNGM 100
++VF+GNL NT + +V +F YG +V C + + + FV + + + +G
Sbjct: 2 SRVFIGNL--NTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGR 59
Query: 101 MVDGKPMKVVVA 112
M+ G+ + + +A
Sbjct: 60 MIAGQVLDINLA 71
>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory
glutamine/lysine-rich protein 1 (SREK1) and similar
proteins. This subfamily corresponds to the RRM2 of
SREK1, also termed serine/arginine-rich-splicing
regulatory protein 86-kDa (SRrp86), or splicing factor
arginine/serine-rich 12 (SFRS12), or splicing regulatory
protein 508 amino acid (SRrp508). SREK1 belongs to a
family of proteins containing regions rich in
serine-arginine dipeptides (SR proteins family), which
is involved in bridge-complex formation and splicing by
mediating protein-protein interactions across either
introns or exons. It is a unique SR family member and it
may play a crucial role in determining tissue specific
patterns of alternative splicing. SREK1 can alter splice
site selection by both positively and negatively
modulating the activity of other SR proteins. For
instance, SREK1 can activate SRp20 and repress SC35 in a
dose-dependent manner both in vitro and in vivo. In
addition, SREK1 contains two (some contain only one) RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and two
serine-arginine (SR)-rich domains (SR domains) separated
by an unusual glutamic acid-lysine (EK) rich region. The
RRM and SR domains are highly conserved among other
members of the SR superfamily. However, the EK domain is
unique to SREK1. It plays a modulatory role controlling
SR domain function by involvement in the inhibition of
both constitutive and alternative splicing and in the
selection of splice-site. .
Length = 85
Score = 37.7 bits (88), Expect = 8e-04
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 47 VFVGNLSDNTRAPEVRELF-----VPYGTVVECDIV-RNYGFVHI-DSPDINKCIKELNG 99
++VGNL T A ++ E F V Y + + Y FV + + +K LNG
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINALK-LNG 65
Query: 100 MMVDGKPMKV 109
M G+P+KV
Sbjct: 66 AMFGGRPLKV 75
>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A subfamily. This subfamily
corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in mRNA
stability in mammalian cells. It has been identified as
the substrate for MAPKAP-K2 and may be involved in the
lipopolysaccharide (LPS)-induced post-transcriptional
regulation of tumor necrosis factor-alpha (TNF-alpha),
cyclooxygenase 2 (COX-2) and macrophage inflammatory
protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic
nuclear RNA-binding protein that may modulate splice
site selection in pre-mRNA splicing. hnRNP A2/B1 is an
RNA trafficking response element-binding protein that
interacts with the hnRNP A2 response element (A2RE).
Many mRNAs, such as myelin basic protein (MBP),
myelin-associated oligodendrocytic basic protein (MOBP),
carboxyanhydrase II (CAII), microtubule-associated
protein tau, and amyloid precursor protein (APP) are
trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 78
Score = 37.4 bits (87), Expect = 8e-04
Identities = 13/46 (28%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ + ++ F ++G++ +C V+K+ +GFV
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFV 46
Score = 30.8 bits (70), Expect = 0.16
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 20/74 (27%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCIKEL 97
K+F+G LS T ++ F +G + +C ++++ +GFV E+
Sbjct: 1 KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTF------ASASEV 54
Query: 98 NGMM------VDGK 105
+ M VDG+
Sbjct: 55 DAAMNARPHKVDGR 68
>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 = 37.3 bits (87), Expect = 8e-04
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDS-PDINKCIKEL 97
+FV NL + + +LF P+G V ++R+ YGFV + + + I L
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63
Query: 98 NGMMVDGKPMKV 109
NG + G+ ++V
Sbjct: 64 NGYRLGGRVLQV 75
>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate
polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF). This subgroup
corresponds to the RRM1 of PSF, also termed proline- and
glutamine-rich splicing factor, or 100 kDa DNA-pairing
protein (POMp100), or 100 kDa subunit of DNA-binding
p52/p100 complex, a multifunctional protein that
mediates diverse activities in the cell. It is
ubiquitously expressed and highly conserved in
vertebrates. PSF binds not only RNA but also both
single-stranded DNA (ssDNA) and double-stranded DNA
(dsDNA) and facilitates the renaturation of
complementary ssDNAs. Besides, it promotes the formation
of D-loops in superhelical duplex DNA, and is involved
in cell proliferation. PSF can also interact with
multiple factors. It is an RNA-binding component of
spliceosomes and binds to insulin-like growth factor
response element (IGFRE). PSF functions as a
transcriptional repressor interacting with Sin3A and
mediating silencing through the recruitment of histone
deacetylases (HDACs) to the DNA binding domain (DBD) of
nuclear hormone receptors. Additionally, PSF is an
essential pre-mRNA splicing factor and is dissociated
from PTB and binds to U1-70K and serine-arginine (SR)
proteins during apoptosis. PSF forms a heterodimer with
the nuclear protein p54nrb, also known as non-POU
domain-containing octamer-binding protein (NonO). The
PSF/p54nrb complex displays a variety of functions, such
as DNA recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which are responsible
for interactions with RNA and for the localization of
the protein in speckles. It also contains an N-terminal
region rich in proline, glycine, and glutamine residues,
which may play a role in interactions recruiting other
molecules. .
Length = 71
Score = 37.2 bits (86), Expect = 9e-04
Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDI--VRNYGFVHIDSPDINKCIK-ELNGMMV 102
++FVGNL + E ++LF YG E I + +GF+ ++S + + K EL+ +
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPM 62
Query: 103 DGKPMKV 109
G+ ++V
Sbjct: 63 RGRQLRV 69
Score = 27.6 bits (61), Expect = 2.2
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGF 345
++F+GN+ + + + LF KYG+ E + K GF
Sbjct: 3 RLFVGNLPADITEDEFKKLFAKYGEPGEVFINKGKGF 39
>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 = 37.1 bits (87), Expect = 9e-04
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 49 VGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDI-NKCIKELNG 99
V NLS++ ++RELF P+G + + ++ + FV + + + I++LNG
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
>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 = 37.2 bits (87), Expect = 0.001
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 22/80 (27%)
Query: 45 TKVFVGNLSDNTRAPEV-----RELFVPYGTVVECDIVRNY---------GFVHIDSP-D 89
T++ V NL +V ELF G V + I NY V + D
Sbjct: 1 TRLRVSNL-----HYDVTEEDLEELFGRVGEVKKVKI--NYDRSGRSEGTADVVFEKRED 53
Query: 90 INKCIKELNGMMVDGKPMKV 109
+ IK+ NG+++DG+PM+V
Sbjct: 54 AERAIKQFNGVLLDGQPMQV 73
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 37.3 bits (87), Expect = 0.001
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 14/78 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----------RNYGFV-HIDSPDINKC 93
++++GNL + +LF YG + + D + R Y FV + K
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60
Query: 94 IKELNGMMVDGKPMKVVV 111
+K LNG GK K+VV
Sbjct: 61 LKSLNGKTALGK--KLVV 76
Score = 30.7 bits (70), Expect = 0.17
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 11/49 (22%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-----------KNYGFV 346
+++IGN++ + + LF KYGK+ + D + + Y FV
Sbjct: 1 RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFV 49
>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 = 36.9 bits (85), Expect = 0.001
Identities = 18/67 (26%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPD-INKCIKELNGMMVDGK 105
+FV NL++ + + F +G + +++Y F+H D D K ++E+NG ++G+
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKELEGE 63
Query: 106 PMKVVVA 112
+++V A
Sbjct: 64 NIEIVFA 70
>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 = 37.2 bits (87), Expect = 0.001
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 14/77 (18%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCIKEL 97
VF+ NL + E++ELF +G V IV++ FV + + KC++
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62
Query: 98 N-----GMMVDGKPMKV 109
+ G+ +DG+ + V
Sbjct: 63 DNAEDSGLSLDGRRLIV 79
Score = 33.7 bits (78), Expect = 0.015
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
+FI N+ + E ++ LF ++G+V +VK+
Sbjct: 3 VFIRNLPFDATEEELKELFSQFGEVKYARIVKD 35
>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 = 36.8 bits (86), Expect = 0.001
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 9/73 (12%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDI-NKCIKE 96
K+F+G L + +V+EL +G + ++V++ Y F P + ++ I
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61
Query: 97 LNGMMVDGKPMKV 109
LNGM + K + V
Sbjct: 62 LNGMQLGDKKLTV 74
Score = 26.8 bits (60), Expect = 4.7
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
KIFIG + S + ++ L E +GK+ ++VK+
Sbjct: 2 KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKD 35
>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 = 36.8 bits (86), Expect = 0.001
Identities = 21/69 (30%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVV--------ECDIVRNYGFVHIDSP-DINKCIK 95
T V++ L NT ++ +L P+G ++ + + + YGFV DSP K I+
Sbjct: 1 TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60
Query: 96 ELNGMMVDG 104
LNG V
Sbjct: 61 GLNGRGVQA 69
>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 = 36.9 bits (86), Expect = 0.001
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 12/78 (15%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----------RNYGFVHIDS-PDIN 91
TT ++VGNL+ + + F +G + I+ RN GFV + D
Sbjct: 1 TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60
Query: 92 KCIKELNGMMVDGKPMKV 109
+ + EL+G V G +K+
Sbjct: 61 RALDELDGKDVMGYELKL 78
>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 = 36.7 bits (85), Expect = 0.001
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+F+G +N TS +R F +YGK+ EC V+ + +GF+
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFI 49
Score = 35.9 bits (83), Expect = 0.003
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKEL 97
K+FVG L+ T +R F YG + EC ++ R +GF+ S D E
Sbjct: 4 KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63
Query: 98 NGMMVDGKPMKV 109
+DG +++
Sbjct: 64 QPHSIDGNQIEL 75
>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 = 36.7 bits (86), Expect = 0.001
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELN 98
+VG+L + + E+F P G V+ + R+ Y +V+ +P D + + LN
Sbjct: 3 YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62
Query: 99 GMMVDGKPMKV 109
++ GKP+++
Sbjct: 63 FDVIKGKPIRI 73
>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 = 36.9 bits (85), Expect = 0.001
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 47 VFVGNLSDNTRAPEVRELF--VPYGTVVECDIVRNYGFVHIDS-PDINKCIKELNGMMVD 103
++V NL +T + + F + G V +R+Y FVH + D + LNG ++D
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSIKPGAVERVKKIRDYAFVHFSNREDAVDAMNALNGKVID 70
Query: 104 GKPMKVVVA 112
G P++V +A
Sbjct: 71 GSPIEVTLA 79
>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 = 36.7 bits (86), Expect = 0.001
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 14/74 (18%)
Query: 48 FVGNLSDNTRAPEVR----ELFVPYGTVVECDIV-----RNYGFVHIDSPDINKCI---K 95
++ NL++ + E++ LF +G V+ DIV + G + D+ +
Sbjct: 3 YINNLNEKIKKDELKRSLYALFSQFGPVL--DIVASKTLKMRGQAFVVFKDVESATNALR 60
Query: 96 ELNGMMVDGKPMKV 109
L G KPM++
Sbjct: 61 ALQGFPFYDKPMRI 74
>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 = 36.3 bits (84), Expect = 0.002
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 9/74 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCI-KEL 97
+++G+L E+++ F +GTV + R+ YGF+ +P++ K +
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 98 NGMMVDGKPMKVVV 111
N ++ GK ++V V
Sbjct: 62 NNYLLMGKVLQVHV 75
>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 = 36.4 bits (85), Expect = 0.002
Identities = 21/64 (32%), Positives = 29/64 (45%), Gaps = 9/64 (14%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY--------GFVHIDS-PDINKCIKE 96
K+FVG L +VR LF YG + E I+R+ FV S + K I+
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60
Query: 97 LNGM 100
L+G
Sbjct: 61 LHGK 64
Score = 33.3 bits (77), Expect = 0.020
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
K+F+G + + E +R LFE+YG + E ++++
Sbjct: 1 KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRD 34
>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 = 36.4 bits (85), Expect = 0.002
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKCIKE 96
++FVG+L + + F Y + + +VR+ YGFV D D K +KE
Sbjct: 8 RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67
Query: 97 LNGMMVDGKPMKV 109
+NG V +P+K+
Sbjct: 68 MNGKYVGNRPIKL 80
Score = 27.2 bits (61), Expect = 3.6
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
F+IF+G++ + E++ F KY + VV K YGFV
Sbjct: 7 FRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFV 53
>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 = 36.3 bits (84), Expect = 0.002
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 14/78 (17%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHI-DSPDIN 91
PNT VFVG + E+R F YG+V E I+ + YGFV D D+
Sbjct: 5 PNT----VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQ 60
Query: 92 KCIKELNGMMVDGKPMKV 109
K ++ + GK +K+
Sbjct: 61 KIVES--QINFHGKKLKL 76
Score = 31.3 bits (71), Expect = 0.14
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 7/44 (15%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+F+G ++ IR F KYG V E ++ K YGFV
Sbjct: 8 VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFV 51
>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding
protein 11 (RBM11). This subfamily corresponds to the
RRM or RBM11, a novel tissue-specific splicing regulator
that is selectively expressed in brain, cerebellum and
testis, and to a lower extent in kidney. RBM11 is
localized in the nucleoplasm and enriched in
SRSF2-containing splicing speckles. It may play a role
in the modulation of alternative splicing during neuron
and germ cell differentiation. RBM11 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM of RBM11 is responsible for RNA binding, whereas
the C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 36.1 bits (83), Expect = 0.002
Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPD-INKCIKELN 98
+FVGNL R + ELF+ G + + I ++ +GFV + + I LN
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63
Query: 99 GMMVDGKPMKV 109
G+ + G+P+KV
Sbjct: 64 GIRLYGRPIKV 74
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and an
RS domain at their C-terminus.
