RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4057
(246 letters)
>gnl|CDD|240923 cd12479, RRM2_SNF, RNA recognition motif 2 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM2 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila 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).
SNF contains two RNA recognition motifs (RRMs); it can
self-associate through RRM1, and each RRM can recognize
poly(U) RNA binding independently. .
Length = 80
Score = 142 bits (358), Expect = 9e-44
Identities = 74/80 (92%), Positives = 77/80 (96%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
EQPPNQILFLTNLPEET+EMMLSMLFNQFPGFKEVRLVP RHDIAFVEFENE+QSAAAK
Sbjct: 1 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEVQSAAAKE 60
Query: 227 ALHGFKITPTHAMKISFAKK 246
AL GFKITPTHAMKI+FAKK
Sbjct: 61 ALQGFKITPTHAMKITFAKK 80
>gnl|CDD|240925 cd12481, RRM2_U2B, RNA recognition motif 2 found in vertebrate U2
small nuclear ribonucleoprotein B" (U2B"). This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B"), a unique protein that comprises the U2 snRNP.
It was initially identified to bind to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA and its nuclear
transport is independent of U2 snRNA binding. U2B"
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). It also contains a nuclear localization signal
(NLS) in the central domain. However, nuclear import of
U2B'' does not depend on this NLS. The N-terminal RRM is
sufficient to direct U2B" to the nucleus. .
Length = 80
Score = 135 bits (341), Expect = 4e-41
Identities = 65/80 (81%), Positives = 72/80 (90%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
+ PPN ILFL NLPEET+EMMLSMLFNQFPGFKEVRLVP RHDIAFVEFENE Q+ AA+
Sbjct: 1 DNPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENEAQAGAARD 60
Query: 227 ALHGFKITPTHAMKISFAKK 246
AL GFKITP+HAMKI++AKK
Sbjct: 61 ALQGFKITPSHAMKITYAKK 80
>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 = 133 bits (336), Expect = 2e-40
Identities = 59/79 (74%), Positives = 73/79 (92%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LK+SLYA+FSQFG ++DIVALKT+KMRGQAFVIFKE++SATNALR +QGFPFY K
Sbjct: 13 IKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNALRQLQGFPFYGK 72
Query: 79 PMRIQYSKTDSDVISKIKG 97
PMRIQY+KTDSD++SK++G
Sbjct: 73 PMRIQYAKTDSDIVSKMRG 91
>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 = 132 bits (334), Expect = 6e-40
Identities = 51/68 (75%), Positives = 62/68 (91%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LK+SLYA+FSQFG ++DIVA KTLKMRGQAFV+FK++ SATNALR++QGFPFYDK
Sbjct: 11 IKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDK 70
Query: 79 PMRIQYSK 86
PMRIQY+K
Sbjct: 71 PMRIQYAK 78
Score = 27.5 bits (62), Expect = 1.9
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 211 AFVEFENEMQSAAAKLALHGFKITPTHAMKISFAK 245
AFV F++ + A AL GF M+I +AK
Sbjct: 45 AFVVFKDVESATNALRALQGFPFYDK-PMRIQYAK 78
>gnl|CDD|240924 cd12480, RRM2_U1A, RNA recognition motif 2 found in vertebrate U1
small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or
U1A). This subgroup corresponds to the RRM2 of U1A
(also termed U1 snRNP A or U1-A), an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. U1A may be
involved in RNA 3'-end processing, specifically
cleavage, splicing and polyadenylation, through
interacting with a large number of non-snRNP proteins,
including polypyrimidine tract binding protein (PTB),
polypyrimidine-tract binding protein-associated factor
(PSF), and non-POU-domain-containing, octamer-binding
(NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5).
U1A also binds to a flavivirus NS5 protein and plays an
important role in virus replication. It contains two RNA
recognition motifs (RRMs); the N-terminal RRM (RRM1)
binds tightly and specifically to the U1 snRNA SLII and
its own 3'-UTR, while in contrast, the C-terminal RRM
(RRM2) does not appear to associate with any RNA and it
may be free for binding other proteins. U1A also
contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 80
Score = 128 bits (322), Expect = 2e-38
Identities = 65/80 (81%), Positives = 73/80 (91%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKL 226
E PPN ILFLTNLPEET+E+MLSMLFNQFPGFKEVRLVP RHDIAFVEF+NE+Q+ AA+
Sbjct: 1 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARE 60
Query: 227 ALHGFKITPTHAMKISFAKK 246
AL GFKIT ++AMKISFAKK
Sbjct: 61 ALQGFKITQSNAMKISFAKK 80
>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM2
of U1A/U2B"/SNF protein family, containing Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs) connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. U2B" does
not require an auxiliary protein for binding to RNA and
its nuclear transport is independent on U2 snRNA
binding. .
Length = 72
Score = 127 bits (321), Expect = 5e-38
Identities = 55/73 (75%), Positives = 59/73 (80%), Gaps = 1/73 (1%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
PN+ILFL NLPEET++ ML MLFNQFPGFKEVRLVP R IAFVEFE E Q+ A AL
Sbjct: 1 PNKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQ 59
Query: 230 GFKITPTHAMKIS 242
GFKITP HAMKIS
Sbjct: 60 GFKITPGHAMKIS 72
Score = 31.0 bits (71), Expect = 0.076
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 3/49 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
K+ L +F+QF ++ + + RG AFV F+ AT AL+++QGF
Sbjct: 16 KEMLEMLFNQFPGFKEV---RLVPRRGIAFVEFETEEQATVALQALQGF 61
>gnl|CDD|240920 cd12476, RRM1_SNF, RNA recognition motif 1 found in Drosophila
melanogaster sex determination protein SNF and similar
proteins. This subgroup corresponds to the RRM1 of SNF
(Sans fille), also termed U1 small nuclear
ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an
RNA-binding protein found in the U1 and U2 snRNPs of
Drosophila. It is essential in Drosophila 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). SNF contains two RNA recognition motifs (RRMs);
it can self-associate through RRM1, and each RRM can
recognize poly(U) RNA binding independently. .
Length = 78
Score = 126 bits (318), Expect = 1e-37
Identities = 58/68 (85%), Positives = 64/68 (94%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
+ +LKKSLYAIFSQFGQI+DIVALKTLKMRGQAFV+FK+I+SATNALRSMQGFPFYDK
Sbjct: 11 VKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVVFKDISSATNALRSMQGFPFYDK 70
Query: 79 PMRIQYSK 86
PMRI YSK
Sbjct: 71 PMRIAYSK 78
>gnl|CDD|240921 cd12477, RRM1_U1A, RNA recognition motif 1 found in vertebrate U1
small nuclear ribonucleoprotein A (U1A). This subgroup
corresponds to the RRM1 of U1A (also termed U1 snRNP A
or U1-A), an RNA-binding protein associated with the U1
snRNP, a small RNA-protein complex involved in pre-mRNA
splicing. U1A binds with high affinity and specificity
to stem-loop II (SLII) of U1 snRNA. It is predominantly
a nuclear protein and it also shuttles between the
nucleus and the cytoplasm independently of interactions
with U1 snRNA. U1A may be involved in RNA 3'-end
processing, specifically cleavage, splicing and
polyadenylation, through interacting with a large
number of non-snRNP proteins, including polypyrimidine
tract binding protein (PTB), polypyrimidine-tract
binding protein-associated factor (PSF), and
non-POU-domain-containing, octamer-binding (NONO), DEAD
(Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also
binds to a flavivirus NS5 protein and plays an
important role in virus replication. U1A contains two
RNA recognition motifs (RRMs); the N-terminal RRM
(RRM1) binds tightly and specifically to the U1 snRNA
SLII and its own 3'-UTR, while in contrast, the
C-terminal RRM (RRM2) does not appear to associate with
any RNA and may be free to bind other proteins. U1A
also contains a proline-rich region, and a nuclear
localization signal (NLS) in the central domain that is
responsible for its nuclear import. .
Length = 89
Score = 125 bits (315), Expect = 3e-37
Identities = 58/75 (77%), Positives = 70/75 (93%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
I +LKKSL+AIFS+FGQI+DI+ ++LKMRGQAFVIFKE++SATNALRSMQGFPFYDK
Sbjct: 15 IKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK 74
Query: 79 PMRIQYSKTDSDVIS 93
PMRIQY+KTDSD+I+
Sbjct: 75 PMRIQYAKTDSDIIA 89
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 64.5 bits (158), Expect = 5e-14
Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
LF+ NLP +T+E L LF++F + +R+V + AFVEFE+E + A AL+
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 230 GFKI 233
G ++
Sbjct: 61 GKEL 64
Score = 53.0 bits (128), Expect = 1e-09
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI--VALKTLKMRGQAFVIFKEIASATNALRSMQ 71
++V ++ ++ L +FS+FG I I V +T + +G AFV F++ A AL ++
Sbjct: 1 LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60
Query: 72 GFPFYDKPMR 81
G + +R
Sbjct: 61 GKELGGRELR 70
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 62.6 bits (153), Expect = 3e-13
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
++V ++ ++ L +FS+FG++ + ++ T K +G AFV F+ A AL ++
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61
Query: 71 QGFPFYDKPMRI 82
G +P+++
Sbjct: 62 NGKELDGRPLKV 73
Score = 57.6 bits (140), Expect = 3e-11
Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 5/65 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ NLP +T+E L LF++F + VRLV ++ AFVEFE+E + A AL
Sbjct: 2 LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61
Query: 229 HGFKI 233
+G ++
Sbjct: 62 NGKEL 66
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes
including mRNA and rRNA processing, RNA export, and RNA
stability. This domain is 90 amino acids in length and
consists of a four-stranded beta-sheet packed against
two alpha-helices. RRM usually interacts with ssRNA,
but is also known to interact with ssDNA as well as
proteins. RRM binds a variable number of nucleotides,
ranging from two to eight. The active site includes
three aromatic side-chains located within the conserved
RNP1 and RNP2 motifs of the domain. The RRM domain is
found in a variety heterogeneous nuclear
ribonucleoproteins (hnRNPs), proteins implicated in
regulation of alternative splicing, and protein
components of small nuclear ribonucleoproteins
(snRNPs).
Length = 72
Score = 59.6 bits (145), Expect = 5e-12
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNALRSMQ 71
++V ++ ++ L +FS+FG+I + ++ K +G AFV F+ A AL ++
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 72 GFPFYDKPMRIQ 83
G + +++
Sbjct: 61 GKELDGRKLKVS 72
Score = 53.5 bits (129), Expect = 7e-10
Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 4/64 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
LF+ NLP +T+E L LF++F + VR+V ++ AFVEFE+ + A AL+
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60
Query: 230 GFKI 233
G ++
Sbjct: 61 GKEL 64
>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding
protein 40 (RBM40) and similar proteins. This
subfamily corresponds to the RRM2 of RBM40 and the RRM
of RBM41. RBM40, also known as RNA-binding
region-containing protein 3 (RNPC3) or U11/U12 small
nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K
protein). It serves as a bridging factor between the
U11 and U12 snRNPs. It contains two RNA recognition
motifs (RRMs), also known as RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), connected by a
linker that includes a proline-rich region. It binds to
the U11-associated 59K protein via its RRM1 and employs
the RRM2 to bind hairpin III of the U12 small nuclear
RNA (snRNA). The proline-rich region might be involved
in protein-protein interactions. RBM41 contains only
one RRM. Its biological function remains unclear. .
Length = 82
Score = 55.6 bits (135), Expect = 1e-10
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQF-------GQIMDIVALKTLKMRGQAFVIFKEIASA 63
+ +YV ++S ++ L IF +F + DI + +M+GQAFV F A
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIA 60
Query: 64 TNALRSMQGFPFYDKPMRIQYS 85
T AL + G+ KPM IQ+
Sbjct: 61 TKALNLVNGYVLKGKPMVIQFG 82
Score = 31.0 bits (71), Expect = 0.10
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 13/73 (17%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-----------AFVEFENEM 219
++ L++ NL + +E L +F +F N DI AFV F +E
Sbjct: 1 SKRLYVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEE 58
Query: 220 QSAAAKLALHGFK 232
+ A ++G+
Sbjct: 59 IATKALNLVNGYV 71
>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 = 54.5 bits (132), Expect = 4e-10
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV-PNRHDIAFVEFENEMQSAAAKLALHGFK 232
LF+ NL T+E L LF++ PGF+ +++ + FVEFE+ + A +L G
Sbjct: 5 LFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGPVCFVEFEDVSFATQALNSLQGAV 64
Query: 233 ITPTH--AMKISFAK 245
++ + ++I +AK
Sbjct: 65 LSSSDRGGIRIEYAK 79
Score = 46.0 bits (110), Expect = 5e-07
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 14/85 (16%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ-----AFVIFKEIASAT 64
N ++V ++ ++ L +FS+ + LKM + FV F++++ AT
Sbjct: 1 PCNTLFVANLGPNTTEEELRQLFSRQ------PGFRRLKMHNKGGGPVCFVEFEDVSFAT 54
Query: 65 NALRSMQGFPFYDK---PMRIQYSK 86
AL S+QG +RI+Y+K
Sbjct: 55 QALNSLQGAVLSSSDRGGIRIEYAK 79
>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 = 52.9 bits (128), Expect = 7e-10
Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
LY +FS FG + I LK K G AFV F +A A++ + G F +P+R+ YS
Sbjct: 1 LYKLFSPFGNVEKIKLLK--KKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
Score = 32.5 bits (75), Expect = 0.019
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 188 LSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKITPTHAMKISFA 244
L LF+ F ++++L+ + AFVEF E + A L+G +++ ++
Sbjct: 1 LYKLFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGG-RPLRVDYS 56
>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding
protein with multiple splicing (RBP-MS)-like proteins.
This subfamily corresponds to the RRM of RNA-binding
proteins with multiple splicing (RBP-MS)-like proteins,
including protein products of RBPMS genes (RBP-MS and
its paralogue RBP-MS2), the Drosophila couch potato
(cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS
may be involved in regulation of mRNA translation and
localization during Xenopus laevis development. It has
also been shown to physically interact with Smad2, Smad3
and Smad4, and stimulates Smad-mediated transactivation.
Cpo may play an important role in regulating normal
function of the nervous system, whereas mutations in
Mec-8 affect mechanosensory and chemosensory neuronal
function. All members contain a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). Some
uncharacterized family members contain two RRMs; this
subfamily includes their RRM1. Their RRM2 shows high
sequence homology to the RRM of yeast proteins scw1,
Whi3, and Whi4.
Length = 79
Score = 52.3 bits (126), Expect = 3e-09
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQSAAAKLA 227
LF++ LP + E L+ LF FPG++ RLV + FV+F + +AAA A
Sbjct: 3 LFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAMDA 62
Query: 228 LHGFKITP 235
L G++ P
Sbjct: 63 LQGYRFDP 70
Score = 26.5 bits (59), Expect = 3.6
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 52 QAFVIFKEIASATNALRSMQGFPF 75
FV F A A+ ++QG+ F
Sbjct: 45 VGFVDFSSAQCAAAAMDALQGYRF 68
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 55.0 bits (131), Expect = 6e-09
Identities = 26/126 (20%), Positives = 57/126 (45%), Gaps = 7/126 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
++V ++ ++ L +F +FG + + + +T K RG AFV F+ SA A+ +
Sbjct: 118 LFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEEL 177
Query: 71 QGFPFYDKPMRIQYSKTD----SDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKA 126
G +P+R+Q ++ S++ + + +F ++ + + D K
Sbjct: 178 NGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKT 237
Query: 127 AKEQAR 132
A+E+
Sbjct: 238 AEEELA 243
Score = 48.0 bits (113), Expect = 1e-06
Identities = 32/161 (19%), Positives = 63/161 (39%), Gaps = 10/161 (6%)
Query: 78 KPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQ 137
+ ++ + + + +K+ + +P +K+ + +
Sbjct: 27 TELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDG 86
Query: 138 QQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPG 197
++ ++ S +P + + N LF+ NLP + +E L LF +F
Sbjct: 87 ERGYTKEFEEELFRSSESPKSRQ-----KSKEENNTLFVGNLPYDVTEEDLRELFKKFGP 141
Query: 198 FKEVRLVPNRH-----DIAFVEFENEMQSAAAKLALHGFKI 233
K VRLV +R AFVEFE+E + A L+G ++
Sbjct: 142 VKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKEL 182
>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 = 50.9 bits (122), Expect = 9e-09
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VY+ +I + ++ L FSQ+G+I + L+ + AFV F I++A A+ ++
Sbjct: 6 VYIGNIDDSLTEEKLRNDFSQYGEIESV---NYLREKNCAFVNFTNISNAIKAIDGVKSH 62
Query: 74 PFYDKPMRIQYSK 86
P + K +I Y K
Sbjct: 63 PLFKK-FKISYGK 74
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 50.2 bits (121), Expect = 1e-08
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 11/86 (12%)
Query: 7 HICVTNFVY-VTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATN 65
+ ++N +Y VT D+ L+ +FS +G + I+ + QA V F + SA N
Sbjct: 3 LVTISNLLYPVTV----DV---LHQVFSPYGAVEKILIFEKNT-GVQALVQFDSVESAEN 54
Query: 66 ALRSMQGFPFYDK--PMRIQYSKTDS 89
A +++ G YD + IQ+S+
Sbjct: 55 AKKALNGRNIYDGCCTLDIQFSRLKE 80
Score = 29.8 bits (68), Expect = 0.29
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 211 AFVEFENEMQSAAAKLALHGFKITPTHA-MKISFAK 245
A V+F++ + AK AL+G I + I F++
Sbjct: 42 ALVQFDSVESAENAKKALNGRNIYDGCCTLDIQFSR 77
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM4 of
polypyrimidine tract-binding protein 1 (PTB or hnRNP I),
polypyrimidine tract-binding protein 2 (PTBP2 or nPTB),
regulator of differentiation 1 (Rod1), and similar
proteins found in Metazoa. PTB is an important negative
regulator of alternative splicing in mammalian cells and
also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 also contains four RRMs. ROD1 coding
protein Rod1 is a mammalian PTB homolog of a regulator
of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset of
differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It may play a role
controlling differentiation in mammals. All members in
this family contain four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 49.2 bits (118), Expect = 3e-08
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGF-KEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
L L+N+P +E L LF Q G K + P +A ++ + ++ A +ALH ++
Sbjct: 2 LHLSNIPPSVTEEDLKELFTQTGGTVKAFKFFPKDRKMALIQMGSVEEAIEALIALHNYQ 61
Query: 233 ITPTHAMKISFAK 245
++ + +++SF+K
Sbjct: 62 LSESSHLRVSFSK 74
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 48.9 bits (117), Expect = 4e-08
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH----DIAFVEFENEMQSAAAKLALH 229
LF++ LP ++ L LF + K VRLV NR +A+VE+ENE ++ A L +
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64
Query: 230 GFKI 233
G +I
Sbjct: 65 GTEI 68
Score = 33.9 bits (78), Expect = 0.012
Identities = 17/74 (22%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
++V+ + + K+ L +F + G + +V ++ K +G A+V ++ +SA+ A+ M
Sbjct: 5 LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64
Query: 72 GFPFYDKPMRIQYS 85
G +K + + S
Sbjct: 65 GTEIKEKTISVAIS 78
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 15 YVTHISSTDLKKSLYAIFSQFGQIMDIVALKT-LKMRGQAFVIFKEIASATNALRSMQGF 73
+V +I+S + L A+F QFG DI L T K RG V + +I +A A R++QG
Sbjct: 5 FVRNINSNVEDEELRALFEQFG---DIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGT 61
Query: 74 PFYDKPMRIQYS 85
+ + I +S
Sbjct: 62 ELGGRKLDIHFS 73
>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 = 46.5 bits (111), Expect = 3e-07
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
V+V +I ++ L IFS+ G ++ + T K +G F F++I +A +A+R++
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60
Query: 71 QGFPFYDKPMRIQYS 85
G+ F + +R+ ++
Sbjct: 61 NGYEFNGRALRVDFA 75
Score = 31.8 bits (73), Expect = 0.043
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 175 FLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALH 229
F+ N+P + +E L +F++ RLV +R F EFE+ +A+A L+
Sbjct: 2 FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61
Query: 230 GFKITPTHAMKISFA 244
G++ A+++ FA
Sbjct: 62 GYEFNG-RALRVDFA 75
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds
to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share
high sequence similarity and are expressed in a wide
variety of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to
poly(C) homopolymers. They are composed of three
N-terminal highly homologous RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be
responsible for interacting with other proteins. In
addition, TIA-1 and TIAR share a potential serine
protease-cleavage site (Phe-Val-Arg) localized at the
junction between their RNA binding domains and their
C-terminal auxiliary domains. This subfamily also
includes a yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1, termed ARS consensus-binding
protein ACBP-60, or poly uridylate-binding protein, or
poly(U)-binding protein, which has been identified as
both a heterogeneous nuclear RNA-binding protein
(hnRNP) and a cytoplasmic mRNA-binding protein (mRNP).