Length = 72
Score = 36.0 bits (83), Expect = 0.002
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHI-DSPDINKCIKELNGM 100
VF GN + R E+ LF YG V D+ + FV++ D D I+ L+
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRVDMKSGFAFVYMEDERDAEDAIRGLDNF 57
Score = 28.2 bits (63), Expect = 1.2
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
+F GN I LF KYG+V D+ + FV
Sbjct: 3 VFCGNFEYDARQSEIERLFGKYGRVDRVDMKSGFAFV 39
>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 = 35.8 bits (83), Expect = 0.003
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---RNYGFVHI--DSPD-INKCIKELN 98
K+ + N+ + R ++ L YGTV C+ V V++ +SP+ + + +LN
Sbjct: 1 RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLN 60
Query: 99 GMMVDGKPMKV 109
G +G +KV
Sbjct: 61 GHEYEGSKLKV 71
Score = 35.0 bits (81), Expect = 0.005
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV 340
KI I N+ P E + L YG V C+ V
Sbjct: 2 KIQISNIPPHVRWEDLDSLLSTYGTVKNCEQV 33
>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 = 35.7 bits (83), Expect = 0.003
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCIK 95
T VFVGN+ + +R+L G V+ V + +GF + P+ + ++
Sbjct: 1 TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60
Query: 96 ELNGMMVDGKPMKVVV 111
LNG+ + GK + V V
Sbjct: 61 LLNGLELGGKKLLVKV 76
Score = 31.0 bits (71), Expect = 0.18
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+F+GN+ G S + IR L EK GKV+ V K +GF
Sbjct: 2 TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFC 47
>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 = 35.7 bits (83), Expect = 0.004
Identities = 12/45 (26%), Positives = 26/45 (57%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+F+ +NP T+ E + +F ++GK+ C+V+++ Y F+
Sbjct: 6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFI 50
Score = 29.5 bits (67), Expect = 0.59
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD 89
P +FV L+ T ++ +F +G + C+++R+ Y F+ ++ +
Sbjct: 2 PENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKE 56
>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein
Musashi homolog Musashi-1, Musashi-2 and similar
proteins. This subfamily corresponds to the RRM1 in
Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is
a neural RNA-binding protein putatively expressed in
central nervous system (CNS) stem cells and neural
progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. It is
evolutionarily conserved from invertebrates to
vertebrates. Musashi-1 is a homolog of Drosophila
Musashi and Xenopus laevis nervous system-specific RNP
protein-1 (Nrp-1). It has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover,
Musashi-1 represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-2
(also termed Msi2) has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Both,
Musashi-1 and Musashi-2, contain two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 75
Score = 35.5 bits (82), Expect = 0.004
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+FIG ++ T+ E +R F K+G++ EC V+++ +GFV
Sbjct: 1 MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFV 45
Score = 35.5 bits (82), Expect = 0.004
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 13/71 (18%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-----INKCI 94
F+G LS T A +RE F +G + EC ++R+ +GFV P + +
Sbjct: 2 FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGP 61
Query: 95 KELNGMMVDGK 105
EL+G +D K
Sbjct: 62 HELDGKKIDPK 72
>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 = 35.7 bits (83), Expect = 0.004
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVEC----DVV----KNYGFV 346
+F+G ++ T+ E +R +F +YG + D+V K Y FV
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFV 50
Score = 33.4 bits (77), Expect = 0.031
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV 83
P +FVG LS T +RE+F YG + +VR+ Y FV
Sbjct: 2 PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFV 50
>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM2 of RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, a novel
mRNA export factor and component of the NXF1 pathway. It
binds to NXF1 and serves as receptor for the RNA export
element RTE. It also possesses mRNA export activity and
can facilitate the access of DEAD-box protein DBP5 to
mRNA at the nuclear pore complex (NPC). RBM15 belongs to
the Spen (split end) protein family, which contain three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 87
Score = 35.7 bits (82), Expect = 0.004
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVR-------NYGFVHIDSPDINKCIK-ELN 98
+F+GNL ++R F +G + E DI R YGF+ ++ D+ K ++
Sbjct: 10 LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69
Query: 99 GMMVDGKPMKV 109
G ++ P+K+
Sbjct: 70 GKVLRRNPIKI 80
>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding
protein Raly. This subgroup corresponds to the RRM of
Raly, also termed autoantigen p542, or heterogeneous
nuclear ribonucleoprotein C-like 2, or hnRNP core
protein C-like 2, or hnRNP associated with lethal yellow
protein homolog, an RNA-binding protein that may play a
critical role in embryonic development. It is encoded by
Raly, a ubiquitously expressed gene of unknown function.
Raly shows a high degree of identity with the 5'
sequences of p542 gene encoding autoantigen, which can
cross-react with EBNA-1 of the Epstein Barr virus. Raly
contains two distinct domains, an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal auxiliary domain that includes a unique
glycine/serine-rich stretch. .
Length = 76
Score = 35.4 bits (81), Expect = 0.004
Identities = 20/42 (47%), Positives = 25/42 (59%), Gaps = 7/42 (16%)
Query: 309 KIFIGNVNPG----TSVELIRPLFEKYGKVVECDVVKNYGFV 346
++FIGN+N + VE I F KYG+VV C V K Y FV
Sbjct: 3 RVFIGNLNTAVVKKSDVETI---FSKYGRVVGCSVHKGYAFV 41
Score = 33.9 bits (77), Expect = 0.015
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 45 TKVFVGNLSDN-TRAPEVRELFVPYGTVVECDIVRNYGFV-HIDSPDINKCIKELNGMMV 102
++VF+GNL+ + +V +F YG VV C + + Y FV + + + NG ++
Sbjct: 2 SRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSVHKGYAFVQYSNERHARGAVIGENGRVL 61
Query: 103 DGKPMKVVVAG 113
G+ + + +AG
Sbjct: 62 AGQTLDINMAG 72
>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells, and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1) and has been implicated in the maintenance of
the stem-cell state, differentiation, and tumorigenesis.
It translationally regulates the expression of a
mammalian numb gene by binding to the 3'-untranslated
region of mRNA of Numb, encoding a membrane-associated
inhibitor of Notch signaling, and further influences
neural development. It represses translation by
interacting with the poly(A)-binding protein and
competes for binding of the eukaryotic initiation
factor-4G (eIF-4G). Musashi-1 contains two conserved
N-terminal tandem RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), along with other domains of
unknown function. .
Length = 74
Score = 35.0 bits (80), Expect = 0.005
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 13/73 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCI--- 94
K+FVG LS NT +V++ F +G V + ++ R +GFV +S DI + +
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 95 --KELNGMMVDGK 105
E+N MV+ K
Sbjct: 61 HFHEINNKMVECK 73
Score = 29.6 bits (66), Expect = 0.44
Identities = 12/26 (46%), Positives = 20/26 (76%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKV 334
KIF+G ++ T+VE ++ FE++GKV
Sbjct: 1 KIFVGGLSVNTTVEDVKQYFEQFGKV 26
>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 = 35.4 bits (81), Expect = 0.005
Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDIN---KCIKELNGMM- 101
K+++GNLS A ++R+LF + ++ G+ +D PD N + I+ L+G +
Sbjct: 3 KLYIGNLSPAVTAEDLRQLFGDRKLPLTGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 62
Query: 102 VDGKPMKV 109
+ GK M+V
Sbjct: 63 LHGKVMEV 70
>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 = 34.5 bits (80), Expect = 0.006
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD 89
++VG L++ + F+P+G + + I R + FV + P+
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51
>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 = 34.5 bits (80), Expect = 0.007
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKC---IK 95
VFVGN+ + ++ E+F G VV +V + YGF + DI I+
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGF--CEFEDIETAASAIR 58
Query: 96 ELNGMMVDGKPMKVVVA 112
LNG +G+ ++V A
Sbjct: 59 NLNGYEFNGRALRVDFA 75
Score = 25.7 bits (57), Expect = 9.6
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+F+GN+ + E + +F + G VV +V K YGF
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFC 45
>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear
polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p)
and similar proteins. This subfamily corresponds to the
RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also
termed cleavage factor IB (CFIB), is a sequence-specific
trans-acting factor that is essential for mRNA 3'-end
formation in yeast Saccharomyces cerevisiae. It can be
UV cross-linked to RNA and specifically recognizes the
(UA)6 RNA element required for both, the cleavage and
poly(A) addition, steps. Moreover, Hrp1p can shuttle
between the nucleus and the cytoplasm, and play an
additional role in the export of mRNAs to the cytoplasm.
Hrp1p also interacts with Rna15p and Rna14p, two
components of CF1A. In addition, Hrp1p functions as a
factor directly involved in modulating the activity of
the nonsense-mediated mRNA decay (NMD) pathway. It binds
specifically to a downstream sequence element
(DSE)-containing RNA and interacts with Upf1p, a
component of the surveillance complex, further
triggering the NMD pathway. Hrp1p contains two central
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and an arginine-glycine-rich region harboring repeats of
the sequence RGGF/Y. .
Length = 76
Score = 34.9 bits (80), Expect = 0.007
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 18/74 (24%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCIKE-- 96
+F+G L+ T +RE F +G V +C ++R+ +GF+ P K + E
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKP---KSVNEVM 57
Query: 97 -----LNGMMVDGK 105
L+G ++D K
Sbjct: 58 KKEHILDGKIIDPK 71
Score = 34.5 bits (79), Expect = 0.010
Identities = 11/33 (33%), Positives = 23/33 (69%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
+FIG +N T+ + +R F ++G+V +C V+++
Sbjct: 1 MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRD 33
>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 = 34.9 bits (81), Expect = 0.007
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+I++ +V+P S + I+ +FE +GK+ C + K YGF+
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFI 47
Score = 33.0 bits (76), Expect = 0.026
Identities = 13/77 (16%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCIK 95
+++V ++ + +++ +F +G + C + + YGF+ ++P I
Sbjct: 1 NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60
Query: 96 ELNGMMVDGKPMKVVVA 112
+N + G+ ++V A
Sbjct: 61 SMNLFDLGGQQLRVGKA 77
>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE. This
subgroup corresponds to the RRM of BOULE, the founder
member of the human DAZ gene family. Invertebrates
contain a single BOULE, while vertebrates, other than
catarrhine primates, possess both BOULE and DAZL genes.
The catarrhine primates possess BOULE, DAZL, and DAZ
genes. BOULE encodes an RNA-binding protein containing
an RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a single copy of the DAZ motif. Although its specific
biochemical functions remains to be investigated, BOULE
protein may interact with poly(A)-binding proteins
(PABPs), and act as translational activators of
specific mRNAs during gametogenesis. .
Length = 81
Score = 34.8 bits (80), Expect = 0.007
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSP-DINKCIKEL 97
++FVG + T ++R+ F YGTV E IV + YGFV ++ D K ++E
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEA 63
Query: 98 N 98
N
Sbjct: 64 N 64
Score = 30.5 bits (69), Expect = 0.21
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+IF+G ++ T+ +R F +YG V E +V K YGFV
Sbjct: 4 RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFV 48
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is a UUAG-specific nuclear RNA
binding protein that may be involved in pre-mRNA
splicing and telomere elongation. hnRNP A/B is an RNA
unwinding protein with a high affinity for G- followed
by U-rich regions. hnRNP A/B has also been identified as
an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 34.5 bits (79), Expect = 0.007
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 13/72 (18%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHI-DSPDINKCIK-- 95
+FVG LS +T +++E F +G VV+C I R +GFV D+ + K +
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60
Query: 96 --ELNGMMVDGK 105
+L+G ++D K
Sbjct: 61 EHKLDGRVIDPK 72
>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 = 34.4 bits (79), Expect = 0.008
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 47 VFVGNLSD-NTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPD 89
+FV N NTR ++ F PYG +V I RN+ FV ++ +
Sbjct: 2 LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNFAFVQYETQE 45
Score = 31.0 bits (70), Expect = 0.11
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 310 IFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKNYGFV 346
+F+ N +P T + FE YGK+V + +N+ FV
Sbjct: 2 LFVINFDPINTRTRDLERHFEPYGKLVNVRIRRNFAFV 39
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2 of
PHIP1. A. thaliana PHIP1 and its homologs represent a
novel class of plant-specific RNA-binding proteins that
may play a unique role in the polarized mRNA transport
to the vicinity of the cell plate. The family members
consist of multiple functional domains, including a
lysine-rich domain (KRD domain) that contains three
nuclear localization motifs (KKKR/NK), two RNA
recognition motifs (RRMs), and three CCHC-type zinc
fingers. PHIP1 is a peripheral membrane protein and is
localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 34.3 bits (79), Expect = 0.008
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 47 VFVGNLSDNTRAPEVRELF-------VPYGTVVECDIVRNYGFVHI-DSPDINKCIKELN 98
V++GNL+ + +VRE F V T E + +G V D ++ +K L+
Sbjct: 2 VYIGNLAWDITEDDVREFFKGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALK-LD 60
Query: 99 GMMVDGKPMKV 109
G ++ G+P+++
Sbjct: 61 GTVLCGRPIRI 71
>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 = 34.6 bits (79), Expect = 0.009
Identities = 12/34 (35%), Positives = 25/34 (73%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
K+F+G+V + + +RP+FE++G V+E ++K+
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKD 34
Score = 28.4 bits (63), Expect = 1.2
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 79
K+FVG++ EVR +F +G V+E I+++
Sbjct: 1 KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKD 34
>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, which is a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP D0 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), in the
middle and an RGG box rich in glycine and arginine
residues in the C-terminal part. Each of RRMs can bind
solely to the UUAG sequence specifically. .