It may be stably bound to a translationally inactive
subpopulation of mRNAs within the cytoplasm. PUB1 is
distributed in both, the nucleus and the cytoplasm, and
binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it
is one of the major cellular proteins cross-linked by
UV light to polyadenylated RNAs in vivo, PUB1 is
nonessential for cell growth in yeast. PUB1 also binds
to T-rich single stranded DNA (ssDNA); however, there
is no strong evidence implicating PUB1 in the mechanism
of DNA replication. PUB1 contains three RRMs, and a GAR
motif (glycine and arginine rich stretch) that is
located between RRM2 and RRM3. .
Length = 73
Score = 46.5 bits (111), Expect = 3e-07
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VYV ++ ++ L FS FG I ++ + K +G AFV F +A A+ ++ G
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEV---RVFKDKGYAFVRFDTHEAAATAIVAVNGT 59
Query: 74 PFYDKPMRIQYSK 86
+ ++ + K
Sbjct: 60 SINGQTVKCSWGK 72
Score = 38.0 bits (89), Expect = 3e-04
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
+++ NLP +E L F+ F +EVR+ ++ AFV F+ +A A +A++G I
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKG-YAFVRFDTHEAAATAIVAVNGTSI 61
Query: 234 TPTHAMKISFAKK 246
+K S+ K+
Sbjct: 62 N-GQTVKCSWGKE 73
>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA
branch site protein p14 (SF3B14) and similar proteins.
This subfamily corresponds to the RRM of SF3B14 (also
termed p14), a 14 kDa protein subunit of SF3B which is
a multiprotein complex that is an integral part of the
U2 small nuclear ribonucleoprotein (snRNP) and the
U11/U12 di-snRNP. SF3B is essential for the accurate
excision of introns from pre-messenger RNA and has been
involved in the recognition of the pre-mRNA's branch
site within the major and minor spliceosomes. SF3B14
associates directly with another SF3B subunit called
SF3B155. It is also present in both U2- and
U12-dependent spliceosomes and may contribute to branch
site positioning in both the major and minor
spliceosome. Moreover, SF3B14 interacts directly with
the pre-mRNA branch adenosine early in spliceosome
assembly and within the fully assembled spliceosome.
SF3B14 contains one well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 77
Score = 46.5 bits (111), Expect = 3e-07
Identities = 22/75 (29%), Positives = 39/75 (52%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
V +YV ++ + LY +F ++G I I T + RG AFV++++I A NA
Sbjct: 1 VNRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDH 60
Query: 70 MQGFPFYDKPMRIQY 84
+ GF ++ + + Y
Sbjct: 61 LSGFNVANRYLVVLY 75
Score = 37.6 bits (88), Expect = 4e-04
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 171 NQILFLTNLPEETSEMMLSMLFNQFPGFKEVRL--VPNRHDIAFVEFENEMQSAAAKLAL 228
N+IL++ NLP + S L LF ++ +++R+ AFV +E+ + A L
Sbjct: 2 NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKETRGTAFVVYEDIYDAKNACDHL 61
Query: 229 HGF 231
GF
Sbjct: 62 SGF 64
>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 = 49.2 bits (117), Expect = 5e-07
Identities = 58/245 (23%), Positives = 100/245 (40%), Gaps = 25/245 (10%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T + L +IFS FGQI+ L T +G F+ F + A A++++
Sbjct: 92 LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151
Query: 71 QGF--PFYDKPMRIQYSKTDSDVISKIKGTFME---RPKKVRKQPAPVEDPAEAKKSKKK 125
G +P+ ++++ S SK + +E P+ R + + A
Sbjct: 152 NGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHA 211
Query: 126 AAKEQ-------ARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT----AGVPEQP-PNQI 173
AA+ + A L QQQ A S PA A A +
Sbjct: 212 AARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYC 271
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+F+ NL +T E +L LF F + V+++ + FV N ++A A L+L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331
Query: 229 HGFKI 233
+G+ +
Sbjct: 332 NGYTL 336
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 22/79 (27%), Positives = 47/79 (59%), Gaps = 3/79 (3%)
Query: 12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALR 68
N ++V+ +S+ +K L A+FS+FG++ +++ +K T + RG FV F+ + A A+R
Sbjct: 2 NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61
Query: 69 SMQGFPFYDKPMRIQYSKT 87
+ G + ++++ +K
Sbjct: 62 DLNGKELEGRVIKVEKAKR 80
Score = 39.9 bits (94), Expect = 7e-05
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAA 224
N+ LF++ L T+E L LF++F +EV L+ + FV FE+ + AA
Sbjct: 1 GNK-LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAA 59
Query: 225 KLALHG 230
L+G
Sbjct: 60 IRDLNG 65
>gnl|CDD|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM2 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 80
Score = 44.6 bits (106), Expect = 1e-06
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK-TLKMRGQAFVIFKEIASATNALRSMQG 72
++V +S K+ L FS+ G+I+++ +K AF+ F+ +A A+ S
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65
Query: 73 FPFYDKPMRIQY 84
+K M +QY
Sbjct: 66 SMLKNKTMHVQY 77
Score = 26.9 bits (60), Expect = 3.5
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV--PNRHDI-AFVEFENEMQSAAA 224
+F+ L + ++ L+ F++ EV L+ N + AF++FE E +A A
Sbjct: 6 IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARA 59
>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 = 43.8 bits (104), Expect = 2e-06
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ +K L+A F FG I DI + +T K RG AFV F+E A A+ +M
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60
Query: 71 QGFPFYDKPMRI 82
+ + +R+
Sbjct: 61 NESELFGRTIRV 72
Score = 29.9 bits (68), Expect = 0.21
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN----RH-DIAFVEFENEMQSAAA 224
L++ L EE E +L F F K++++ + +H AFVEFE +AAA
Sbjct: 1 LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAA 56
>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 = 43.8 bits (104), Expect = 3e-06
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR------GQAFVIFKEIASATNAL 67
+YV ++ + L IFS+FG++ I K + G AFV FK+ +SA NAL
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62
Query: 68 RSMQGFPFYDKPMRIQ 83
+ G + + +
Sbjct: 63 -QLNGTELGGRKISVS 77
Score = 30.3 bits (69), Expect = 0.17
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 174 LFLTNLPEETSEMMLSMLFNQF--------PGFKEVRLVPNRHDIAFVEFENEMQSAAAK 225
+++ NL + E L +F++F P ++ + + AFV F++ SA
Sbjct: 3 IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDA-SSAENA 61
Query: 226 LALHGFKI 233
L L+G ++
Sbjct: 62 LQLNGTEL 69
>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 = 43.3 bits (103), Expect = 3e-06
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 32 FSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF--YDKPMRIQYSK 86
F +FG I I R A++ ++ I +A A +++GFP + +R+ ++
Sbjct: 19 FDRFGAIRRI---DYDPGRNYAYIEYESIEAAQAAKEALRGFPLGGPGRRLRVDFAD 72
Score = 34.1 bits (79), Expect = 0.006
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
L++ L TS L F++F + + P R + A++E+E+ + AAK AL GF +
Sbjct: 1 LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGR-NYAYIEYESIEAAQAAKEALRGFPL 59
Query: 234 T-PTHAMKISFAK 245
P +++ FA
Sbjct: 60 GGPGRRLRVDFAD 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 = 43.4 bits (103), Expect = 3e-06
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
+L++ NLP T+E L LF+++ + V+ + D AFV FE + A ++G +
Sbjct: 3 VLYVRNLPLSTTEEQLRELFSEYGEVERVKKIK---DYAFVHFEERDDAVKAMEEMNGKE 59
Query: 233 ITPTHAMKISFAK 245
+ + +++S AK
Sbjct: 60 LEGS-PIEVSLAK 71
Score = 34.5 bits (80), Expect = 0.005
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+YV ++ + ++ L +FS++G++ + K++ AFV F+E A A+ M G
Sbjct: 4 LYVRNLPLSTTEEQLRELFSEYGEVERVK-----KIKDYAFVHFEERDDAVKAMEEMNGK 58
Query: 74 PFYDKPMRIQYSK 86
P+ + +K
Sbjct: 59 ELEGSPIEVSLAK 71
>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible
RNA binding protein (CIRBP), RNA binding motif protein
3 (RBM3) and similar proteins. This subfamily
corresponds to the RRM domain of two structurally
related heterogenous nuclear ribonucleoproteins, CIRBP
(also termed CIRP or A18 hnRNP) and RBM3 (also termed
RNPL), both of which belong to a highly conserved cold
shock proteins family. The cold shock proteins can be
induced after exposure to a moderate cold-shock and
other cellular stresses such as UV radiation and
hypoxia. CIRBP and RBM3 may function in
posttranscriptional regulation of gene expression by
binding to different transcripts, thus allowing the
cell to response rapidly to environmental signals.
However, the kinetics and degree of cold induction are
different between CIRBP and RBM3. Tissue distribution
of their expression is different. CIRBP and RBM3 may be
differentially regulated under physiological and stress
conditions and may play distinct roles in cold
responses of cells. CIRBP, also termed glycine-rich
RNA-binding protein CIRP, is localized in the nucleus
and mediates the cold-induced suppression of cell cycle
progression. CIRBP also binds DNA and possibly serves
as a chaperone that assists in the folding/unfolding,
assembly/disassembly and transport of various proteins.
RBM3 may enhance global protein synthesis and the
formation of active polysomes while reducing the levels
of ribonucleoprotein complexes containing microRNAs.
RBM3 may also serve to prevent the loss of muscle mass
by its ability to decrease cell death. Furthermore,
RBM3 may be essential for cell proliferation and
mitosis. Both, CIRBP and RBM3, contain an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), that
is involved in RNA binding, and C-terminal glycine-rich
domain (RGG motif) that probably enhances RNA-binding
via protein-protein and/or protein-RNA interactions.
Like CIRBP, RBM3 can also bind to both RNA and DNA via
its RRM domain. .