Length = 74
Score = 34.2 bits (78), Expect = 0.010
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 13/72 (18%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHI-DSPDINKCIKE- 96
+F+G LS +T ++++ F +G VV+C + R +GFV +S ++K + +
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60
Query: 97 ---LNGMMVDGK 105
LNG ++D K
Sbjct: 61 EHKLNGKVIDPK 72
>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 = 34.3 bits (78), Expect = 0.010
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 9/71 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKCIKEL 97
VFVG+LS +++ F P+G + + +V++ YGFV + D I +
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 98 NGMMVDGKPMK 108
G + G+ ++
Sbjct: 64 GGQWLGGRQIR 74
Score = 34.3 bits (78), Expect = 0.013
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
F +F+G+++P + E I+ F +GK+ + VVK+ YGFV
Sbjct: 2 FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFV 48
>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A3 which is a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 81
Score = 34.3 bits (78), Expect = 0.010
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 15/72 (20%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCIKEL 97
K+F+G LS T +RE F +GT+ +C ++R+ +GFV C++E+
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFV------TYSCVEEV 57
Query: 98 NGMMVDGKPMKV 109
+ M +P KV
Sbjct: 58 DAAMS-ARPHKV 68
Score = 28.9 bits (64), Expect = 0.80
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ + +R FEK+G + +C V+++ +GFV
Sbjct: 4 KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFV 49
>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 = 34.4 bits (79), Expect = 0.010
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 79
K+FVG + + ++RELF YG V + +++R+
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRD 36
Score = 29.4 bits (66), Expect = 0.64
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
K+F+G + S + +R LFE+YG V + +V+++
Sbjct: 3 KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRD 36
>gnl|CDD|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subgroup corresponds to the RRM2 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA binding
motif protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear envelope
as well as the binding to mRNA export factors NXF1 and
Aly/REF. RBM15B belongs to the Spen (split end) protein
family, which shares a domain architecture comprising of
three N-terminal RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 85
Score = 34.6 bits (79), Expect = 0.011
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR-------NYGFVHIDSPDINKCIK- 95
T +F+GNL N E+R F YG + E I R Y F+ + D+ K
Sbjct: 8 TRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKV 67
Query: 96 ELNGMMVDGKPMKV 109
++G ++ P+K+
Sbjct: 68 AMSGRVIGRNPIKI 81
>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 = 34.6 bits (80), Expect = 0.011
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVR-----NYGFV 83
++VG + +T E+R+ F P+G + E + NYGFV
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFV 46
Score = 30.8 bits (70), Expect = 0.21
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVK-----NYGFV 346
I++G + T+ +R F+ +G++ E + NYGFV
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFV 46
>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), which is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus plays an
important role in apoB mRNA editing. hnRNP A/B contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long C-terminal glycine-rich domain that
contains a potential ATP/GTP binding loop. .
Length = 75
Score = 34.2 bits (78), Expect = 0.011
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHIDSPD-INKCIKE 96
K+FVG LS +T ++++ F +G V +C I R +GF+ + K +++
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60
Query: 97 ----LNGMMVDGK 105
L+G ++D K
Sbjct: 61 KEHRLDGRLIDPK 73
Score = 27.3 bits (60), Expect = 3.1
Identities = 10/31 (32%), Positives = 21/31 (67%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDV 339
K+F+G ++ TS + ++ F K+G+V +C +
Sbjct: 1 KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTI 31
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 34.2 bits (79), Expect = 0.012
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 48 FVGNLSDNTRAPEVRELF----VPYGTVV---ECDIVRNYGFVHIDSPDINKCIKELNGM 100
FVGNL NT ++ +F V +V E D + + +V + + K E +G
Sbjct: 5 FVGNLPFNTVQGDLDAIFKDLSVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDGA 64
Query: 101 MVDGKPMKVVVA 112
+ D + ++V +A
Sbjct: 65 LFDDRSLRVDIA 76
>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 = 34.2 bits (79), Expect = 0.012
Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 10/73 (13%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVE-CDIVRN--------YGFVHIDSPDI-NKCIKE 96
+F+GNL + + F +G +++ I+R+ + F+ DS + + I+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63
Query: 97 LNGMMVDGKPMKV 109
+NG + +P+ V
Sbjct: 64 MNGQYLCNRPITV 76
Score = 28.8 bits (65), Expect = 0.95
Identities = 10/46 (21%), Positives = 21/46 (45%), Gaps = 9/46 (19%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVV---------ECDVVKNYGFV 346
+FIGN++P +L+ F +G ++ + K + F+
Sbjct: 4 LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFI 49
>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 = 33.9 bits (78), Expect = 0.013
Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 9/73 (12%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINK-CIKE 96
+V+VG++S +R+ F P+G + D+ + + FV + P+ + +++
Sbjct: 2 RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61
Query: 97 LNGMMVDGKPMKV 109
+NG+M+ G+ +KV
Sbjct: 62 MNGVMLGGRNIKV 74
>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 = 33.8 bits (78), Expect = 0.013
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCIKEL 97
V+V NL + ++ ++F YG VV+ IV++ F+ +D D +KC+K L
Sbjct: 4 VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63
Query: 98 NGMMVDGKPMKVVVA 112
N + G+ +K +A
Sbjct: 64 NNKELFGRTLKCSIA 78
Score = 29.2 bits (66), Expect = 0.71
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 324 IRPLFEKYGKVVECDVVKN 342
+ +F KYGKVV+ +VK+
Sbjct: 18 LHKIFSKYGKVVKVTIVKD 36
>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 = 33.8 bits (78), Expect = 0.014
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDI---VRNYGFVHIDSPDI 90
KVFVG L+++ ++R+ F +G V + I R + FV P++
Sbjct: 1 RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEV 49
Score = 31.5 bits (72), Expect = 0.087
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 7/43 (16%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDV-----VKNYGFV 346
K+F+G + + E +R F ++G+V DV + + FV
Sbjct: 2 KVFVGRLTEDMTEEDLRQYFSQFGEV--TDVYIPKPFRAFAFV 42
>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras
GTPase-activating protein-binding protein 2 (G3BP2) and
similar proteins. This subgroup corresponds to the RRM
of G3BP2, also termed GAP SH3 domain-binding protein 2,
a cytoplasmic protein that interacts with both
IkappaBalpha and IkappaBalpha/NF-kappaB complexes,
indicating that G3BP2 may play a role in the control of
nucleocytoplasmic distribution of IkappaBalpha and
cytoplasmic anchoring of the IkappaBalpha/NF-kappaB
complex. G3BP2 contains an N-terminal nuclear transfer
factor 2 (NTF2)-like domain, an acidic domain, a domain
containing five PXXP motifs, an RNA recognition motif
(RRM domain), and an Arg-Gly-rich region (RGG-rich
region, or arginine methylation motif). It binds to the
SH3 domain of RasGAP, a multi-functional protein
controlling Ras activity, through its N-terminal
NTF2-like domain. The acidic domain is sufficient for
the interaction of G3BP2 with the IkappaBalpha
cytoplasmic retention sequence. Furthermore, G3BP2
might influence stability or translational efficiency
of particular mRNAs by binding to RNA-containing
structures within the cytoplasm through its RNA-binding
domain.
Length = 83
Score = 34.2 bits (78), Expect = 0.014
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 8/52 (15%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHIDSPD 89
++FVGNL + E++E F+ +G VVE I + N+GFV D +
Sbjct: 7 QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSE 58
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and
similar proteins. PABPs are highly conserved proteins
that bind to the poly(A) tail present at the 3' ends of
most eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. ePABP-2 is
predominantly located in the cytoplasm and PABP-2 is
located in the nucleus. In contrast to the type I PABPs
containing four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), the type II PABPs contains
a single highly-conserved RRM. This subfamily also
includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C)
gene encoding cytoplasmic mRNA-binding protein Rbp29
that binds preferentially to poly(A). Although not
essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 33.8 bits (78), Expect = 0.014
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 8/72 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCIKELN 98
+FVGN+ T E++E F GT+ I+ + + ++ + LN
Sbjct: 2 IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61
Query: 99 GMMVDGKPMKVV 110
G+ +KV
Sbjct: 62 ESEFRGRQIKVT 73
>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 = 33.6 bits (77), Expect = 0.016
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 9/71 (12%)
Query: 47 VFVGNLSDNTRAPE----VRELFVPYG-TVVECDI--VRNYGFVHIDSP-DINKCIKELN 98
+FVGNL+ N E + E F V + I + +G+V +S D+ K + EL
Sbjct: 3 LFVGNLNPNKDFDELKTAISEFFSKKNLAVQDVRIGSSKKFGYVDFESAEDLEKAL-ELT 61
Query: 99 GMMVDGKPMKV 109
G + G +K+
Sbjct: 62 GKKLLGNEIKL 72
>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 = 33.5 bits (77), Expect = 0.018
Identities = 16/69 (23%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHI---DSPDINKCIKELNGM 100
+T +++G+LS +++ LF YG + D++ G ++ D ++ +++L +
Sbjct: 2 STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRGCAYVCMETRQDAHRALQKLRNV 61
Query: 101 MVDGKPMKV 109
+ GK +KV
Sbjct: 62 KLAGKKIKV 70
Score = 30.0 bits (68), Expect = 0.32
Identities = 10/35 (28%), Positives = 23/35 (65%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYG 344
++IG+++ + E ++ LFE+YG++ D++ G
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPRG 39
>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A0 (hnRNP A0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A0, a low abundance hnRNP protein that has been
implicated in mRNA stability in mammalian cells. It has
been identified as the substrate for MAPKAP-K2 and may
be involved in the lipopolysaccharide (LPS)-induced
post-transcriptional regulation of tumor necrosis
factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and
macrophage inflammatory protein 2 (MIP-2). hnRNP A0
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 33.7 bits (77), Expect = 0.018
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD 89
K+FVG L + ++ E F +G V + +++ R +GFV+ + D
Sbjct: 1 KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHD 52
>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 = 33.6 bits (77), Expect = 0.019
Identities = 16/46 (34%), Positives = 29/46 (63%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+F+G ++ T+ E +R F +YG+VV+C ++K+ +GFV
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFV 46
Score = 33.6 bits (77), Expect = 0.021
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 19/77 (24%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCIK-- 95
K+FVG LS T +R F YG VV+C I+++ +GFV P+ C+
Sbjct: 1 KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPN---CVGTV 57
Query: 96 ------ELNGMMVDGKP 106
L+G +D KP
Sbjct: 58 LAGGPHTLDGRTIDPKP 74
>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM2 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1), and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 80
Score = 33.5 bits (76), Expect = 0.019
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 9/71 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH-IDSPDINKCIKEL 97
VFVG+LS +++ F P+G + + +V++ YGFV + D I+++
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 98 NGMMVDGKPMK 108
G + G+ ++
Sbjct: 64 GGQWLGGRQIR 74
Score = 31.6 bits (71), Expect = 0.11
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
F +F+G+++P + + I+ F +G++ + VVK+ YGFV
Sbjct: 2 FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 48
>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein
homolog beta (TRA-2 beta) and similar proteins. This
subgroup corresponds to the RRM of TRA2-beta or
TRA-2-beta, also termed splicing factor,
arginine/serine-rich 10 (SFRS10), or transformer-2
protein homolog B, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-beta is a
serine/arginine-rich (SR) protein that controls the
pre-mRNA alternative splicing of the
calcitonin/calcitonin gene-related peptide (CGRP), the
survival motor neuron 1 (SMN1) protein and the tau
protein. It contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. TRA2-beta
specifically binds to two types of RNA sequences, the
CAA and (GAA)2 sequences, through the RRMs in different
RNA binding modes. .
Length = 89
Score = 33.9 bits (77), Expect = 0.020
Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDS 87
+R P+ P + V LS T ++RE+F YG + + IV R + FV+ ++
Sbjct: 2 NRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60
Query: 88 PDINKCIKE-LNGMMVDGKPMKV 109
D K KE NGM +DG+ ++V
Sbjct: 61 VDDAKEAKERANGMELDGRRIRV 83
>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor. This
model describes the sex-lethal family of splicing
factors found in Dipteran insects. The sex-lethal
phenotype, however, may be limited to the Melanogasters
and closely related species. In Drosophila the protein
acts as an inhibitor of splicing. This subfamily is most
closely related to the ELAV/HUD subfamily of splicing
factors (TIGR01661).
Length = 346
Score = 36.1 bits (83), Expect = 0.021
Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 9/83 (10%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-D 89
N T + V L + E+ LF G + C I+R+ Y FV S D
Sbjct: 102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEAD 161
Query: 90 INKCIKELNGMMVDGKPMKVVVA 112
+ IK LNG+ V K +KV A
Sbjct: 162 SQRAIKNLNGITVRNKRLKVSYA 184
Score = 35.8 bits (82), Expect = 0.028
Identities = 31/109 (28%), Positives = 52/109 (47%), Gaps = 12/109 (11%)
Query: 15 AIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC 74
AIK LNG V K LK+ A G + T ++V NL ++ +F YG +V+
Sbjct: 165 AIKNLNGITVRNKRLKVSYARP-GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQK 223
Query: 75 DIVRN--------YGFVHIDS-PDINKCIKELNGMMVDG--KPMKVVVA 112
+I+R+ FV + + + I LN ++ +G +P+ V +A
Sbjct: 224 NILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLA 272
>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 = 33.5 bits (77), Expect = 0.021
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 12/77 (15%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPDINKC---I 94
T +++ NL + ++ + PYG V+ I+R+ GF ++S + KC I
Sbjct: 1 TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESRE--KCEDII 58
Query: 95 KELNGMMVDGKPMKVVV 111
+ NG + G+ ++V
Sbjct: 59 SKFNGKYLKGEGEPLLV 75
>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 = 33.0 bits (76), Expect = 0.022
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYG-----FVHIDSPDINKCIKELNG 99
T++ V NL + ++ ELF G + +VR G +V D D I + N
Sbjct: 1 TRLVVSNLHPSVTEDDIVELFSAIGALKRARLVRP-GVAEVVYVRKD--DALTAIDKYNN 57
Query: 100 MMVDGKPMKV 109
+DG+PMK
Sbjct: 58 RELDGQPMKC 67
>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 = 33.2 bits (76), Expect = 0.024
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYG----FVHIDSP-DINKCIKELNGM 100
+++VGNL + R ++ +LF YG + + D+ G FV + P D + +G
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60
Query: 101 MVDGKPMKV 109
DG ++V
Sbjct: 61 DYDGYRLRV 69
Score = 28.6 bits (64), Expect = 1.1
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYG 344
+I++GN+ P + I LF KYG + + D+ G
Sbjct: 1 RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRG 36
>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 = 33.0 bits (75), Expect = 0.025
Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDIN---KCIKELNGMM- 101
K+++GNLS+N ++ +F + G+ +D PD + K I L+G +
Sbjct: 3 KLYIGNLSENASPLDLESIFKDSKIPFSGPFLVKSGYAFVDCPDESWAMKAIDTLSGKVE 62
Query: 102 VDGKPMKV 109
+ GK ++V
Sbjct: 63 LHGKVIEV 70
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 33.0 bits (75), Expect = 0.027
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 13/76 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHI-DSPDINKCIK- 95
K+F+G LS +T ++ E +G V++C I R +GFV D+ ++K ++
Sbjct: 1 KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60
Query: 96 ---ELNGMMVDGKPMK 108
+L+G ++D K K
Sbjct: 61 KEHKLDGKLIDPKRAK 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 = 33.7 bits (78), Expect = 0.027
Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 15/77 (19%)
Query: 47 VFVGNLSDNTRAPEV---RELFVPYGTVVECDIVRN--YGFVHIDS----------PDIN 91
V+V L EV E F YG + + I RN Y S D
Sbjct: 8 VYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRKEDAL 67
Query: 92 KCIKELNGMMVDGKPMK 108
+CI+ ++G +DG+ +K
Sbjct: 68 RCIQAVDGFYLDGRLLK 84
>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 = 33.2 bits (76), Expect = 0.028
Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHI-DSPDINKCIKEL 97
K+FV L + E+ +LF +G V +V N +V + ++ + ++
Sbjct: 4 KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63
Query: 98 NGMMVDGKPMKVVVA 112
+G + K + V ++
Sbjct: 64 DGTEIKEKTISVAIS 78
>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 = 33.1 bits (76), Expect = 0.029
Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 12/81 (14%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHID-SPDINKC 93
P +++F+ + ++RE F P+G + + +V++ +V + +
Sbjct: 2 PNSRLFI-VCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60
Query: 94 IKELNGMMV--DGKPMKVVVA 112
++E+NG + D KP+KV++A
Sbjct: 61 MEEMNGKCLGGDTKPLKVLIA 81
>gnl|CDD|240882 cd12436, RRM1_2_MATR3_like, RNA recognition motif 1 and 2 in the
matrin 3 family of nuclear proteins. This subfamily
corresponds to the RRM of the matrin 3 family of nuclear
proteins consisting of Matrin 3 (MATR3), nuclear protein
220 (NP220) and similar proteins. MATR3 is a highly
conserved inner nuclear matrix protein that has been
implicated in various biological processes. NP220 is a
large nucleoplasmic DNA-binding protein that binds to
cytidine-rich sequences, such as CCCCC (G/C), in
double-stranded DNA (dsDNA). Both, Matrin 3 and NP220,
contain two RNA recognition motif (RRM), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a Cys2-His2 zinc finger-like motif at the
C-terminal region. .