Length = 80
Score = 43.3 bits (102), Expect = 5e-06
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 26 KSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
+SL +FS++GQI ++V +K T + RG FV F+ A +A+ +M G + +R+
Sbjct: 15 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRV 74
Score = 29.8 bits (67), Expect = 0.32
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ L +T+E L +F+++ EV +V +R FV FEN + A +A+
Sbjct: 3 LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62
Query: 229 HG 230
+G
Sbjct: 63 NG 64
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM2 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 71
Score = 42.2 bits (100), Expect = 1e-05
Identities = 22/57 (38%), Positives = 30/57 (52%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
L + NL S+ L LF+QF K++R P R FVEF + + AA AL+G
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQKFVEFYDIRAAEAALDALNG 60
Score = 41.4 bits (98), Expect = 2e-05
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+ V ++ S + L ++FSQFG++ DI +T Q FV F +I +A AL ++ G
Sbjct: 4 LLVFNLDSPISDQELRSLFSQFGEVKDIR--ETPLRPSQKFVEFYDIRAAEAALDALNGR 61
Query: 74 PFYDKPMRIQ 83
PF ++++
Sbjct: 62 PFLGGRLKVK 71
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
L + LP++ ++ L LF + ++V +R FV++ +E + A L
Sbjct: 3 LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTL 62
Query: 229 HGFKITPTHAMKISFA 244
+GF+I +K+S+A
Sbjct: 63 NGFEIRNKR-LKVSYA 77
Score = 27.3 bits (61), Expect = 1.9
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 28 LYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
L ++F G I + T + G FV + + A A+ ++ GF +K +++ Y
Sbjct: 17 LRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSY 76
>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 = 41.8 bits (99), Expect = 1e-05
Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 3/46 (6%)
Query: 26 KSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALR 68
SL FSQFG+I + V + +T K RG FV FK+ SA A +
Sbjct: 15 DSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60
Score = 26.8 bits (60), Expect = 3.0
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+F+ LP T++ L F+QF +E ++ +R FV F++ +A+ A
Sbjct: 3 IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKD---KESAERAC 59
>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 = 41.5 bits (98), Expect = 2e-05
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRS 69
F+Y H+ + + LY +F+ FG ++ V T + + FV + SA A+++
Sbjct: 2 FIY--HLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKA 59
Query: 70 MQGFPFYDKPMRIQ 83
M GF K +++Q
Sbjct: 60 MNGFQVGGKRLKVQ 73
Score = 29.9 bits (68), Expect = 0.22
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ +LP E ++ L LF F ++ +++ FV ++N + AA A+
Sbjct: 1 LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60
Query: 229 HGFKI 233
+GF++
Sbjct: 61 NGFQV 65
>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 = 41.3 bits (97), Expect = 2e-05
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF 231
L++ P +TSE + +F+ + KEV+++ N AFVEFE+ + AK ++HG
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN---FAFVEFESLESAIRAKDSVHGK 56
Score = 35.1 bits (81), Expect = 0.003
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+YV + ++ IFS +G + ++ + AFV F+ + SA A S+ G
Sbjct: 2 LYVRPFPPDTSESAIREIFSPYGAVKEVKMISNF-----AFVEFESLESAIRAKDSVHGK 56
Query: 74 PFYDKPMRIQY 84
+ P+ + Y
Sbjct: 57 VLNNNPLYVTY 67
>gnl|CDD|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM1 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind
to the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs),
including polyadenylate-binding protein 1 (PABP-1 or
PABPC1), polyadenylate-binding protein 3 (PABP-3 or
PABPC3), polyadenylate-binding protein 4 (PABP-4 or
APP-1 or iPABP), polyadenylate-binding protein 5
(PABP-5 or PABPC5), polyadenylate-binding protein
1-like (PABP-1-like or PABPC1L), polyadenylate-binding
protein 1-like 2 (PABPC1L2 or RBM32),
polyadenylate-binding protein 4-like (PABP-4-like or
PABPC4L), yeast polyadenylate-binding protein,
cytoplasmic and nuclear (PABP or ACBP-67), and similar
proteins. PABP-1 is a ubiquitously expressed
multifunctional protein that may play a role in 3' end
formation of mRNA, translation initiation, mRNA
stabilization, protection of poly(A) from nuclease
activity, mRNA deadenylation, inhibition of mRNA
decapping, and mRNP maturation. Although PABP-1 is
thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains), a
less well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. Moreover, PABP-1 possesses an A-rich sequence
in its 5'-UTR and allows binding of PABP and blockage
of translation of its own mRNA. In contrast, PABP-3
lacks the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to
be identical. PABP-5 is encoded by PABPC5 gene within
the X-specific subinterval, and expressed in fetal
brain and in a range of adult tissues in mammals, such
as ovary and testis. It may play an important role in
germ cell development. Moreover, unlike other PABPs,
PABP-5 contains only four RRMs, but lacks both the
linker region and the CTD. PABP-1-like and PABP-1-like
2 are the orthologs of PABP-1. PABP-4-like is the
ortholog of PABP-5. Their cellular functions remain
unclear. The family also includes yeast PABP, a
conserved poly(A) binding protein containing poly(A)
tails that can be attached to the 3'-ends of mRNAs. The
yeast PABP and its homologs may play important roles in
the initiation of translation and in mRNA decay. Like
vertebrate PABP-1, the yeast PABP contains four RRMs, a
linker region, and a proline-rich CTD as well. The
first two RRMs are mainly responsible for specific
binding to poly(A). The proline-rich region may be
involved in protein-protein interactions. .
Length = 80
Score = 41.8 bits (99), Expect = 2e-05
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 9/67 (13%)
Query: 28 LYAIFSQFGQIM------DIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
LY IFS G ++ D++ T + G A+V F+ A A AL ++ KP+R
Sbjct: 16 LYEIFSPAGPVLSIRVCRDLI---TRRSLGYAYVNFQNPADAERALDTLNFDVIKGKPIR 72
Query: 82 IQYSKTD 88
I +S+ D
Sbjct: 73 IMWSQRD 79
Score = 27.5 bits (62), Expect = 1.9
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVR----LVPNRH-DIAFVEFENEMQSAAAKLA 227
L++ +L + +E ML +F+ +R L+ R A+V F+N A A+ A
Sbjct: 1 SLYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQN---PADAERA 57
Query: 228 L 228
L
Sbjct: 58 L 58
>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 = 41.0 bits (97), Expect = 3e-05
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIV-AL--KTLKMRGQAFVIFKEIASATNALRSM 70
+YV ++S ++ +Y +FS+ G I I+ L T G FV + A NA++ +
Sbjct: 1 LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60
Query: 71 QGFPFYDKPMRI 82
G D+ +R+
Sbjct: 61 NGTKLDDRIIRV 72
>gnl|CDD|240754 cd12308, RRM1_Spen, RNA recognition motif 1 in the Spen (split
end) protein family. This subfamily corresponds to the
RRM1 domain in the Spen (split end) family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B), and similar
proteins found in Metazoa. RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, is a novel mRNA export factor and component
of the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RNA-binding protein 15B (RBM15B),
also known as one twenty-two 3 (OTT3), is a paralog of
RBM15 and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15
the association with the splicing factor compartment
and the nuclear envelope as well as the binding to mRNA
export factors NXF1 and Aly/REF. Members in this family
belong- to the Spen (split end) protein family, which
share a domain architecture comprising of three
N-terminal RNA recognition motifs (RRMs), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain), and a C-terminal SPOC (Spen paralog and
ortholog C-terminal) domain. .
Length = 79
Score = 40.3 bits (95), Expect = 5e-05
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNAL 67
+CV+N + +S D++ LY F +FG + V R A+V F+ A A
Sbjct: 4 LCVSNLP--SKLSDEDIEDVLYHEFKKFGDVSVRVLHDGEDER-VAYVNFRHPEDAREAK 60
Query: 68 RSMQGFPFYDKPMRIQYSK 86
+ +D+P+ ++
Sbjct: 61 HAKGRLVLFDRPLNVEPVY 79
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 39.8 bits (94), Expect = 5e-05
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH---DIAFVEFENEMQSAAAKLALHG 230
L++ NLP +E L F+ + + VRLV N+ AFVEF + + AA L+G
Sbjct: 1 LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60
Query: 231 FKI 233
+
Sbjct: 61 LVL 63
Score = 34.4 bits (80), Expect = 0.005
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 9/67 (13%)
Query: 14 VYVT----HISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALR 68
+YV ++ DL++ FS +G++ + + + RG AFV F A AL+
Sbjct: 1 LYVRNLPPSVTEEDLRE----FFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALK 56
Query: 69 SMQGFPF 75
+ G
Sbjct: 57 KLNGLVL 63
>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 = 40.0 bits (94), Expect = 6e-05
Identities = 16/63 (25%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
VYV+++ + L+ IFS++G+++ + +K T K +G AF++F + A +++
Sbjct: 3 TVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKA 62
Query: 70 MQG 72
+
Sbjct: 63 LNN 65
>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 = 39.6 bits (93), Expect = 8e-05
Identities = 18/72 (25%), Positives = 35/72 (48%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+YV ++ T + L +FSQ G I ++ AFV + + SA AL++M G
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60
Query: 74 PFYDKPMRIQYS 85
+ +++ ++
Sbjct: 61 LILGQEIKVNWA 72
Score = 31.1 bits (71), Expect = 0.075
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV--PNRHDIAFVEFENEMQSAAAKLALHGF 231
L++ NL +E +L+ LF+Q K +L+ AFVE+ + +AAA ++G
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNGR 60
Query: 232 KITPTHAMKISFA 244
I +K+++A
Sbjct: 61 LIL-GQEIKVNWA 72
>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 = 39.7 bits (93), Expect = 9e-05
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQG 72
I + L+ + F+ FG+I D +K T K +G FV F + A NA++SM G
Sbjct: 11 IDTETLRAA----FAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNG 63
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
K+ L IFS++G+I+ I K G FV F A A+ G + + I
Sbjct: 15 KEDLEEIFSKYGKILGISLHK-----GYGFVQFDNEEDARAAVAGENGREIAGQKLDI 67
Score = 26.0 bits (58), Expect = 4.4
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
+F+ NL T ++ L F + ++ + FV+F+NE + AA +G
Sbjct: 3 VFVGNLN--TDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDARAAVAGENG 57
>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 = 39.5 bits (93), Expect = 1e-04