Length = 76
Score = 33.0 bits (76), Expect = 0.029
Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 46 KVFVGNL-SDNTRAPEVRELFVPYGTVVECDIVRNY--GFVHIDSPDINK---CIKELNG 99
V + NL E+ +L P+G V + N F+ ++SP+ + +
Sbjct: 2 VVRLSNLPEGGYTEAELLKLAEPFGKVDHYIFLPNRNKAFIEMESPEDAQALVSFYKTYP 61
Query: 100 MMVDGKPMKVVVA 112
+ + GK +KV ++
Sbjct: 62 LTIGGKSIKVALS 74
>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 = 33.1 bits (76), Expect = 0.030
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHIDSPDI---NKCIK 95
T ++V N++D TR ++R LF YG +V+ I ++ GF ++ D+ +
Sbjct: 1 TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60
Query: 96 ELNGMMVDGKPMKVVVA 112
L+ G+ +++ A
Sbjct: 61 YLDRTRFLGREIEIQFA 77
Score = 28.9 bits (65), Expect = 1.0
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVE 336
+++ NV T + +R LF KYG +V+
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVD 29
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0, a UUAG-specific nuclear RNA binding
protein that may be involved in pre-mRNA splicing and
telomere elongation. hnRNP A/B is an RNA unwinding
protein with a high affinity for G- followed by U-rich
regions. It has also been identified as an
APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis at
the transcriptional and post-transcriptional levels. All
memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and a
glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 32.7 bits (75), Expect = 0.033
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVE 336
KIF+G ++P T+ E IR F K+G +VE
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVE 28
Score = 31.6 bits (72), Expect = 0.078
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKEL 97
K+FVG LS T ++RE F +G +VE ++ R + F+ DS + K I E
Sbjct: 1 KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60
Query: 98 NGMMVDGKPMKVVVA 112
++ GK ++V A
Sbjct: 61 QFHVIGGKKVEVKKA 75
>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 = 33.0 bits (76), Expect = 0.033
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTV 71
VFVGNL T+ ++++LF +G +
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPI 27
Score = 30.7 bits (70), Expect = 0.28
Identities = 7/25 (28%), Positives = 17/25 (68%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKV 334
+F+GN+ T + ++ LF+++G +
Sbjct: 3 VFVGNLPLTTKKKDLKKLFKQFGPI 27
>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 = 0.034
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 47 VFVGNLSDNTRAPEVRELF--VPYGTVVECDIVRNYGFVHI-DSPDINKCIKELNGMMVD 103
++V NL T + + F G V +R+Y FVH D D K + ELNG ++
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDREDAVKAMDELNGKELE 295
Query: 104 GKPMKVVVA 112
G ++V +A
Sbjct: 296 GSEIEVTLA 304
>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 = 32.6 bits (75), Expect = 0.036
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI--VRNYGFVHIDSPDINK-CIKELNGMMV- 102
++VG L T E+ F +G + D RNY ++ +S + + + L G +
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLG 60
Query: 103 -DGKPMKV 109
G+ ++V
Sbjct: 61 GPGRRLRV 68
Score = 28.7 bits (65), Expect = 0.88
Identities = 9/39 (23%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDV--VKNYGFV 346
+++G + P TS+ + F+++G + D +NY ++
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGRNYAYI 39
>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding
protein MRN1 and similar proteins. This subgroup
corresponds to the RRM2 of MRN1, also termed multicopy
suppressor of RSC-NHP6 synthetic lethality protein 1,
or post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 78
Score = 32.8 bits (75), Expect = 0.038
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSPDINKCIK 95
V++GNL ++ E+RE +G + + IV +N FVH S I IK
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFVHFLS--IANAIK 54
Score = 28.9 bits (65), Expect = 0.85
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
++IGN+ S E +R EK+G + + +V KN FV
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKNIAFV 44
>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich
splicing factor 12 (SRSF12) and similar proteins. This
subgroup corresponds to the RRM of SRSF12, also termed
35 kDa SR repressor protein (SRrp35), or splicing
factor, arginine/serine-rich 13B (SFRS13B), or splicing
factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a
serine/arginine (SR) protein-like alternative splicing
regulator that antagonizes authentic SR proteins in the
modulation of alternative 5' splice site choice. For
instance, it activates distal alternative 5' splice site
of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains
a single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 32.7 bits (74), Expect = 0.042
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHIDSPDI---NKCIK 95
T +FV N++D TR ++R F YG +V+ + ++ GF +I D+ +
Sbjct: 1 TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60
Query: 96 ELNGMMVDGKPMKVVVA 112
LN V G+ +++ A
Sbjct: 61 NLNRKWVCGRQIEIQFA 77
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously expressed
pre-mRNA splicing factor that enhances messenger RNA
(mRNA) splicing in a cell-specific manner or in a
certain developmental process, such as spermatogenesis.
It interacts with splicing factors SAP145 (the
spliceosomal splicing factor 3b subunit 2) and SRp20,
and may play a more specific role in meiosis entry and
progression. Together with additional testis-specific
RNA-binding proteins, RBM7 may regulate the splicing of
specific pre-mRNA species that are important in the
meiotic cell cycle. RBM11 is a novel tissue-specific
splicing regulator that is selectively expressed in
brain, cerebellum and testis, and to a lower extent in
kidney. It is localized in the nucleoplasm and enriched
in SRSF2-containing splicing speckles. It may play a
role in the modulation of alternative splicing during
neuron and germ cell differentiation. Both, RBM7 and
RBM11, contain an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a region lacking known
homology at the C-terminus. The RRM is responsible for
RNA binding, whereas the C-terminal region permits
nuclear localization and homodimerization. .
Length = 75
Score = 32.3 bits (74), Expect = 0.047
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI-------VRNYGFV-HIDSPDINKCIKELN 98
+FVGNL + ELF+ G + I +++ FV + I+ LN
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63
Query: 99 GMMVDGKPMKV 109
G+ + G+ +++
Sbjct: 64 GIRLFGRELRI 74
>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM1 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core protein
A1, and is an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced transcripts
of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can
shuttle between the nucleus and the cytoplasm. Thus, it
may be involved in transport of cellular RNAs, including
the packaging of pre-mRNA into hnRNP particles and
transport of poly A+ mRNA from the nucleus to the
cytoplasm. The cytoplasmic hnRNP A1 has high affinity
with AU-rich elements, whereas the nuclear hnRNP A1 has
high affinity with a polypyrimidine stretch bordered by
AG at the 3' ends of introns. hnRNP A1 is also involved
in the replication of an RNA virus, such as mouse
hepatitis virus (MHV), through an interaction with the
transcription-regulatory region of viral RNA. hnRNP A1,
together with the scaffold protein septin 6, serves as
host protein to form a complex with NS5b and viral RNA,
and further plays important roles in the replication of
Hepatitis C virus (HCV). hnRNP A1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. The
RRMs of hnRNP A1 play an important role in silencing the
exon and the glycine-rich domain is responsible for
protein-protein interactions. .
Length = 81
Score = 32.3 bits (73), Expect = 0.048
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 15/72 (20%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCIKEL 97
K+F+G LS T +R F +GT+ +C ++R+ +GFV S + E+
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVE------EV 57
Query: 98 NGMMVDGKPMKV 109
+ M + +P KV
Sbjct: 58 DAAM-NARPHKV 68
Score = 29.6 bits (66), Expect = 0.45
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV
Sbjct: 4 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 49
>gnl|CDD|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast
nucleolar protein 13 (Nop13p) and similar proteins.
This subfamily corresponds to the RRM2 of Nop13p encoded
by YNL175c from Saccharomyces cerevisiae. It shares high
sequence similarity with nucleolar protein 12 (Nop12p).
Both Nop12p and Nop13p are not essential for growth.
However, unlike Nop12p that is localized to the
nucleolus, Nop13p localizes primarily to the nucleolus
but is also present in the nucleoplasm to a lesser
extent. Nop13p contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 32.0 bits (73), Expect = 0.054
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVEC------DIVRNYGFVHIDSPDINKCIKELNGM 100
+FVGNLS T E+R F G + D + GF +D +I L G
Sbjct: 1 LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60
Query: 101 MVDGKPMKV 109
++G+ ++V
Sbjct: 61 HLNGRALRV 69
>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 1 (Musashi-1) and similar proteins.
This subgroup corresponds to the RRM1 of Musashi-1. The
mammalian MSI1 gene encoding Musashi-1 (also termed
Msi1) is a neural RNA-binding protein putatively
expressed in central nervous system (CNS) stem cells and
neural progenitor cells and associated with asymmetric
divisions in neural progenitor cells. Musashi-1 is
evolutionarily conserved from invertebrates to
vertebrates. It is a homolog of Drosophila Musashi and
Xenopus laevis nervous system-specific RNP protein-1
(Nrp-1). Musashi-1 has been implicated in the
maintenance of the stem-cell state, differentiation, and
tumorigenesis. It translationally regulates the
expression of a mammalian numb gene by binding to the
3'-untranslated region of mRNA of Numb, encoding a
membrane-associated inhibitor of Notch signaling, and
further influences neural development. Moreover, it
represses translation by interacting with the
poly(A)-binding protein and competes for binding of the
eukaryotic initiation factor-4G (eIF-4G). Musashi-1
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 77
Score = 32.3 bits (73), Expect = 0.059
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV-HIDSPDINKCI-- 94
K+F+G LS T +RE F +G V EC ++R+ +GFV +D ++K +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 95 --KELNGMMVDGK 105
EL+ +D K
Sbjct: 62 SRHELDSKTIDPK 74
Score = 29.6 bits (66), Expect = 0.53
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ E +R F ++G+V EC V+++ +GFV
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 47
>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 = 34.9 bits (80), Expect = 0.061
Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 9/78 (11%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGF-VHIDSPDINKCIKE 96
++++GNL +++EL +G + +++++ Y F + D + I
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356
Query: 97 LNGMMVDGKPMKVVVAGF 114
LNG + V A
Sbjct: 357 LNGKDTGDNKLHVQRACV 374
>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 = 31.9 bits (72), Expect = 0.075
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 47 VFVGNLSDNTRAPEVRELFVPY--GTVVECDIVRNYGFVHIDS-PDINKCIKELNGMMVD 103
++V NL T +++ F + G V +R+Y FVH S D + LNG ++
Sbjct: 4 LYVRNLMIETSEDTIKKTFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELE 63
Query: 104 GKPMKVVVA 112
G ++V +A
Sbjct: 64 GSCIEVTLA 72
>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 = 31.9 bits (73), Expect = 0.076
Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRNYGFVHIDSPDIN---KCIKELNGMMVD 103
FV N++ N E+R LF +G + ++ GF+ + DI + + L G +
Sbjct: 5 FVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTELG 64
Query: 104 GKPMKV 109
G+ + +
Sbjct: 65 GRKLDI 70
Score = 31.5 bits (72), Expect = 0.084
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVEC-DVVKNYGFV 346
+F+ N+N E +R LFE++G + K+ GF+
Sbjct: 4 LFVRNINSNVEDEELRALFEQFGDIRTLYTACKHRGFI 41
>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 = 32.0 bits (73), Expect = 0.077
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
K+F+G + + +RPLFE++GK+ E V+K+
Sbjct: 7 KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKD 40
Score = 27.0 bits (60), Expect = 5.3
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 79
K+FVG + N ++R LF +G + E ++++
Sbjct: 6 IKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKD 40
>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the
RRM2 of hnRNP A2/B1, an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor
suppressors, such as BIN1, WWOX, the antiapoptotic
proteins c-FLIP and caspase-9B, the insulin receptor
(IR), and the RON proto-oncogene among others.
Overexpression of hnRNP A2/B1 has been described in
many cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. .