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 28 LYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
L +FS++G I + + KT + RG FV F+ + A A + G + +R+ Y
Sbjct: 16 LREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVDY 75
Query: 85 SKT 87
S T
Sbjct: 76 SIT 78
>gnl|CDD|240869 cd12423, RRM3_PTBP1_like, RNA recognition motif 3 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM3 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 39.2 bits (92), Expect = 1e-04
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 30 AIFSQFGQIMDIVALKTL-KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
A+F+ FG D+V +K L + A + + A AL + G + K +R+ SK
Sbjct: 16 ALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGIRLHGKKLRVTLSK 73
Score = 28.8 bits (65), Expect = 0.58
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 173 ILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF 231
+L ++NL EE + L LF + V+++ N+ D A ++ + Q+ A L+G
Sbjct: 1 VLLVSNLNEEMVTPDALFTLFGVYGDVVRVKILFNKKDTALIQMADPQQAQTALTHLNGI 60
Query: 232 KI 233
++
Sbjct: 61 RL 62
>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in
RNA-binding protein MRN1 and similar proteins. This
subgroup corresponds to the RRM2 and RRM4 of MRN1, also
termed multicopy suppressor of RSC-NHP6 synthetic
lethality protein 1, or post-transcriptional regulator
of 69 kDa, and is an RNA-binding protein found in
yeast. Although its specific biological role remains
unclear, MRN1 might be involved in translational
regulation. Members in this family contain four copies
of conserved RNA recognition motif (RRM), also known as
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 82
Score = 39.5 bits (92), Expect = 1e-04
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
+K L ++G+I I + L+ + AF+ F I +A AL+++ G YD +RI Y
Sbjct: 21 EKELRKECEKYGEIESI---RILREKACAFINFMNIPNAIAALQTLNGKKPYDTIVRINY 77
Query: 85 SK 86
K
Sbjct: 78 GK 79
>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 = 39.3 bits (92), Expect = 1e-04
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
SL FSQ+G+I D V +K T + RG FV F + A+ +
Sbjct: 15 SLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60
>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 = 42.3 bits (99), Expect = 1e-04
Identities = 58/257 (22%), Positives = 101/257 (39%), Gaps = 37/257 (14%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQ 71
V+V I + L +F + G I ++ + + RG AFV F A A++ +
Sbjct: 61 VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120
Query: 72 GFPFYDKPMRIQYSKTDSDVI-------SKIKGTFMERPKKVRKQPAPV---EDPAEAKK 121
+ + D+ + +K + +E KV + V A+ KK
Sbjct: 121 NYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKK 180
Query: 122 ----------SKKKAAKEQARLMQAQQQQM-QALSVQ-QPPVSQPAPPAPMATAGVPEQP 169
S + AA + +LM + Q ++V P + MA
Sbjct: 181 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDV-MAKV------ 233
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
+IL++ NL T+E ++ F++F PG +V V D AFV FE+ + A L
Sbjct: 234 --KILYVRNLMTTTTEEIIEKSFSEFKPG--KVERVKKIRDYAFVHFEDREDAVKAMDEL 289
Query: 229 HGFKITPTHAMKISFAK 245
+G K ++++ AK
Sbjct: 290 NG-KELEGSEIEVTLAK 305
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 19/60 (31%), Positives = 24/60 (40%), Gaps = 5/60 (8%)
Query: 177 TNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGF 231
TNL E+ E L LF F V L ++ AFV F + A L+GF
Sbjct: 5 TNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64
Score = 36.0 bits (84), Expect = 0.002
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 16 VTHISSTDLKKSLYAIFSQFGQIMDI-VAL--KTLKMRGQAFVIFKEIASATNALRSMQG 72
VT++S + L +F FG I + +A +T + RG AFV F A A+ + G
Sbjct: 4 VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
Query: 73 FPFYDKPMRIQYSK 86
F + + + ++++K
Sbjct: 64 FGYDNLILSVEWAK 77
>gnl|CDD|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog
subfamily C member 17. The CD corresponds to the RRM
of some eukaryotic DnaJ homolog subfamily C member 17
and similar proteins. DnaJ/Hsp40 (heat shock protein
40) proteins are highly conserved and play crucial
roles in protein translation, folding, unfolding,
translocation, and degradation. They act primarily by
stimulating the ATPase activity of Hsp70s, an important
chaperonine family. Members in this family contains an
N-terminal DnaJ domain or J-domain, which mediates the
interaction with Hsp70. They also contains a RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), at the
C-terminus, which may play an essential role in RNA
binding. .
Length = 74
Score = 38.8 bits (91), Expect = 1e-04
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
+ L IFS++G + D+V K +G A V F +A A+ + G P P+ +
Sbjct: 18 EDELRKIFSKYGDVSDVVVSS--KKKGSAIVEFASKKAAEAAVENECGLP--SNPLLVS 72
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNA 66
V N Y T + DL++ +F ++G++ D+ + T + RG AFV F + A +A
Sbjct: 3 VDNLTYRT--TPDDLRR----VFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDA 56
Query: 67 LRSMQGFPFYDKPMRIQ 83
+ +M G + +R+Q
Sbjct: 57 MDAMDGKELDGRELRVQ 73
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 13/85 (15%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ---------AFVIFKEIA 61
TN +YV +++ ++ L F +FG + ++K + R + FV F A
Sbjct: 2 TN-LYVGNLNPKVTEEVLCQEFGRFG---PLASVKIMWPRTEEERRRNRNCGFVAFMNRA 57
Query: 62 SATNALRSMQGFPFYDKPMRIQYSK 86
A AL + G +++ + K
Sbjct: 58 DAERALDELDGKDVMGYELKLGWGK 82
Score = 31.1 bits (71), Expect = 0.100
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD--------IAFVEFENEMQSAAAK 225
L++ NL + +E +L F +F V+++ R + FV F N + A
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63
Query: 226 LALHGFKITPTHAMKISFAK 245
L G K + +K+ + K
Sbjct: 64 DELDG-KDVMGYELKLGWGK 82
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 38.7 bits (91), Expect = 2e-04
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 176 LTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
L N+ + +E + F + P +++ L P+ H+ A VEFE+ + A L+L+G
Sbjct: 5 LFNVSDTVNEEQIKAFFEKIGPDVRKIELFPD-HEGALVEFESPSDAGKASLSLNG 59
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 38.8 bits (90), Expect = 2e-04
Identities = 20/77 (25%), Positives = 38/77 (49%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
PP+ L L+N+P+ +E L LF G + H +A ++ ++ A + L
Sbjct: 1 PPSATLHLSNIPQSVTEEDLRTLFANTGGTVKAFKFFQDHKMALLQMSTVEEAIQALIDL 60
Query: 229 HGFKITPTHAMKISFAK 245
H + + H +++SF+K
Sbjct: 61 HNYNLGENHHLRVSFSK 77
>gnl|CDD|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding
protein 28 (RBM28) and similar proteins. This
subfamily corresponds to the RRM2 of RBM28 and Nop4p.
RBM28 is a specific nucleolar component of the
spliceosomal small nuclear ribonucleoproteins (snRNPs),
possibly coordinating their transition through the
nucleolus. It specifically associates with U1, U2, U4,
U5, and U6 small nuclear RNAs (snRNAs), and may play a
role in the maturation of both small nuclear and
ribosomal RNAs. RBM28 has four RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and an extremely acidic
region between RRM2 and RRM3. The family also includes
nucleolar protein 4 (Nop4p or Nop77p) encoded by
YPL043W from Saccharomyces cerevisiae. It is an
essential nucleolar protein involved in processing and
maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p also contains four RRMs. .
Length = 76
Score = 38.8 bits (91), Expect = 2e-04
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 6/60 (10%)
Query: 22 TDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKP 79
DLKK +FS FG + ++ + K +G AFV F A A A++ + G +P
Sbjct: 14 ADLKK----LFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP 69
>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and
CTD-associated factor 4 (SCAF4), SR-related and
CTD-associated factor 8 (SCAF8) and similar proteins.
This subfamily corresponds to the RRM in a new class of
SCAFs (SR-like CTD-associated factors), including
SCAF4, SCAF8 and similar proteins. The biological role
of SCAF4 remains unclear, but it shows high sequence
similarity to SCAF8 (also termed CDC5L
complex-associated protein 7, or RNA-binding motif
protein 16, or CTD-binding SR-like protein RA8). SCAF8
is a nuclear matrix protein that interacts specifically
with a highly serine-phosphorylated form of the
carboxy-terminal domain (CTD) of the largest subunit of
RNA polymerase II (pol II). The pol II CTD plays a role
in coupling transcription and pre-mRNA processing. In
addition, SCAF8 co-localizes primarily with
transcription sites that are enriched in nuclear matrix
fraction, which is known to contain proteins involved
in pre-mRNA processing. Thus, SCAF8 may play a direct
role in coupling with both, transcription and pre-mRNA
processing, processes. SCAF8 and SCAF4 both contain a
conserved N-terminal CTD-interacting domain (CID), an
atypical RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNPs (ribonucleoprotein
domain), and serine/arginine-rich motifs.
Length = 77
Score = 38.5 bits (90), Expect = 2e-04
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
+++ H+S ++ L +F ++G+I I + RG A+V + A AL+ +
Sbjct: 5 LWIGHLSKKVTEEDLKNLFEEYGEIQSI---DMIPPRGCAYVCMETRQDAHRALQKL 58
>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 = 38.4 bits (90), Expect = 2e-04
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 7/67 (10%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPF 75
I+ DL+ IF FG+I + + T + +G F+ F + A AL + GF
Sbjct: 10 ITEDDLR----GIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFEL 65
Query: 76 YDKPMRI 82
+P+++
Sbjct: 66 AGRPIKV 72
>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 = 38.8 bits (90), Expect = 3e-04
Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 5/83 (6%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLV-PNRHDIA---FVEFENEMQSA 222
+Q N+ LFL NL +E L F++F EV + P R + F++FEN +
Sbjct: 3 DQRANRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAH 62
Query: 223 AAKLALHGFKITPTHAMKISFAK 245
AKLA+ G K+ + +KI + K
Sbjct: 63 RAKLAMSG-KVLRRNPIKIGYGK 84
>gnl|CDD|240879 cd12433, RRM_Yme2p_like, RNA recognition motif in yeast
mitochondrial escape protein 2 (Yme2p) and similar
proteins. This subfamily corresponds to the RRM of
Yme2p, also termed protein RNA12, an inner
mitochondrial membrane protein that plays a critical
role in mitochondrial DNA transactions. It may serve as
a mediator of nucleoid structure and number in
mitochondria of the yeast Saccharomyces cerevisiae.
Yme2p contains an exonuclease domain, an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal domain. .
Length = 86
Score = 38.4 bits (90), Expect = 3e-04
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKP--MRIQYS 85
LY++F +G+I DI + A V F+ I A +A + GF + + IQY
Sbjct: 21 LYSLFRPYGKIKDITPPPPDSLPRYATVTFRRIRGAISAKNCLHGFELNEGKTRLHIQYE 80
Query: 86 K 86
Sbjct: 81 P 81
>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 = 38.5 bits (90), Expect = 3e-04
Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV +++ L +F ++G I+D+ + T + RG A+V F+++ A +AL +
Sbjct: 3 LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62
Query: 71 QGFPFYDKPMRIQYSKTD 88
F + + IQ+++ D
Sbjct: 63 DRTRFLGREIEIQFAQGD 80
>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1,
2, 3, 4 family. These eukaryotic proteins recognize the
poly-A of mRNA and consists of four tandem RNA
recognition domains at the N-terminus (rrm: pfam00076)
followed by a PABP-specific domain (pfam00658) at the
C-terminus. The protein is involved in the transport of
mRNA's from the nucleus to the cytoplasm. There are four
paralogs in Homo sapiens which are expressed in testis
(GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ),
broadly expressed (SP:P11940_PABP1) and of unknown
tissue range (SP:Q15097_PABP2).
Length = 562
Score = 40.9 bits (96), Expect = 4e-04
Identities = 28/159 (17%), Positives = 53/159 (33%), Gaps = 11/159 (6%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVAL--KTLKMRGQAFVIFKEIASATNALRSMQGFPFY 76
++ L++ +FS+ G+I + + RG FV F A A+ M G
Sbjct: 297 VTDEKLRE----LFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLG 352
Query: 77 DKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQA 136
KP+ + ++ + ++ FM+ ++R+ P P + + +
Sbjct: 353 GKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMG--SPMGGAMGQPPYYGQGPQQQFN 410
Query: 137 QQQQMQALSVQQPPVSQP-APPAPMATAGVPEQ--PPNQ 172
Q P P P P A + P
Sbjct: 411 GQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRN 449
Score = 33.6 bits (77), Expect = 0.077
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 26 KSLYAIFSQFGQIMDI--VALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
K+L+ FS+FG I+ + K RG FV F++ SA A++ + G DK
Sbjct: 103 KALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK 157
Score = 33.6 bits (77), Expect = 0.088
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIM------DIVALKTLKMRGQAFVIFKEIASATNAL 67
+YV + + LY +F FG ++ D V ++L G +V F+ A A AL
Sbjct: 3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSL---GYGYVNFQNPADAERAL 59
Query: 68 RSMQGFPFYDKPMRIQYSKTDSD 90
+M KP+RI +S+ D
Sbjct: 60 ETMNFKRLGGKPIRIMWSQRDPS 82
Score = 29.0 bits (65), Expect = 3.0
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVA--LKTLKMRGQAFVIFKEIASATNALR 68
TN +YV ++ + + L +F++FG+I + + RG AFV F++ A A+
Sbjct: 179 TN-LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVE 237
Query: 69 SMQG--FPFYDKPMRI 82
M G + ++
Sbjct: 238 EMNGKKIGLAKEGKKL 253
Score = 28.6 bits (64), Expect = 3.1
Identities = 20/74 (27%), Positives = 29/74 (39%), Gaps = 4/74 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKE--VRLVPNR--HDIAFVEFENEMQSAAAKLALH 229
L++ NL +E L LF +F V + AFV FE +A A ++
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240
Query: 230 GFKITPTHAMKISF 243
G KI K +
Sbjct: 241 GKKIGLAKEGKKLY 254
>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 = 37.6 bits (88), Expect = 5e-04
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE--MQSA 222
LF+ L +T+E L F ++ K +RLV ++ AF+EFE+E M++A
Sbjct: 4 LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAA 59
>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 = 37.1 bits (86), Expect = 6e-04
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VYV +I + L +F FG I++ + RG AFV A A+ +QGF
Sbjct: 3 VYVGNIPPYTTQADLIPLFQNFGYILEF---RHQPDRGFAFVKLDTHEQAAMAIVQLQGF 59
Query: 74 PFYDKPMRIQYSK 86
P + +P+R + K
Sbjct: 60 PVHGRPLRCGWGK 72
Score = 30.1 bits (68), Expect = 0.21
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 175 FLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF 231
++ N+P T++ L LF F E R P+R AFV+ + Q+A A + L GF
Sbjct: 4 YVGNIPPYTTQADLIPLFQNFGYILEFRHQPDR-GFAFVKLDTHEQAAMAIVQLQGF 59
>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 = 6e-04
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 25 KKSLYAIFSQFGQI--MDIVALK-TLKMRGQAFVIFKEIASATNALRS 69
++ L +FSQFG++ IV K T +G AFV FK SA L +
Sbjct: 14 EEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEA 61
Score = 27.9 bits (63), Expect = 1.1
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENE 218
+F+ NLP + +E L LF+QF K R+V + AFV+F+ +
Sbjct: 2 TVFIRNLPFDATEEELKELFSQFGEVKYARIVKD-KLTGHSKGTAFVKFKTK 52
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 38.5 bits (89), Expect = 8e-04
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 22 TDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
TD SL F+ FG ++D IV +T + RG FV F + +AT A+ M G +
Sbjct: 46 TD-DASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGR 104
Query: 79 PMRI 82
+R+
Sbjct: 105 HIRV 108
>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in
RNA-binding protein 5 (RBM5) and similar proteins. This
subfamily includes the RRM1 and RRM2 of RNA-binding
protein 5 (RBM5 or LUCA15 or H37) and RNA-binding
protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding
protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs
share high sequence homology and may play an important
role in regulating apoptosis. RBM5 is a known modulator
of apoptosis. It may also act as a tumor suppressor or
an RNA splicing factor. RBM6 has been predicted to be a
nuclear factor based on its nuclear localization signal.
Both, RBM6 and RBM5, specifically bind poly(G) RNA.
RBM10 is a paralog of RBM5. It may play an important
role in mRNA generation, processing and degradation in
several cell types. The rat homolog of human RBM10 is
protein S1-1, a hypothetical RNA binding protein with
poly(G) and poly(U) binding capabilities. All family
members contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two C2H2-type zinc fingers,
and a G-patch/D111 domain. .
Length = 84
Score = 37.1 bits (87), Expect = 8e-04
Identities = 21/74 (28%), Positives = 29/74 (39%), Gaps = 10/74 (13%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGF--KEVRLVPNR-----HDIAFVEF---ENEM 219
P L L L T+E + + K+VRL+ ++ AFVEF E+
Sbjct: 1 PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60
Query: 220 QSAAAKLALHGFKI 233
Q A L F I
Sbjct: 61 QWMDALNNLDPFVI 74
>gnl|CDD|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and
cytoplasmic polyadenylated RNA-binding protein PUB1 and
similar proteins. This subgroup corresponds to the
RRM2 of yeast protein PUB1, also termed ARS
consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein.
PUB1 has been identified as both, a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP), which may be stably bound
to a translationally inactive subpopulation of mRNAs
within the cytoplasm. It is distributed in both, the
nucleus and the cytoplasm, and binds to poly(A)+ RNA
(mRNA or pre-mRNA). Although it is one of the major
cellular proteins cross-linked by UV light to
polyadenylated RNAs in vivo, PUB1 is nonessential for
cell growth in yeast. PUB1 also binds to T-rich single
stranded DNA (ssDNA). However, there is no strong
evidence implicating PUB1 in the mechanism of DNA
replication. PUB1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a GAR motif (glycine
and arginine rich stretch) that is located between RRM2
and RRM3. .
Length = 75
Score = 36.3 bits (84), Expect = 0.001
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
++V +S +L+A FS F D + K+ + RG FV F+ A NA+ M
Sbjct: 2 IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61
Query: 71 QGFPFYDKPMRIQY 84
G +P+R +
Sbjct: 62 NGKWLGSRPIRCNW 75
>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM1 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 80
Score = 36.6 bits (85), Expect = 0.001
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
VYV+ I ++ L A+FS GQ++D + +R AF+ F + A AL S+
Sbjct: 5 VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRF-AFIEFTDEEGARAAL-SLS 62
Query: 72 GFPFYDKPMRIQYSKT 87
G P+R+ SKT
Sbjct: 63 GTMLGFYPVRVLPSKT 78
>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 = 36.1 bits (84), Expect = 0.001
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRS 69
FVY ++ + L+ +FS FG + + I L T K +G FV A +A+ S
Sbjct: 5 FVY--NLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62
Query: 70 MQGFPFYDKPMRIQY 84
+ G+ + +++ +
Sbjct: 63 LNGYRLGGRVLQVSF 77
Score = 27.7 bits (62), Expect = 1.4
Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 11/67 (16%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI--------AFVEFENEMQSAAAK 225
+F+ NLP + E +L LF+ F V+++ D+ FV N ++ +A
Sbjct: 4 IFVYNLPPDADESLLWQLFSPFGAVTNVKVI---RDLTTNKCKGYGFVTMTNYEEAYSAI 60
Query: 226 LALHGFK 232
+L+G++
Sbjct: 61 ASLNGYR 67
>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 = 36.1 bits (84), Expect = 0.002
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIA----FVEFEN----EMQS 221
PN+I F+ +P +T+E L F++F K+V+++ +R ++ FV FE E
Sbjct: 2 PNRI-FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKIL 60
Query: 222 AAAKLALHGFKITPTHAMK 240
A L G K+ A++
Sbjct: 61 AMGNLNFRGKKLNIGPAIR 79
Score = 30.7 bits (70), Expect = 0.14
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 12 NFVYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRS 69
N ++V I ++ L FS+FG + D I+ + +G FV F+ A + +
Sbjct: 3 NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEK-ILA 61
Query: 70 MQGFPFYDKPMRI 82
M F K + I
Sbjct: 62 MGNLNFRGKKLNI 74
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 36.5 bits (85), Expect = 0.002
Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 30 AIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
+FSQ+G+I+DI + KT K +G AF+ +++ S A+ ++ G + +R+
Sbjct: 28 CVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83
>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 = 36.0 bits (84), Expect = 0.002
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKM----RGQAFVIFKEIASATNALRS 69
++V ++ K L IFS +G + D V L + RG A+V F+ A A++
Sbjct: 1 LHVGKLTRNVNKDHLKEIFSNYGTVKD-VDLPIDREVNLPRGYAYVEFESPEDAEKAIKH 59
Query: 70 MQG 72
M G
Sbjct: 60 MDG 62
>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 = 36.1 bits (84), Expect = 0.002
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 14/80 (17%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ-------AFVIFKEIASATNA 66