Length = 80
Score = 32.0 bits (72), Expect = 0.084
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD 89
K+FVG + ++T +R+ F YG + +I+ R +GFV D D
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHD 53
Score = 28.9 bits (64), Expect = 0.94
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
K+F+G + T +R FE+YGK+ +++ +
Sbjct: 2 KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITD 35
>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 = 31.4 bits (72), Expect = 0.086
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCIKE-L 97
V++G+L PE+R+ F +GTV + R+ Y FV +SP++ K + E +
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 98 NGMMVDGKPMKV 109
N ++ + +K
Sbjct: 62 NNYLLFERLLKC 73
>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate
serine/arginine-rich splicing factor 3 (SRSF3). This
subgroup corresponds to the RRM of SRSF3, also termed
pre-mRNA-splicing factor SRp20, a splicing regulatory
serine/arginine (SR) protein that modulates alternative
splicing by interacting with RNA cis-elements in a
concentration- and cell differentiation-dependent
manner. It is also involved in termination of
transcription, alternative RNA polyadenylation, RNA
export, and protein translation. SRSF3 is critical for
cell proliferation and tumor induction and maintenance.
SRSF3 can shuttle between the nucleus and cytoplasm. It
contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal RS domain
rich in serine-arginine dipeptides. The RRM domain is
involved in RNA binding, and the RS domain has been
implicated in protein shuttling and protein-protein
interactions. .
Length = 81
Score = 31.6 bits (71), Expect = 0.091
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHI-DSPDINKCIKELNGMM 101
KV+VGNL +N E+ F YG + + RN + FV D D ++EL+G
Sbjct: 6 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 65
Query: 102 VDGKPMKV 109
+ G ++V
Sbjct: 66 LCGCRVRV 73
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 31.7 bits (73), Expect = 0.093
Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 15/78 (19%)
Query: 46 KVFVGNLSDNTRAPEVRELF-----------VPYGTVVECDIV--RNYGFVHIDSPDI-N 91
+++VGNL E+ + F P V+ I +N+ FV + +
Sbjct: 3 RLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKNFAFVEFRTVEEAT 62
Query: 92 KCIKELNGMMVDGKPMKV 109
+ L+G++ G+P+K+
Sbjct: 63 AALA-LDGIIFKGQPLKI 79
>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA
annealing protein YRA1 (Yra1p), yeast mRNA export
protein mlo3 and similar proteins. This subfamily
corresponds to the RRM of Yra1p and mlo3. Yra1p is an
essential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA1 gene. It belongs to the
evolutionarily conserved REF (RNA and export factor
binding proteins) family of hnRNP-like proteins. Yra1p
possesses potent RNA annealing activity and interacts
with a number of proteins involved in nuclear transport
and RNA processing. It binds to the mRNA export factor
Mex67p/TAP and couples transcription to export in yeast.
Yra1p is associated with Pse1p and Kap123p, two members
of the beta-importin family, further mediating transport
of Yra1p into the nucleus. In addition, the
co-transcriptional loading of Yra1p is required for
autoregulation. Yra1p consists of two highly conserved
N- and C-terminal boxes and a central RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). This subfamily includes
RNA-annealing protein mlo3, also termed mRNA export
protein mlo3, which has been identified in fission yeast
as a protein that causes defects in chromosome
segregation when overexpressed. It shows high sequence
similarity with Yra1p. .
Length = 77
Score = 31.6 bits (72), Expect = 0.097
Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 46 KVFVGNLSDNTRAPEVRELFVP-YGTVVECDIVRN-----YGFVHI---DSPDINKCIKE 96
KV V NL + ++RE FV G + + N G +I + D K +
Sbjct: 1 KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60
Query: 97 LNGMMVDGK-PMKVVV 111
NG + DG MKV V
Sbjct: 61 FNGRIDDGNRKMKVEV 76
>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 = 31.5 bits (72), Expect = 0.099
Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 10/76 (13%)
Query: 47 VFVGNLSDNTRAPEVRELFVP-YGTVVECDIV--------RNYGFVHI-DSPDINKCIKE 96
+FVG+L+ + ++E F Y +V +V + YGFV D + ++ + E
Sbjct: 4 IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63
Query: 97 LNGMMVDGKPMKVVVA 112
+NG+ +PM+V A
Sbjct: 64 MNGVYCSSRPMRVSPA 79
Score = 26.9 bits (60), Expect = 4.3
Identities = 8/28 (28%), Positives = 18/28 (64%)
Query: 8 NDEEGRTAIKELNGQIVNEKPLKIEAAT 35
+++E A+ E+NG + +P+++ AT
Sbjct: 53 DEDERDRALTEMNGVYCSSRPMRVSPAT 80
>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 = 31.4 bits (71), Expect = 0.10
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 9/76 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDS-PDINKCIK 95
T ++V NL E+R++F YG +V+C+++R+ FV D + I
Sbjct: 1 TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60
Query: 96 ELNGMMVDGKPMKVVV 111
LNG + G M + V
Sbjct: 61 SLNGTIPPGSTMPLSV 76
>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 = 31.4 bits (72), Expect = 0.10
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 7/52 (13%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDI-------VRNYGFVHIDSPD 89
TK+ V N+ E+RELF P+G V + R + FV +
Sbjct: 1 TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQ 52
>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 = 31.2 bits (71), Expect = 0.11
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-DINKCIKELN 98
+FV NL +++E+F G VV DI R G V + P + + I N
Sbjct: 1 IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60
Query: 99 GMMVDGKPMKV 109
G M+ +PM+V
Sbjct: 61 GQMLFDRPMRV 71
>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A3 (hnRNP A3) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A3, a novel RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE) independently of hnRNP A2 and
participates in the trafficking of A2RE-containing RNA.
hnRNP A3 can shuttle between the nucleus and the
cytoplasm. It contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a long
glycine-rich region at the C-terminus. .
Length = 80
Score = 31.5 bits (71), Expect = 0.12
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
KIF+G + T +R FEKYGK+ +V+++
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMED 35
Score = 31.1 bits (70), Expect = 0.16
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD 89
K+FVG + ++T +R+ F YG + +++ R + FV D D
Sbjct: 2 KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHD 53
>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 = 31.2 bits (70), Expect = 0.13
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR 78
K+F+G +S ++R +F P+G + EC I+R
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEECRILR 35
Score = 28.1 bits (62), Expect = 1.9
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK 341
K+FIG V+ + IR +F +G++ EC +++
Sbjct: 3 KLFIGMVSKKCNENDIRVMFSPFGQIEECRILR 35
>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 = 31.2 bits (71), Expect = 0.13
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHI---DSPDINKCI 94
T ++FV NL + + ++ +LF +G + E + + GF ++ D D K
Sbjct: 2 TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61
Query: 95 KELNGMMVDGKPMKV 109
KEL+G + G+ + +
Sbjct: 62 KELDGKVFQGRLIHI 76
Score = 27.4 bits (61), Expect = 3.5
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV 340
T ++F+ N+ + + LF K+G++ E V
Sbjct: 2 TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVA 35
>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger.
Length = 17
Score = 29.7 bits (68), Expect = 0.14
Identities = 6/13 (46%), Positives = 10/13 (76%)
Query: 129 RCGRGGHWSKECP 141
CG+ GH +++CP
Sbjct: 4 NCGKEGHIARDCP 16
>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 = 31.5 bits (71), Expect = 0.14
Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 14/86 (16%)
Query: 47 VFVGNLSDNTRAPEVRE----LFVPYGTVVECDIV-------RNYGFVHIDS-PDINKCI 94
+++ NL+D + E++ LF +G VV DIV R FV +
Sbjct: 4 IYINNLNDKIKKEELKRSLYALFSQFGHVV--DIVALKTMKMRGQAFVIFKELSSATNAL 61
Query: 95 KELNGMMVDGKPMKVVVAGFISSILS 120
++L G GKPM++ A S I+S
Sbjct: 62 RQLQGFPFYGKPMRIQYAKTDSDIVS 87
>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 = 31.1 bits (70), Expect = 0.14
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMM 101
KV+VGNL E+ F YG + I RN + FV + P D ++ L+G +
Sbjct: 1 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 60
Query: 102 VDGKPMKVVVA 112
+ G ++V ++
Sbjct: 61 ICGSRVRVELS 71
>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 = 31.1 bits (71), Expect = 0.14
Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 13/76 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-----------YGFV-HIDSPDINKC 93
+++V NL ++R +F +G V I + + FV D+
Sbjct: 2 EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61
Query: 94 IKELNGMMVDGKPMKV 109
+ +LNG + G+ + V
Sbjct: 62 L-QLNGTELGGRKISV 76
>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein
Musashi homolog 2 (Musashi-2 ) and similar proteins.
This subgroup corresponds to the RRM2 of Musashi-2 (also
termed Msi2) which has been identified as a regulator of
the hematopoietic stem cell (HSC) compartment and of
leukemic stem cells after transplantation of cells with
loss and gain of function of the gene. It influences
proliferation and differentiation of HSCs and myeloid
progenitors, and further modulates normal hematopoiesis
and promotes aggressive myeloid leukemia. Musashi-2
contains two conserved N-terminal tandem RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), along with other
domains of unknown function. .
Length = 76
Score = 31.2 bits (70), Expect = 0.14
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 13/73 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCI-- 94
K+F+G LS T +R+ F +G + EC ++R+ +GFV P ++K +
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60
Query: 95 --KELNGMMVDGK 105
EL+ +D K
Sbjct: 61 PHHELDSKTIDPK 73
Score = 30.4 bits (68), Expect = 0.26
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ TS + +R F K+G++ EC V+++ +GFV
Sbjct: 1 KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFV 46
>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein M (hnRNP M).
This subgroup corresponds to the RRM2 of hnRNP M, a
pre-mRNA binding protein that may play an important role
in the pre-mRNA processing. It also preferentially binds
to poly(G) and poly(U) RNA homopolymers. hnRNP M is able
to interact with early spliceosomes, further influencing
splicing patterns of specific pre-mRNAs. It functions as
the receptor of carcinoembryonic antigen (CEA) that
contains the penta-peptide sequence PELPK signaling
motif. In addition, hnRNP M and another splicing factor
Nova-1 work together as dopamine D2 receptor (D2R)
pre-mRNA-binding proteins. They regulate alternative
splicing of D2R pre-mRNA in an antagonistic manner.
hnRNP M contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an unusual
hexapeptide-repeat region rich in methionine and
arginine residues (MR repeat motif). .
Length = 76
Score = 31.1 bits (70), Expect = 0.15
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 8/73 (10%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-DINKCIKE 96
+ VFV NL +++E+F G VV DI+ R G V + P + + I
Sbjct: 1 STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISM 60
Query: 97 LNGMMVDGKPMKV 109
NG ++ +PM V
Sbjct: 61 FNGQLLFDRPMHV 73
>gnl|CDD|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM3 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 72
Score = 30.8 bits (70), Expect = 0.16
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTV 71
T + V N T A E+R+LF P+G +
Sbjct: 1 TTILVKNFPYGTTAEELRDLFEPHGKL 27
Score = 28.5 bits (64), Expect = 0.96
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKV 334
I + N GT+ E +R LFE +GK+
Sbjct: 3 ILVKNFPYGTTAEELRDLFEPHGKL 27
>gnl|CDD|240971 cd12527, RRM2_EAR1_like, RNA recognition motif 2 in terminal
EAR1-like proteins. This subgroup corresponds to the
RRM2 of terminal EAR1-like proteins, including terminal
EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land
plants. They may play a role in the regulation of leaf
initiation. The terminal EAR1-like proteins are putative
RNA-binding proteins carrying three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and TEL characteristic
motifs that allow sequence and putative functional
discrimination between the terminal EAR1-like proteins
and Mei2-like proteins. .
Length = 71
Score = 30.9 bits (70), Expect = 0.16
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 306 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVE 336
GT IF N++P S E +R +F+ YG V E
Sbjct: 2 GTLVIF--NLDPTVSSETLRSIFQVYGDVKE 30
Score = 29.4 bits (66), Expect = 0.49
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 49 VGNLSDNTRAPEVRELFVPYGTVV---ECDIVRNYGFVHI-DSPDINKCIKELNGMMVDG 104
+ NL + +R +F YG V E R FV D D K ++ +NG + G
Sbjct: 6 IFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKEISG 65
Query: 105 KPMKV 109
KP+ +
Sbjct: 66 KPVVI 70
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in
serine/arginine-rich splicing factor 10 (SRSF10) and
similar proteins. This subgroup corresponds to the RRM
of SRSF10, also termed 40 kDa SR-repressor protein
(SRrp40), or FUS-interacting serine-arginine-rich
protein 1 (FUSIP1), or splicing factor SRp38, or
splicing factor, arginine/serine-rich 13A (SFRS13A), or
TLS-associated protein with Ser-Arg repeats (TASR).
SRSF10 is a serine-arginine (SR) protein that acts as a
potent and general splicing repressor when
dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator
of cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is
required for proper Ca2+ handling during embryonic
heart development. In contrast, the phosphorylated
SRSF10 functions as a sequence-specific splicing
activator in the presence of a nuclear cofactor. It
activates distal alternative 5' splice site of
adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10
strengthens pre-mRNA recognition by U1 and U2 snRNPs.
SRSF10 localizes to the nuclear speckles and can
shuttle between nucleus and cytoplasm. It contains a
single N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. .
Length = 84
Score = 31.1 bits (70), Expect = 0.18
Identities = 14/52 (26%), Positives = 30/52 (57%), Gaps = 6/52 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY------GFVHIDSPDI 90
+ +FV N++D+TR+ ++R F YG +V+ + ++ GF ++ D+
Sbjct: 1 SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDV 52
>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A/B (hnRNP A/B) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A/B, also termed APOBEC1-binding protein 1
(ABBP-1), an RNA unwinding protein with a high affinity
for G- followed by U-rich regions. hnRNP A/B has also
been identified as an APOBEC1-binding protein that
interacts with apolipoprotein B (apoB) mRNA transcripts
around the editing site and thus plays an important role
in apoB mRNA editing. hnRNP A/B contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long C-terminal glycine-rich domain that contains a
potential ATP/GTP binding loop. .