+YV ++ T L FSQ G++ K ++M G AFV F E S NA
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEV------KYVRMAGDETQPTRYAFVEFAEQTSVINA 60
Query: 67 LRSMQGFPFYDKPMRIQYSK 86
L+ + G F +P+++ +S
Sbjct: 61 LK-LNGAMFGGRPLKVNHSN 79
>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 = 35.8 bits (83), Expect = 0.002
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
T +++ ++ T L F +FG+I+DI K AF+ + +IAS A+R M
Sbjct: 2 TRTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPAYAFIQYADIASVVKAMRKM 61
Query: 71 QG 72
G
Sbjct: 62 DG 63
>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8 and similar proteins. This subfamily
corresponds to the RRM3 of NGR1 and NAM8. NGR1, also
termed RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA) in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 72
Score = 35.7 bits (83), Expect = 0.002
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
V+V + + L ++F FG +IV +K +G FV F A+A A++ +QG
Sbjct: 4 VFVGGLDPAVTEDELRSLFGPFG---EIVYVKIPPGKGCGFVQFVHRAAAEAAIQQLQGT 60
Query: 74 PFYDKPMRIQY 84
+R+ +
Sbjct: 61 IIGGSRIRLSW 71
>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 = 35.6 bits (83), Expect = 0.002
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 28 LYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQG 72
+ A+F ++G I ++ ++ T + +G AFV F A A+ ++ G
Sbjct: 16 VRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63
Score = 28.7 bits (65), Expect = 0.67
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ LP+ +E + LF ++ +EV ++ ++ AFV+F + ++ A AL
Sbjct: 2 LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61
Query: 229 HGFKITP 235
HG P
Sbjct: 62 HGKVTMP 68
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM2 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 79
Score = 35.8 bits (83), Expect = 0.002
Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMDI-VAL--KTLKMRGQAFVIFKEIASATNA 66
V N Y DL+K +FS+FG++ ++ VA+ K+ K +G A+V+F + A A
Sbjct: 7 VRNLPYSC--KEDDLEK----LFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60
Query: 67 LRSMQGFPFYDKPMRI 82
+ + G F + + I
Sbjct: 61 YKELDGKVFQGRLIHI 76
Score = 28.5 bits (64), Expect = 0.70
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ NLP E L LF++F EV + ++ A+V F + + A L
Sbjct: 5 LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64
Query: 229 HG 230
G
Sbjct: 65 DG 66
>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 = 35.7 bits (83), Expect = 0.002
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 31 IFSQFGQI--MDIVALKTLKMRGQ----AFVIFKEIASATNALRSMQG 72
+FS++G+I D + K+ ++GQ FV F+ A AL+S+ G
Sbjct: 19 LFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNG 66
>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 = 35.7 bits (83), Expect = 0.002
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 26 KSLYAIFSQFGQIMDIVAL----KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
K LY FS FG I+ + T +G AF+ + ++ A+ +M G ++P+
Sbjct: 16 KLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPIT 75
Query: 82 IQYS 85
+ Y+
Sbjct: 76 VSYA 79
>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 = 35.6 bits (83), Expect = 0.002
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY--DKPMRIQYS 85
L A+ S FG++ + L+ + QA V + SA + + P + + IQYS
Sbjct: 16 LIALVSPFGKV---TNVLLLRGKNQALVEMDSVESAKSMVDYYLTVPALIRGRRVYIQYS 72
Query: 86 K 86
Sbjct: 73 N 73
Score = 28.7 bits (65), Expect = 0.54
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAA 224
+L L NLP + +E L L + F V L+ ++ A VE ++ +SA +
Sbjct: 1 VLHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQ-ALVEMDSV-ESAKS 50
>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2
protein homolog alpha (TRA-2 alpha) and similar
proteins. This subgroup corresponds to the RRM of
TRA2-alpha or TRA-2-alpha, also termed transformer-2
protein homolog A, a mammalian homolog of Drosophila
transformer-2 (Tra2). TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein (SRp40) that
specifically binds to gonadotropin-releasing hormone
(GnRH) exonic splicing enhancer on exon 4 (ESE4) and is
necessary for enhanced GnRH pre-mRNA splicing. It
strongly stimulates GnRH intron A excision in a
dose-dependent manner. In addition, TRA2-alpha can
interact with either 9G8 or SRp30c, which may also be
crucial for ESE-dependent GnRH pre-mRNA splicing.
TRA2-alpha contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 79
Score = 35.7 bits (82), Expect = 0.002
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 9 CVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATN 65
C+ F + + DL++ +FS++G + + + +T + RG AFV F+ I +
Sbjct: 1 CLGVFGLSLYTTERDLRE----VFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKE 56
Query: 66 ALRSMQGFPFYDKPMRIQYSKT 87
A+ G + +R+ YS T
Sbjct: 57 AMEHANGMELDGRRIRVDYSIT 78
>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM2 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 96
Score = 35.9 bits (83), Expect = 0.002
Identities = 28/87 (32%), Positives = 43/87 (49%), Gaps = 10/87 (11%)
Query: 2 NIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIA 61
N +L + V N Y + D+ L+ IFS+FG ++ I+ T + QA + F +
Sbjct: 1 NTVL-RVIVENMTYPV---TLDV---LHQIFSKFGTVLKIITF-TKNNQFQALIQFADAV 52
Query: 62 SATNALRSMQGFPFYDK--PMRIQYSK 86
SA A S+ G Y+ +RI YSK
Sbjct: 53 SAQAAKLSLDGQNIYNGCCTLRIDYSK 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 = 35.3 bits (82), Expect = 0.002
Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
TN V++ + + ++ L FS++G ++ +V + RGQA V F ++ +A A+ M
Sbjct: 7 TNCVWLDGLDESVTEQYLTRHFSRYGPVVHVV---IDRQRGQALVFFDKVEAAQAAVNEM 63
Query: 71 QGFPFYDKPMRIQY 84
+G + +++ +
Sbjct: 64 KGRKLGGRKLQVDF 77
>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 = 35.1 bits (81), Expect = 0.003
Identities = 21/61 (34%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 174 LFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
LF+ P T E + LF F + R AFVEFE+ + A ALHG +
Sbjct: 2 LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI---RKTFAFVEFEDSEDATKALEALHGSR 58
Query: 233 I 233
I
Sbjct: 59 I 59
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 35.2 bits (82), Expect = 0.003
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVR---LVPNRHD-IAFVEFENEMQSAAAKLAL 228
L++TN P + + LF Q+ +R L N+ +V+F + +SAAA +AL
Sbjct: 2 TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSP-ESAAAAVAL 60
Query: 229 HGFKITPTHAM--KIS 242
K+ + + KIS
Sbjct: 61 LNGKLGEGYKLVVKIS 76
>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 = 35.3 bits (82), Expect = 0.003
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
T +V+ ++ LKK+ FS FG I++I K + FV F+++ SA A+ +
Sbjct: 6 TLYVHGYGLTEEILKKA----FSPFGNIINI---SMEKEKNCGFVTFEKMESADRAIAEL 58
Query: 71 QGFPFYDKPMRIQYSK 86
G +++ ++
Sbjct: 59 NGTTVQGVQLKVSLAR 74
>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP A and
hnRNP D subfamilies and similar proteins. This
subfamily corresponds to the RRM1 in the hnRNP A
subfamily which includes hnRNP A0, hnRNP A1, hnRNP
A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low
abundance hnRNP protein that has been implicated in
mRNA stability in mammalian cells. hnRNP A1 is an
abundant eukaryotic nuclear RNA-binding protein that
may modulate splice site selection in pre-mRNA
splicing. hnRNP A2/B1 is an RNA trafficking response
element-binding protein that interacts with the hnRNP
A2 response element (A2RE). hnRNP A3 is also a RNA
trafficking response element-binding protein that
participates in the trafficking of A2RE-containing RNA.
The hnRNP A subfamily is characterized by two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a long glycine-rich region at the
C-terminus. The hnRNP D subfamily includes hnRNP D0,
hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a
UUAG-specific nuclear RNA binding protein that may be
involved in pre-mRNA splicing and telomere elongation.
hnRNP A/B is an RNA unwinding protein with a high
affinity for G- followed by U-rich regions. hnRNP A/B
has also been identified as an APOBEC1-binding protein
that interacts with apolipoprotein B (apoB) mRNA
transcripts around the editing site and thus, plays an
important role in apoB mRNA editing. hnRNP DL (or hnRNP
D-like) is a dual functional protein that possesses
DNA- and RNA-binding properties. It has been implicated
in mRNA biogenesis at the transcriptional and
post-transcriptional levels. All members in this
subfamily contain two putative RRMs and a glycine- and
tyrosine-rich C-terminus. The family also contains
DAZAP1 (Deleted in azoospermia-associated protein 1),
RNA-binding protein Musashi homolog Musashi-1,
Musashi-2 and similar proteins. They all harbor two
RRMs. .
Length = 72
Score = 35.3 bits (82), Expect = 0.003
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 25 KKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRS 69
++SL FS++G+++D V +K T + RG FV F + +S L +
Sbjct: 12 EESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59
>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 = 34.9 bits (81), Expect = 0.004
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
LF+ NLP + +E LF+++ EV L F+ + + AK L G
Sbjct: 4 LFVGNLPNDITEEEFKELFSKYGEVSEVFL-NKEKGFGFIRLDTRTNAEKAKAELDG 59
>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA
cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6),
pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or
CPSF7), and similar proteins. This subfamily
corresponds to the RRM of cleavage factor Im (CFIm)
subunits. Cleavage factor Im (CFIm) is a highly
conserved component of the eukaryotic mRNA 3'
processing machinery that functions in UGUA-mediated
poly(A) site recognition, the regulation of alternative
poly(A) site selection, mRNA export, and mRNA splicing.
It is a complex composed of a small 25 kDa (CFIm25)
subunit and a larger 59/68/72 kDa subunit. Two separate
genes, CPSF6 and CPSF7, code for two isoforms of the
large subunit, CFIm68 and CFIm59. Structurally related
CFIm68 and CFIm59, also termed cleavage and
polyadenylation specificity factor subunit 6 (CPSF7),
or cleavage and polyadenylation specificity factor 59
kDa subunit (CPSF59), are functionally redundant. Both
contains an N-terminal RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a central proline-rich
region, and a C-terminal RS-like domain. Their
N-terminal RRM mediates the interaction with CFIm25,
and also serves to enhance RNA binding and facilitate
RNA looping. .