Length = 80
Score = 30.7 bits (69), Expect = 0.19
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKV 334
KIF+G +NP + E IR F ++G++
Sbjct: 6 KIFVGGLNPEATEEKIREYFGEFGEI 31
Score = 26.5 bits (58), Expect = 6.6
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTV 71
P K+FVG L+ ++RE F +G +
Sbjct: 3 PVKKIFVGGLNPEATEEKIREYFGEFGEI 31
>gnl|CDD|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative
RNA-binding protein 15B (RBM15B) from vertebrate. This
subgroup corresponds to the RRM3 of RBM15B, also termed
one twenty-two 3 (OTT3), a paralog of RNA binding motif
protein 15 (RBM15), also known as One-twenty two
protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 76
Score = 30.8 bits (69), Expect = 0.19
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR--NYGFVHIDSPD 89
PTT+++VG L NT + F +G++ D V+ ++ ++ +S D
Sbjct: 1 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDYVKGDSFAYIQYESLD 49
>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 = 30.5 bits (69), Expect = 0.19
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 8/61 (13%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI-------VRNYGFVHI-DSPDINKCIKELN 98
++V TRA ++ F YG +V CDI R + FV D +E++
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEMH 61
Query: 99 G 99
G
Sbjct: 62 G 62
>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 = 30.5 bits (69), Expect = 0.20
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFV 83
+++VGNL + R ++ +LF YG + + ++ G V
Sbjct: 1 RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLV 38
>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved in
eukaryotic gene regulation, such as C. elegans GLH-1.
Structure is an 18-residue zinc finger.
Length = 18
Score = 29.0 bits (66), Expect = 0.20
Identities = 6/13 (46%), Positives = 10/13 (76%)
Query: 129 RCGRGGHWSKECP 141
CG+ GH +++CP
Sbjct: 5 NCGKEGHLARDCP 17
>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM1 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver.
It is involved in the regulation of mRNA splicing
probably via its complex formation with RNA-binding
protein with a serine-rich domain (RNPS1), a
pre-mRNA-splicing factor. SART3 has also been
identified as a nuclear Tat-interacting protein that
regulates Tat transactivation activity through direct
interaction and functions as an important cellular
factor for HIV-1 gene expression and viral replication.
In addition, SART3 is required for U6 snRNP targeting
to Cajal bodies. It binds specifically and directly to
the U6 snRNA, interacts transiently with the U6 and
U4/U6 snRNPs, and promotes the reassembly of U4/U6
snRNPs after splicing in vitro. SART3 contains an
N-terminal half-a-tetratricopeptide repeat (HAT)-rich
domain, a nuclearlocalization signal (NLS) domain, and
two C-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 72
Score = 30.3 bits (69), Expect = 0.23
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYG 81
VFV NL + E+R+LF G + + +V+NY
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK 36
>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 = 30.2 bits (69), Expect = 0.24
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYG--FVHIDS 87
+ + NL + ++ L P+G V ++R V +DS
Sbjct: 2 LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQALVEMDS 44
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to the
RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein and
is localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 30.4 bits (69), Expect = 0.24
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKELN 98
V+VG + + E+R F G + E D++ R F+ + + K L+
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60
Query: 99 GMMVDGKPMKV 109
G + G+ +KV
Sbjct: 61 GEDMGGRFLKV 71
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 30.4 bits (69), Expect = 0.27
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECD-------IVRNYGFV-HIDSPDINKCIKE 96
+++ V NL + ++R+LF +GT+ + R +GFV + + K +K
Sbjct: 1 SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60
Query: 97 LNGMMVDGKPMKV 109
N +D + V
Sbjct: 61 FNNSFIDTSKITV 73
>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein A1 (hnRNP A1) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP A1, also termed helix-destabilizing protein, or
single-strand RNA-binding protein, or hnRNP core
protein A1, an abundant eukaryotic nuclear RNA-binding
protein that may modulate splice site selection in
pre-mRNA splicing. hnRNP A1 has been characterized as a
splicing silencer, often acting in opposition to an
activating hnRNP H. It silences exons when bound to
exonic elements in the alternatively spliced
transcripts of c-src, HIV, GRIN1, and beta-tropomyosin.
hnRNP A1 can shuttle between the nucleus and the
cytoplasm. Thus, it may be involved in transport of
cellular RNAs, including the packaging of pre-mRNA into
hnRNP particles and transport of poly A+ mRNA from the
nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has
high affinity with AU-rich elements, whereas the
nuclear hnRNP A1 has high affinity with a
polypyrimidine stretch bordered by AG at the 3' ends of
introns. hnRNP A1 is also involved in the replication
of an RNA virus, such as mouse hepatitis virus (MHV),
through an interaction with the
transcription-regulatory region of viral RNA. Moreover,
hnRNP A1, together with the scaffold protein septin 6,
serves as host proteins to form a complex with NS5b and
viral RNA, and further play important roles in the
replication of Hepatitis C virus (HCV). hnRNP A1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a long glycine-rich region at the
C-terminus. The RRMs of hnRNP A1 play an important role
in silencing the exon and the glycine-rich domain is
responsible for protein-protein interactions. .
Length = 77
Score = 30.3 bits (68), Expect = 0.28
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD 89
K+FVG + ++T +R+ F YG + +I+ R + FV D D
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 53
Score = 28.8 bits (64), Expect = 0.97
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYG 344
KIF+G + T +R FE+YGK+ +++ + G
Sbjct: 2 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG 37
>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and
similar proteins. This subgroup corresponds to the RRM1
of hnRNP A2/B1 which is an RNA trafficking response
element-binding protein that interacts with the hnRNP A2
response element (A2RE). Many mRNAs, such as myelin
basic protein (MBP), myelin-associated oligodendrocytic
basic protein (MOBP), carboxyanhydrase II (CAII),
microtubule-associated protein tau, and amyloid
precursor protein (APP) are trafficked by hnRNP A2/B1.
hnRNP A2/B1 also functions as a splicing factor that
regulates alternative splicing of the tumor suppressors,
such as BIN1, WWOX, the antiapoptotic proteins c-FLIP
and caspase-9B, the insulin receptor (IR), and the RON
proto-oncogene among others. Moreover, the
overexpression of hnRNP A2/B1 has been described in many
cancers. It functions as a nuclear matrix protein
involving in RNA synthesis and the regulation of
cellular migration through alternatively splicing
pre-mRNA. It may play a role in tumor cell
differentiation. hnRNP A2/B1 contains two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), followed
by a long glycine-rich region at the C-terminus. .
Length = 81
Score = 30.5 bits (68), Expect = 0.28
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ E +R +E++GK+ +C V+++ +GFV
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFV 49
Score = 28.5 bits (63), Expect = 1.1
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 20/74 (27%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDINKCIKEL 97
K+F+G LS T +R + +G + +C ++R+ +GFV C+ E+
Sbjct: 4 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF------SCMNEV 57
Query: 98 NGMM------VDGK 105
+ M +DG+
Sbjct: 58 DAAMAARPHTIDGR 71
>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 = 32.7 bits (74), Expect = 0.29
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+I++ +V+P S I+ +FE +G++V+C + K YGF+
Sbjct: 205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFI 251
Score = 31.2 bits (70), Expect = 0.88
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 9/73 (12%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKE- 96
+V+VG++S R +R F P+G + ++ + + FV + P+ + E
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168
Query: 97 LNGMMVDGKPMKV 109
+NG M+ G+ +KV
Sbjct: 169 MNGQMLGGRNIKV 181
>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 = 30.2 bits (69), Expect = 0.32
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RN------YGFVHIDSP-DINKCIK 95
++VGNLS T ++ ELF G + I+ R + FV + D +K
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58
Query: 96 ELNGMMVDGKPMKV 109
LNG +D + ++V
Sbjct: 59 YLNGTKLDDRIIRV 72
>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 = 29.8 bits (68), Expect = 0.33
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 75 DIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMKV 109
DI + FV + K I+ LNG + GK ++V
Sbjct: 36 DIFDKFSFVEVPEEVAEKVIEALNGKKIKGKKVRV 70
>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 = 30.3 bits (69), Expect = 0.36
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 11/73 (15%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELN 98
FV L+ +T ++R F YG + +VR+ Y F+ + D+ K +
Sbjct: 5 FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64
Query: 99 GMMVDGKPMKVVV 111
G +DG+ +V+V
Sbjct: 65 GKKIDGR--RVLV 75
>gnl|CDD|237446 PRK13612, PRK13612, photosystem II reaction center protein Psb28;
Provisional.
Length = 113
Score = 30.3 bits (69), Expect = 0.44
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 9 DEEGRTAIKELNGQIVNEKPLKIEA 33
DEEG +E+ + VN KP +EA
Sbjct: 58 DEEGEIVTREVKAKFVNGKPSALEA 82
>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 = 29.6 bits (67), Expect = 0.44
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHIDSPDI-NKCIKEL 97
+FVGNLS + + E F YG + + + +G+V S + + L
Sbjct: 1 LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60
Query: 98 NGMMVDGKPMKV 109
G + G+P+++
Sbjct: 61 GGTDLLGRPVRL 72
>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 = 29.9 bits (68), Expect = 0.49
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 48 FVGNL-SDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-DINKCIKELN 98
FV L +R+LF G C + R + FV + D + + LN
Sbjct: 6 FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALN 65
Query: 99 GMMVDGKPMKV 109
G + G P++V
Sbjct: 66 GHSLQGSPIRV 76
>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 = 29.4 bits (66), Expect = 0.50
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKEL 97
+FV NL+ + ++ + F + +V R YGFV D + + +L
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 98 NGMMVDGKPMKVVVA 112
+ G+ +++ +A
Sbjct: 62 KNKKLHGRILRLDIA 76
>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 = 29.5 bits (66), Expect = 0.51
Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVV--ECDIVRNYGFVHIDSPDINKCIKELNGM 100
P+ + + NL E+ EL P+G +V +C++ N ++ D+N+ I ++
Sbjct: 1 PSKVLHLRNLPWECTEEELIELCKPFGKIVNTKCNVGANRNQAFVEFADLNQAIAMVSYY 60
Query: 101 MVDGKPMKV 109
+P +V
Sbjct: 61 ASSSEPAQV 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 = 29.2 bits (66), Expect = 0.52
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 49 VGNLSDNTRAPEVRELFVPYGTVVECDI--------VRNYGFVHI-DSPDINKCIKELNG 99
V NL+ T ++R +F YG V + I R + FV D D + ++G
Sbjct: 3 VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62
Query: 100 MMVDGKPMKV 109
+DG+ ++V
Sbjct: 63 KELDGRELRV 72
>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 = 29.4 bits (66), Expect = 0.55
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKEL 97
+F+ +L E+ ++F+P+G V+ + + +GFV D+P I+ +
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66
Query: 98 NGMMVDGKPMKV 109
NG + K +KV
Sbjct: 67 NGFQIGMKRLKV 78
>gnl|CDD|227000 COG4653, COG4653, Predicted phage phi-C31 gp36 major capsid-like
protein [General function prediction only].
Length = 422
Score = 31.7 bits (72), Expect = 0.56
Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 13/75 (17%)
Query: 272 FKQTKTTIVWSPRYQS------FGTVVVIEARNMPG------FSSVGTFKIFIGNVNPGT 319
FK +W P S G V E M ++G FK F V+ T
Sbjct: 322 FKDANGAYIWPPLLASGQPPTLLGKPVT-EDEAMDDVGANNFPIALGDFKQFYLIVDVRT 380
Query: 320 SVELIRPLFEKYGKV 334
V ++ + + G+V
Sbjct: 381 GVRVLPDPYTEKGQV 395
>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 = 29.4 bits (67), Expect = 0.62
Identities = 16/63 (25%), Positives = 22/63 (34%), Gaps = 12/63 (19%)
Query: 60 EVRELFVPYGTVVECDIVR---------NYGFVHI---DSPDINKCIKELNGMMVDGKPM 107
+V+E YG V+ I R G V + D D K L G DG+ +
Sbjct: 27 DVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTV 86
Query: 108 KVV 110
Sbjct: 87 VAS 89
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains). The
RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 29.2 bits (66), Expect = 0.63
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 312 IGNVNPGTSVELIRPLFEKYGKVVECDV 339
+ NV+P + E +R LF GK+ E +
Sbjct: 4 VTNVSPQATEEQMRTLFGFLGKIEELRL 31
>gnl|CDD|241067 cd12623, RRM_PPARGC1A, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator
1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar
proteins. This subgroup corresponds to the RRM of
PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect
modulator 6, a member of a family of transcription
coactivators that plays a central role in the regulation
of cellular energy metabolism. As an inducible
transcription coactivator, PGC-1alpha can interact with
a broad range of transcription factors involved in a
wide variety of biological responses, such as adaptive
thermogenesis, skeletal muscle fiber type switching,
glucose/fatty acid metabolism, and heart development.
PGC-1alpha stimulates mitochondrial biogenesis and
promotes oxidative metabolism. It participates in the
regulation of both carbohydrate and lipid metabolism and
plays a role in disorders such as obesity, diabetes, and
cardiomyopathy. PGC-1alpha is a multi-domain protein
containing an N-terminal activation domain region, a
central region involved in the interaction with at least
a nuclear receptor, and a C-terminal domain region. The
N-terminal domain region consists of three leucine-rich
motifs (L1, NR box 2 and 3), among which the two last
are required for interaction with nuclear receptors,
potential nuclear localization signals (NLS), and a
proline-rich region overlapping a putative repression
domain. The C-terminus of PGC-1alpha is composed of two
arginine/serine-rich regions (SR domains), a putative
dimerization domain, and an RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). PGC-1alpha could interact
favorably with single-stranded RNA. .
Length = 91
Score = 29.5 bits (66), Expect = 0.64
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-----KNYGFV 346
I++G + P T+ +R FE +G++ EC V +YGF+
Sbjct: 5 IYVGKIRPDTTRTELRDRFEVFGEIEECTVNLRDDGDSYGFI 46
Score = 26.8 bits (59), Expect = 6.2
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 5/42 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI-VR----NYGFV 83
++VG + +T E+R+ F +G + EC + +R +YGF+
Sbjct: 5 IYVGKIRPDTTRTELRDRFEVFGEIEECTVNLRDDGDSYGFI 46
>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 = 28.7 bits (65), Expect = 0.83
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVR 78
VFVGNL + E+R+ F G V IVR
Sbjct: 2 VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVR 33
>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 = 29.3 bits (65), Expect = 0.86
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCIKEL 97
+FV NLS ++ + +LF P+G V ++R+ +GFV + + D I L
Sbjct: 6 IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 98 NGMMVDGKPMKV 109
NG + + ++V
Sbjct: 66 NGYRLGDRVLQV 77
>gnl|CDD|239157 cd02756, MopB_Arsenite-Ox, Arsenite oxidase (Arsenite-Ox) oxidizes
arsenite to the less toxic arsenate; it transfers the
electrons obtained from the oxidation of arsenite
towards the soluble periplasmic electron carriers
cytochrome c and/or amicyanin. Arsenite oxidase is a
heterodimeric enzyme containing a large and a small
subunit. The large catalytic subunit harbors the
molybdopterin cofactor and the [3Fe-4S] cluster; and the
small subunit belongs to the structural class of the
Rieske proteins. The small subunit is not included in
this alignment. Members of MopB_Arsenite-Ox CD belong to
the molybdopterin_binding (MopB) superfamily of
proteins.
Length = 676
Score = 31.3 bits (71), Expect = 0.87
Identities = 14/31 (45%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 209 GAVGGPGP-LDRFGYPREAYPRDPYPPPPPP 238
G +G PG R G +E Y R P PPPP
Sbjct: 387 GNIGRPGTGCVRQGGHQEGYVRPPPPPPPWY 417
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 28.9 bits (65), Expect = 0.88
Identities = 13/54 (24%), Positives = 29/54 (53%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIKELNGM 100
V++GN+ D+ ++R F YG + + +R ++ +I+ IK ++G+
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDGV 59
>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall
integrity protein scw1 and similar proteins. This
subfamily corresponds to the RRM of the family
including yeast cell wall integrity protein scw1, yeast
Whi3 protein, yeast Whi4 protein and similar proteins.
The strong cell wall protein 1, scw1, is a nonessential
cytoplasmic RNA-binding protein that regulates
septation and cell-wall structure in fission yeast. It
may function as an inhibitor of septum formation, such
that its loss of function allows weak SIN signaling to
promote septum formation. It's RRM domain shows high
homology to two budding yeast proteins, Whi3 and Whi4.
Whi3 is a dose-dependent modulator of cell size and has
been implicated in cell cycle control in the yeast
Saccharomyces cerevisiae. It functions as a negative
regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3),
a G1 cyclin that promotes transcription of many genes
to trigger the G1/S transition in budding yeast. It
specifically binds the CLN3 mRNA and localizes it into
discrete cytoplasmic loci that may locally restrict
Cln3 synthesis to modulate cell cycle progression.
Moreover, Whi3 plays a key role in cell fate
determination in budding yeast. The RRM domain is
essential for Whi3 function. Whi4 is a partially
redundant homolog of Whi3, also containing one RRM.
Some uncharacterized family members of this subfamily
contain two RRMs; their RRM1 shows high sequence
homology to the RRM of RNA-binding protein with
multiple splicing (RBP-MS)-like proteins.
Length = 79
Score = 28.7 bits (65), Expect = 0.95
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELF 65
P +FV NL NT E+R+LF
Sbjct: 1 PCNTLFVANLGPNTTEEELRQLF 23
>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of
histone-lysine N-methyltransferases. This subfamily
corresponds to the RRM of the Set1-like family of
histone-lysine N-methyltransferases which includes Set1A
and Set1B that are ubiquitously expressed vertebrates
histone methyltransferases exhibiting high homology to
yeast Set1. Set1A and Set1B proteins exhibit a largely
non-overlapping subnuclear distribution in euchromatic
nuclear speckles, strongly suggesting that they bind to
a unique set of target genes and thus make non-redundant
contributions to the epigenetic control of chromatin
structure and gene expression. With the exception of the
catalytic component, the subunit composition of the
Set1A and Set1B histone methyltransferase complexes are
identical. Each complex contains six human homologs of
the yeast Set1/COMPASS complex, including Set1A or
Set1B, Ash2 (homologous to yeast Bre2), CXXC finger
protein 1 (CFP1; homologous to yeast Spp1), Rbbp5
(homologous to yeast Swd1), Wdr5 (homologous to yeast
Swd3), and Wdr82 (homologous to yeast Swd2). The genomic
targeting of these complexes is determined by the
identity of the catalytic subunit present in each
histone methyltransferase complex. Thus, the Set1A and
Set1B complexes may exhibit both overlapping and
non-redundant properties. Both Set1A and Set1B contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), an N- SET domain, and a C-terminal catalytic
SET domain followed by a post-SET domain. In contrast to
Set1B, Set1A additionally contains an HCF-1 binding
motif that interacts with HCF-1 in vivo. .
Length = 93
Score = 29.2 bits (66), Expect = 0.96
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKC 93
P +V NL+DN ++++ YG V E I + V DS +C
Sbjct: 1 PPREVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRC 60
Query: 94 IKELNGMMVDGKPMKVVV 111
+++LN V GK +KV +
Sbjct: 61 VEKLNQTSVMGKIIKVFL 78
>gnl|CDD|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome
proliferator-activated receptor gamma coactivator 1-beta
(PGC-1-beta) and similar proteins. This subfamily
corresponds to the RRM of PGC-1beta, also termed
PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or
PGC-1-related estrogen receptor alpha coactivator, which
is one of the members of PGC-1 transcriptional
coactivators family, including PGC-1alpha and
PGC-1-related coactivator (PRC). PGC-1beta plays a
nonredundant role in controlling mitochondrial oxidative
energy metabolism and affects both, insulin sensitivity
and mitochondrial biogenesis, and functions in a number
of oxidative tissues. It is involved in maintaining
baseline mitochondrial function and cardiac contractile
function following pressure overload hypertrophy by
preserving glucose metabolism and preventing oxidative
stress. PGC-1beta induces hypertriglyceridemia in
response to dietary fats through activating hepatic
lipogenesis and lipoprotein secretion. It can stimulate
apolipoprotein C3 (APOC3) expression, further mediating
hypolipidemic effect of nicotinic acid. PGC-1beta also
drives nuclear respiratory factor 1 (NRF-1) target gene
expression and NRF-1 and estrogen related receptor alpha
(ERRalpha)-dependent mitochondrial biogenesis. The
modulation of the expression of PGC-1beta can trigger
ERRalpha-induced adipogenesis. PGC-1beta is also a
potent regulator inducing angiogenesis in skeletal
muscle. The transcriptional activity of PGC-1beta can be
increased through binding to host cell factor (HCF), a
cellular protein involved in herpes simplex virus (HSV)
infection and cell cycle regulation. PGC-1beta is a
multi-domain protein containing an N-terminal activation
domain, an LXXLL coactivator signature, a tetrapeptide
motif (DHDY) responsible for HCF binding, two
glutamic/aspartic acid-rich acidic domains, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha, PGC-1beta lacks most of the
arginine/serine (SR)-rich domain that is responsible for
the regulation of RNA processing. .
Length = 79
Score = 28.7 bits (64), Expect = 0.98
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-----KNYGFV 346
I+I N++ S ++ FE +G++ EC V+ + YGF+
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGEKYGFI 46
Score = 28.7 bits (64), Expect = 1.1
Identities = 11/42 (26%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----RNYGFV 83
+++ NLS + + E+++ F +G + EC ++ YGF+
Sbjct: 5 IYIRNLSSSMSSTELKKRFEVFGEIEECKVLIKSRGEKYGFI 46
>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 = 28.9 bits (64), Expect = 0.98
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCIKEL 97
+FV NLS + +LF P+G V ++R+ +GFV + + D I L
Sbjct: 4 IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63
Query: 98 NGMMVDGKPMKV 109
NG + + ++V
Sbjct: 64 NGYRLGDRVLQV 75
>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM2 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for the
correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA)
is the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the cytoplasm,
Hu proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. Also included in this subfamily is the
sex-lethal protein (SXL) from Drosophila melanogaster.
SXL governs sexual differentiation and X chromosome
dosage compensation in flies. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 79
Score = 28.7 bits (64), Expect = 0.98
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 11/79 (13%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDS-PDINKCIK 95
++V L E+ +LF YG ++ I+ R GF+ D + + IK
Sbjct: 1 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60
Query: 96 ELNGMMVDG--KPMKVVVA 112
LNG +G +P+ V A
Sbjct: 61 GLNGQKPEGASEPITVKFA 79
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 28.8 bits (64), Expect = 0.99
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKV 334
KIF+G ++P T E IR F +G+V
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEV 26
Score = 27.7 bits (61), Expect = 2.1
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTV 71
K+FVG LS +T ++RE F +G V
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGAFGEV 26
>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 = 28.8 bits (65), Expect = 1.0
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCIKEL 97
++V L E+ LF PYG ++ I+ R GF+ D + IK L
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 98 NGMMVDGKPMKVVV 111
NG + G + V
Sbjct: 63 NGTIPPGATEPITV 76
>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 = 28.2 bits (63), Expect = 1.2
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTV 71
++VGNL +N R + E F YG V
Sbjct: 2 LWVGNLPENVREERISEHFKRYGRV 26
>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 = 28.2 bits (63), Expect = 1.2
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI-DSPDINKCIKEL 97
VFVGN+ +++++F G VV +V + YGF D ++ L
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 98 NGMMVDGKPMKV 109
NG ++G+ ++V
Sbjct: 61 NGYELNGRQLRV 72
>gnl|CDD|241164 cd12720, RRM_SYNJ2, RNA recognition motif in synaptojanin-2 and
similar proteins. This subgroup corresponds to the RRM
of synaptojanin-2, also termed synaptic
inositol-1,4,5-trisphosphate 5-phosphatase 2, an
ubiquitously expressed central regulatory enzyme in the
phosphoinositide-signaling cascade. As a novel Rac1
effector regulating the early step of clathrin-mediated
endocytosis, synaptojanin-2 acts as a
polyphosphoinositide phosphatase directly and
specifically interacting with Rac1 in a GTP-dependent
manner. It mediates the inhibitory effect of Rac1 on
endocytosis and plays an important role in the
Rac1-mediated control of cell growth. Synaptojanin-2
shows high sequence homology to the N-terminal Sac1p
homology domain, the central inositol 5-phosphatase
domain, the putative RNA recognition motif (RRM) of
synaptojanin-1, but differs in the proline-rich region.
.
Length = 78
Score = 28.2 bits (63), Expect = 1.3
Identities = 13/50 (26%), Positives = 21/50 (42%)
Query: 60 EVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMKV 109
E+ + YG VV I V + +L+G+ V GK +K+
Sbjct: 26 ELLQTLEGYGDVVLVRIAGGQMIVTFADSRSALEVLDLDGIKVLGKTVKI 75
>gnl|CDD|177050 CHL00128, psbW, photosystem II protein W; Reviewed.
Length = 113
Score = 28.9 bits (65), Expect = 1.3
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 9 DEEGRTAIKELNGQIVNEKPLKIEA 33
DEEG + +++N + +N KP IEA
Sbjct: 58 DEEGELSTRDVNAKFINGKPQAIEA 82
>gnl|CDD|176458 cd03468, PolY_like, DNA Polymerase Y-family. Y-family DNA
polymerases are a specialized subset of polymerases that
facilitate translesion synthesis (TLS), a process that
allows the bypass of a variety of DNA lesions. Unlike
replicative polymerases, TLS polymerases lack
proofreading activity and have low fidelity and low
processivity. They use damaged DNA as templates and
insert nucleotides opposite the lesions. The active
sites of TLS polymerases are large and flexible to allow
the accomodation of distorted bases. Expression of
Y-family polymerases is often induced by DNA damage and
is believed to be highly regulated. TLS is likely
induced by the monoubiquitination of the replication
clamp PCNA, which provides a scaffold for TLS
polymerases to bind in order to access the lesion.
Because of their high error rates, TLS polymerases are
potential targets for cancer treatment and prevention.
Length = 335
Score = 30.4 bits (69), Expect = 1.3
Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 204 CSRRFGAVGGPGPLDR--FGYPREAYPRDPYPPPPPPSFLRDRM 245
+RRFG L R Y R+ P PPPP F +
Sbjct: 205 LARRFG----LALLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQ 244
>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin
expression factor 2 (MEF-2). This subgroup corresponds
to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a
sequence-specific single-stranded DNA (ssDNA) binding
protein that binds specifically to ssDNA derived from
the proximal (MB1) element of the myelin basic protein
(MBP) promoter and represses transcription of the MBP
gene. MEF-2 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which may be responsible
for its ssDNA binding activity. .
Length = 76
Score = 28.4 bits (63), Expect = 1.4
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI-------VRNYGFVHIDSP-DINKCIKELN 98
+FV NL +++E+F GTV DI R G V + P + + I N
Sbjct: 3 IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62
Query: 99 GMMVDGKPMKV 109
G + +PM V
Sbjct: 63 GQFLFDRPMHV 73
>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 = 28.1 bits (63), Expect = 1.7
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVEC 337
++FI N+ + E + LF KYG + E
Sbjct: 4 RLFIRNLAYTCTEEDLEKLFSKYGPLSEV 32
>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 = 28.3 bits (62), Expect = 1.9
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP 88
T +++ L NT ++ +L PYG +V + + YGFV DSP
Sbjct: 8 TNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 59
>gnl|CDD|190791 pfam03912, Psb28, Psb28 protein. Psb28 is a 13 kDa soluble
protein that is directly assembled in dimeric PSII
supercomplexes. The negatively charged N-terminal
region is essential for this process. This protein was
formerly known as PsbW, but PsbW is now reserved for
pfam07123.
Length = 108
Score = 28.4 bits (64), Expect = 2.0
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 8 NDEEGRTAIKELNGQIVNEKPLKIEA 33
DEEG + + ++ + VN +P +EA
Sbjct: 54 IDEEGEISTRPVSAKFVNGEPKAVEA 79
>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 = 27.6 bits (62), Expect = 2.1
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 3/74 (4%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYG--FVHIDSPDI-NKCIK 95
G + PT V++ L ++ + F YG VV I R G V D + +
Sbjct: 2 GKSMPTNCVWLDGLDESVTEQYLTRHFSRYGPVVHVVIDRQRGQALVFFDKVEAAQAAVN 61
Query: 96 ELNGMMVDGKPMKV 109
E+ G + G+ ++V
Sbjct: 62 EMKGRKLGGRKLQV 75
>gnl|CDD|240739 cd12293, RRM_Rrp7p, RNA recognition motif in yeast ribosomal
RNA-processing protein 7 (Rrp7p) and similar proteins.
This subfamily corresponds to the RRM of Rrp7p which is
encoded by YCL031C gene from Saccharomyces cerevisiae.
It is an essential yeast protein involved in pre-rRNA
processing and ribosome assembly, and is speculated to
be required for correct assembly of rpS27 into the
pre-ribosomal particle. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain. .
Length = 96
Score = 28.1 bits (63), Expect = 2.3
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVE 336
+F+ N+ T+ +R LF G ++E
Sbjct: 3 LFLVNLPVDTTERHLRKLFGSGGGIIE 29
>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 = 27.6 bits (62), Expect = 2.4
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY---GFVHIDSP-DINKCIKELNGMM 101
+V V L + ++++ G V D+ R+ G V S D+ + +++L+G
Sbjct: 2 RVVVSGLPEGASWQDLKDFGRQAGDVTYADVDRDQEGEGVVEFTSQEDMERALRKLDGTE 61
Query: 102 VDGKPMKVV 110
G+ ++V
Sbjct: 62 FRGRRVRVE 70
>gnl|CDD|149426 pfam08357, SEFIR, SEFIR domain. This family comprises IL17
receptors (IL17Rs) and SEF proteins. The latter are
feedback inhibitors of FGF signalling and are also
thought to be receptors. Due to its similarity to the
TIR domain (pfam01582), the SEFIR region is thought to
be involved in homotypic interactions with other
SEFIR/TIR-domain-containing proteins. Thus, SEFs and
IL17Rs may be involved in TOLL/IL1R-like signalling
pathways.
Length = 150
Score = 28.9 bits (65), Expect = 2.4
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 9/64 (14%)
Query: 165 ALVLWED-------QDLWTGLVKGTSDLVVVIASPIHQAHCDSFLCCSRRFGAVGGPGPL 217
AL LWE W +D V+++ S +A CD +R G VG
Sbjct: 34 ALDLWELNEISAIGPVAWLERQIQEADKVIIVCSKGAKAICDK--KADKRKGGVGTESQH 91
Query: 218 DRFG 221
D F
Sbjct: 92 DLFI 95
>gnl|CDD|241194 cd12750, RRM5_RBM12B, RNA recognition motif 5 in RNA-binding
protein 12B (RBM12B) and similar proteins. This
subgroup corresponds to the RRM5 of RBM12B which
contains five distinct RNA binding motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Its biological role
remains unclear. .
Length = 77
Score = 27.6 bits (61), Expect = 2.5
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKI 31
MEN E AI ELN + + + +K+
Sbjct: 48 AMENYYEAMAAINELNDRPIGPRKVKL 74
>gnl|CDD|202795 pfam03880, DbpA, DbpA RNA binding domain. This RNA binding domain
is found at the C-terminus of a number of DEAD helicase
proteins. It is sufficient to confer specificity for
hairpin 92 of 23S rRNA, which is part of the ribosomal
A-site. However, several members of this family lack
specificity for 23S rRNA. These can proteins can
generally be distinguished by a basic region that
extends beyond this domain [Karl Kossen, unpublished
data].
Length = 74
Score = 27.4 bits (62), Expect = 2.6
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 75 DIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMKVVVA 112
DI N+ FV + +K +K L + G+ +K+ A
Sbjct: 37 DIFDNFSFVEVPEDMADKVLKALKKGKIKGRKLKIEPA 74
>gnl|CDD|177673 PLN00039, PLN00039, photosystem II reaction center Psb28 protein;
Provisional.
Length = 111
Score = 28.2 bits (63), Expect = 2.6
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 8 NDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
DEEG +++ + VN KP IEA + P
Sbjct: 55 IDEEGVLQTVDVSAKFVNGKPAGIEAKYVMRSPR 88
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in
vertebrate. It has been reported to be involved in
pre-splicesome assembly and to interact with the
Ca2+-signaling protein ALG-2. It also plays an
important role in embryogenesis. RBM22 contains a
conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), a zinc finger of the unusual type
C-x8-C-x5-C-x3-H, and a C-terminus that is unusually
rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 27.2 bits (61), Expect = 2.7
Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFV 83
T ++VG L + ++R+ F +G + +V + FV
Sbjct: 2 TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQCAFV 42
>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 = 27.3 bits (60), Expect = 2.8
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
++ G V G + +L+R F +G+++E V K Y FV
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDKGYSFV 41
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional
and post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus.
.
Length = 75
Score = 27.3 bits (60), Expect = 2.9
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTV 71
KVFVG LS +T +++E F +G +
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEI 26
Score = 27.3 bits (60), Expect = 3.5
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKV 334
K+F+G ++P T+ E I+ F +G++
Sbjct: 1 KVFVGGLSPDTTEEQIKEYFGAFGEI 26
>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 = 27.4 bits (60), Expect = 3.1
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCIKEL 97
+FV NL+ + + ++F P+G V ++R+ +GFV + + D I L
Sbjct: 6 IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65
Query: 98 NGMMVDGKPMKV 109
NG + + ++V
Sbjct: 66 NGYRLGDRVLQV 77
>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces
cerevisiae nucleolar protein 6 (Nop6) and similar
proteins. This subfamily corresponds to the RRM of
Nop6, also known as Ydl213c, a component of 90S
pre-ribosomal particles in yeast S. cerevisiae. It is
enriched in the nucleolus and is required for 40S
ribosomal subunit biogenesis. Nop6 is a non-essential
putative RNA-binding protein with two N-terminal
putative nuclear localisation sequences (NLS-1 and
NLS-2) and an RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). It binds to the pre-rRNA early during
transcription and plays an essential role in pre-rRNA
processing. .
Length = 74
Score = 26.9 bits (60), Expect = 3.3
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD 89
+FVGNL +T A ++ F G ++ + FV D+ +
Sbjct: 3 LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAE 53
>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 = 27.2 bits (60), Expect = 3.5
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
+F+GN++P + ELI LF + G V++ + K+
Sbjct: 4 LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD 36
>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM3 of RBM39, also
termed hepatocellular carcinoma protein 1, or
RNA-binding region-containing protein 2, or splicing
factor HCC1, ia nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 27.1 bits (61), Expect = 3.6
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 60 EVRELFVPYGTVVECDIVRNY--GFVHI---DSPDINKCIKELNGMMVDGKPMKVVVAGF 114
+V E +G V + +N G V++ KCI+ LNG DG+ + A +
Sbjct: 27 DVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQ---ITAEY 83
Query: 115 IS 116
+
Sbjct: 84 VD 85
>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 = 27.6 bits (62), Expect = 4.0
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 7 ENDEEGRTAIKELNGQIVNEKPLKIE 32
E +E+ A++ LNG+ +PL E
Sbjct: 74 ETEEDAEAALQALNGRYYAGRPLYPE 99
>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 = 27.2 bits (60), Expect = 4.1
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDI-VR----NYGFV 83
V++G + E+++ F +G + EC I R NYGFV
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDNYGFV 46
Score = 26.4 bits (58), Expect = 8.6
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV-----KNYGFV 346
++IG + + ++ F +G++ EC + NYGFV
Sbjct: 5 VYIGKIPSRMTRSELKDRFSVFGEIEECTIHFRSEGDNYGFV 46
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein
(UMSBP); Provisional.
Length = 148
Score = 27.8 bits (62), Expect = 4.5
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 129 RCGRGGHWSKECPRA 143
+CG GH S+ECP A
Sbjct: 32 KCGEPGHLSRECPSA 46
Score = 27.8 bits (62), Expect = 5.6
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 129 RCGRGGHWSKECPRAGNFRSSG---CY 152
RCG GH S+ECP + ++ CY
Sbjct: 5 RCGGVGHQSRECPNSAPAGAAKARPCY 31
>gnl|CDD|213763 TIGR03047, PS_II_psb28, photosystem II reaction center protein
Psb28. Members of this protein family are the Psb28
protein of photosystem II. Two different protein
families, apparently without homology between them,
have been designated PsbW. Cyanobacterial proteins
previously designated PsbW are members of the family
described here. However, while members of the plant
PsbW family are not found (so far) in Cyanobacteria,
members of the present family do occur in plants. We
therefore support the alternative designation that has
emerged for this protein family, Psp28, rather than
PsbW [Energy metabolism, Photosynthesis].
Length = 109
Score = 27.2 bits (61), Expect = 4.7
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 9 DEEGRTAIKELNGQIVNEKPLKIEA 33
DEEG + +E+ + VN KP +EA
Sbjct: 55 DEEGEISTREVKAKFVNGKPKALEA 79
>gnl|CDD|129050 smart00814, Alpha_TIF, Alpha trans-inducing protein (Alpha-TIF).
Alpha-TIF (VP16) from Herpes Simplex virus is an
essential tegument protein involved in the
transcriptional activation of viral immediate early (IE)
promoters (alpha genes) during the lytic phase of viral
infection. VP16 associates with cellular transcription
factors to enhance transcription rates, including the
general transcription factor TFIIB and the
transcriptional coactivator PC4. The N-terminal residues
of VP16 confer specificity for the IE genes, while the
C-terminal residues are responsible for transcriptional
activation. Within the C-terminal region are two
activation regions that can independently and
cooperatively activate transcription. VP16 forms a
transcriptional regulatory complex with two cellular
proteins, the POU-domain transcription factor Oct-1 and
the cell-proliferation factor HCF-1. VP16 is an
alpha/beta protein with an unusual fold. Other
transcription factors may have a similar topology.
Length = 356
Score = 28.5 bits (64), Expect = 4.8
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 208 FGAVGGPGPLDRFGYPREAYPRDPYPPPPPPSFLRDRMM 246
G G + GYP A P P P P+ L R++
Sbjct: 2 LGNPGAAALVYAPGYPSSAQLALPPPRPASPAALYQRLL 40
>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 = 26.1 bits (58), Expect = 6.3
Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 62 RELFVPYGTVVECDIV--RNYGFV-HIDSPDINKCIKELNGMMVDGKPMKV 109
++F +G +++ +V +NYG+ + D + I L+G V+G +KV
Sbjct: 17 EDVFCRFGGLIDVYLVPGKNYGYAKYADRESAERAITTLHGKEVNGVKLKV 67
>gnl|CDD|99960 cd03784, GT1_Gtf_like, This family includes the Gtfs, a group of
homologous glycosyltransferases involved in the final
stages of the biosynthesis of antibiotics vancomycin and
related chloroeremomycin. Gtfs transfer sugar moieties
from an activated NDP-sugar donor to the oxidatively
cross-linked heptapeptide core of vancomycin group
antibiotics. The core structure is important for the
bioactivity of the antibiotics.
Length = 401
Score = 28.5 bits (64), Expect = 6.4
Identities = 15/46 (32%), Positives = 18/46 (39%), Gaps = 2/46 (4%)
Query: 206 RRFGAVGGPGPLDRFGYPREAYPRDPYPPPPPPSFLRDRMMGGYPM 251
RR G P L E Y P PPPP + R ++ GY
Sbjct: 175 RRLGL--PPLSLLDGSDVPELYGFSPAVLPPPPDWPRFDLVTGYGF 218
>gnl|CDD|234094 TIGR03026, NDP-sugDHase, nucleotide sugar dehydrogenase. Enzymes
in this family catalyze the NAD-dependent
alcohol-to-acid oxidation of nucleotide-linked sugars.
Examples include UDP-glucose 6-dehydrogenase (1.1.1.22)
, GDP-mannose 6-dehydrogenase (1.1.1.132) ,
UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136),
UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase and
UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase.
These enzymes are most often involved in the
biosynthesis of polysaccharides and are often found in
operons devoted to that purpose. All of these enzymes
contain three Pfam domains, pfam03721, pfam00984, and
pfam03720 for the N-terminal, central, and C-terminal
regions respectively.
Length = 409
Score = 28.3 bits (64), Expect = 7.1
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 315 VNPGTSVELIRPLFEKYGKVVECDV 339
V PGT+ E+++P+ E+ G + D
Sbjct: 122 VPPGTTEEVVKPILERSGLKLGEDF 146
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 28.4 bits (63), Expect = 7.3
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 228 PRDPYPPPPPPSF 240
P +P PPPPPP F
Sbjct: 6 PGNPPPPPPPPGF 18
>gnl|CDD|223006 PHA03179, PHA03179, UL43 envelope protein; Provisional.
Length = 387
Score = 27.9 bits (62), Expect = 7.4
Identities = 12/34 (35%), Positives = 13/34 (38%), Gaps = 2/34 (5%)
Query: 206 RRFGAVGGPGPLDRFGYPREAYPRDPYPPPPPPS 239
RR +G L R P E R P P PP
Sbjct: 198 RRGCVIGAGESLSR--RPPEDAERPTAPDPEPPP 229
>gnl|CDD|219897 pfam08549, SWI-SNF_Ssr4, Fungal domain of unknown function
(DUF1750). This is a fungal domain of unknown function.
Length = 669
Score = 28.1 bits (62), Expect = 8.6
Identities = 7/26 (26%), Positives = 9/26 (34%)
Query: 214 PGPLDRFGYPREAYPRDPYPPPPPPS 239
PGP R+ + P PP
Sbjct: 217 PGPYPNAMVGRQPFYPQPGAVAGPPK 242
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.140 0.445
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,163,585
Number of extensions: 1766083
Number of successful extensions: 2573
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2496
Number of HSP's successfully gapped: 426
Length of query: 346
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 248
Effective length of database: 6,590,910
Effective search space: 1634545680
Effective search space used: 1634545680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.6 bits)