Length = 76
Score = 35.0 bits (81), Expect = 0.004
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 15/72 (20%)
Query: 22 TDLKKSLYAIFSQFGQIMDIVALKTL---------KMRGQAFVIFKEIASATNALRSMQG 72
TD + L ++ G +V +K++ K +G A+V F A+A ++G
Sbjct: 11 TD--EDLEGALAEAG----VVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEG 64
Query: 73 FPFYDKPMRIQY 84
F K + Y
Sbjct: 65 REFNGKKCVVTY 76
>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA
repair protein alkB homolog 8 (ALKBH8) and similar
proteins. This subfamily corresponds to the RRM of
ALKBH8, also termed alpha-ketoglutarate-dependent
dioxygenase ABH8, or S-adenosyl-L-methionine-dependent
tRNA methyltransferase ABH8, expressed in various types
of human cancers. It is essential in urothelial
carcinoma cell survival mediated by NOX-1-dependent ROS
signals. ALKBH8 has also been identified as a tRNA
methyltransferase that catalyzes methylation of tRNA to
yield 5-methylcarboxymethyl uridine (mcm5U) at the
wobble position of the anticodon loop. Thus, ALKBH8
plays a crucial role in the DNA damage survival pathway
through a distinct mechanism involving the regulation
of tRNA modification. ALKBH8 localizes to the
cytoplasm. It contains the characteristic AlkB domain
that is composed of a tRNA methyltransferase motif, a
motif homologous to the bacterial AlkB DNA/RNA repair
enzyme, and a dioxygenase catalytic core domain
encompassing cofactor-binding sites for iron and
2-oxoglutarate. In addition, unlike other AlkB
homologs, ALKBH8 contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a C-terminal
S-adenosylmethionine (SAM)-dependent methyltransferase
(MT) domain. .
Length = 80
Score = 34.9 bits (81), Expect = 0.004
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 11/68 (16%)
Query: 7 HICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ--AFVIFKEIASAT 64
H+ V N +S ++ L +F ++G + D+V G+ FV + I A
Sbjct: 3 HLVVANGGLGNGVS----REELLRVFEKYGTVEDLVMP-----PGKPYCFVSYSSIEDAA 53
Query: 65 NALRSMQG 72
A ++ G
Sbjct: 54 AAYDALNG 61
>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 = 35.6 bits (83), Expect = 0.004
Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 13/87 (14%)
Query: 12 NFVYVTHISSTD-----LKKSLYAIFSQFGQIMDIVALKTLKMRGQ------AFVIFKEI 60
N VYV + LKK Y F Q+G+I IV + G A+V +
Sbjct: 6 NLVYVVGLPPRLADEEVLKKPEY--FGQYGKIKKIVINRNTSYNGSQGPSASAYVTYSRK 63
Query: 61 ASATNALRSMQGFPFYDKPMRIQYSKT 87
A ++++ GF + ++ + T
Sbjct: 64 EDALRCIQAVDGFYLDGRLLKASFGTT 90
>gnl|CDD|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding
protein with multiple splicing (RBP-MS). This subfamily
corresponds to the RRM of RBP-MS, also termed heart and
RRM expressed sequence (hermes), an RNA-binding proteins
found in various vertebrate species. It contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). RBP-MS
physically interacts with Smad2, Smad3 and Smad4 and
plays a role in regulation of Smad-mediated
transcriptional activity. In addition, RBP-MS may be
involved in regulation of mRNA translation and
localization during Xenopus laevis development. .
Length = 76
Score = 35.0 bits (80), Expect = 0.004
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRL-VPNRHDIAFVEFENEMQSAAAKLALHG 230
+ LF++ LP + L +LF F G++ + + ++ + FV F++ ++ AAK AL+G
Sbjct: 2 RTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNG 61
Query: 231 FKITP 235
+ P
Sbjct: 62 IRFDP 66
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both nuclear
and cytoplasmic roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 86
Score = 35.0 bits (81), Expect = 0.004
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYS 85
+Y I + G+++ IV + K QA V F + SA A ++ G Y ++I+Y+
Sbjct: 20 IYTICNPHGKVLRIVIFR--KNGVQAMVEFDSVDSAQRAKAALNGADIYAGCCTLKIEYA 77
Query: 86 KTDS 89
K D
Sbjct: 78 KPDR 81
Score = 27.7 bits (62), Expect = 1.7
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 211 AFVEFENEMQSAAAKLALHGFKITP-THAMKISFAK 245
A VEF++ + AK AL+G I +KI +AK
Sbjct: 43 AMVEFDSVDSAQRAKAALNGADIYAGCCTLKIEYAK 78
>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 = 34.9 bits (81), Expect = 0.004
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
L++ NLP +E L LF QF R++ +R FVE E ++ AA L
Sbjct: 2 LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61
Query: 229 HGF 231
+G
Sbjct: 62 NGT 64
Score = 30.7 bits (70), Expect = 0.13
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 9/76 (11%)
Query: 10 VTNFVYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNA 66
V N Y DLK +F QFG++ I +T + RG FV + A A
Sbjct: 4 VGNLPYNVT--EEDLK----DLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57
Query: 67 LRSMQGFPFYDKPMRI 82
+ + G F + + +
Sbjct: 58 IEKLNGTDFGGRTLTV 73
>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding
protein 7 (RBM7) and similar proteins. This subfamily
corresponds to the RRM of RBM7, RBM11 and their
eukaryotic homologous. RBM7 is an ubiquitously
expressed pre-mRNA splicing factor that enhances
messenger RNA (mRNA) splicing in a cell-specific manner
or in a certain developmental process, such as
spermatogenesis. It interacts with splicing factors
SAP145 (the spliceosomal splicing factor 3b subunit 2)
and SRp20, and may play a more specific role in meiosis
entry and progression. Together with additional
testis-specific RNA-binding proteins, RBM7 may regulate
the splicing of specific pre-mRNA species that are
important in the meiotic cell cycle. RBM11 is a novel
tissue-specific splicing regulator that is selectively
expressed in brain, cerebellum and testis, and to a
lower extent in kidney. It is localized in the
nucleoplasm and enriched in SRSF2-containing splicing
speckles. It may play a role in the modulation of
alternative splicing during neuron and germ cell
differentiation. Both, RBM7 and RBM11, contain an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a region lacking known homology at the C-terminus.
The RRM is responsible for RNA binding, whereas the
C-terminal region permits nuclear localization and
homodimerization. .
Length = 75
Score = 34.6 bits (80), Expect = 0.005
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQ 71
++V ++ + ++ LY +F Q G + + K K + AFV FK S A++ +
Sbjct: 4 LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63
Query: 72 GFPFYDKPMRIQ 83
G + + +RI+
Sbjct: 64 GIRLFGRELRIK 75
>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 = 34.7 bits (80), Expect = 0.005
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VY+ ++ + ++ L +FG I I K +K + AFV F IA+A + ++
Sbjct: 6 VYIGNLPESYSEEELREDLEKFGPIDQI---KIVKEKNIAFVHFLSIANAIKVVTTLPCE 62
Query: 74 PFYDKPMRIQYSK 86
P Y RI Y K
Sbjct: 63 PDY-ASRRIFYGK 74
>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 = 34.9 bits (81), Expect = 0.006
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 14/77 (18%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-------AFVEFENE--MQ 220
P LF+ L +T+E L +F+++ + +RLV R + AFVE+E+E
Sbjct: 2 PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLV--RDIVTGFSKGYAFVEYEHERDAL 59
Query: 221 SA---AAKLALHGFKIT 234
A A KL + G +I
Sbjct: 60 RAYRDAHKLVIDGSEIF 76
Score = 34.5 bits (80), Expect = 0.007
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIM------DIVALKTLKMRGQAFVIFKEIASATNAL 67
++V +S +++L +FS++G I DIV T +G AFV ++ A A
Sbjct: 6 LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIV---TGFSKGYAFVEYEHERDALRAY 62
Query: 68 RSMQ 71
R
Sbjct: 63 RDAH 66
>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic
activator RIM4 and similar proteins. This subfamily
corresponds to the RRM1 of RIM4, also termed regulator
of IME2 protein 4, a putative RNA binding protein that
is expressed at elevated levels early in meiosis. It
functions as a meiotic activator required for both the
IME1- and IME2-dependent pathways of meiotic gene
expression, as well as early events of meiosis, such as
meiotic division and recombination, in Saccharomyces
cerevisiae. RIM4 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The family also includes a
putative RNA-binding protein termed multicopy
suppressor of sporulation protein Msa1. It is a
putative RNA-binding protein encoded by a novel gene,
msa1, from the fission yeast Schizosaccharomyces pombe.
Msa1 may be involved in the inhibition of sexual
differentiation by controlling the expression of
Ste11-regulated genes, possibly through the
pheromone-signaling pathway. Like RIM4, Msa1 also
contains two RRMs, both of which are essential for the
function of Msa1. .
Length = 86
Score = 34.7 bits (80), Expect = 0.006
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 14 VYVTHISST----DLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
V+V + ++ +L+ ++ FS++G ++ + L+ + R AFV F A NAL
Sbjct: 5 VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQRPYAFVQFTNDDDAKNALAK 64
Query: 70 MQGFPFYDKPMRIQYSK 86
QG + +R + +K
Sbjct: 65 GQGTILDGRHIRCERAK 81
>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 = 34.6 bits (80), Expect = 0.006
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 9/67 (13%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI-------AFVEFENEMQSAAAKL 226
L + NLP E ++ L + F + LV + FVE+ ++ + AK
Sbjct: 2 LCVGNLPLEFTDEQFRELVSPFGAVERCFLV--YSESTGESKGYGFVEYASKASALKAKN 59
Query: 227 ALHGFKI 233
L G +I
Sbjct: 60 QLDGKQI 66
>gnl|CDD|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate
RNA-binding protein with multiple splicing 2 (RBP-MS2).
This subfamily corresponds to the RRM of RBP-MS2,
encoded by RBPMS2 gene, a paralog of RNA-binding protein
with multiple splicing (RBP-MS). The biological function
of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 76
Score = 34.2 bits (78), Expect = 0.007
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRL-VPNRHDIAFVEFENEMQSAAAKLALHG 230
+ LF++ LP + L +LF F G++ + + ++ + FV F++ + AAK AL+G
Sbjct: 2 RTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVTFDSRAGAEAAKNALNG 61
Query: 231 FKITP 235
+ P
Sbjct: 62 IRFDP 66
>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 = 34.2 bits (78), Expect = 0.009
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 25 KKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMR 81
++ L +FS++G I D+ + ++ + RG AFV F+ + A A G + +R
Sbjct: 23 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 82
Query: 82 IQYSKT 87
+ +S T
Sbjct: 83 VDFSIT 88
>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 = 33.7 bits (78), Expect = 0.010
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKMRGQAFVIFKEIASATNALRSMQG 72
VYV ++ K+ L F ++G + + VA G AFV F++ A +A+R++ G
Sbjct: 2 VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNP---PGFAFVEFEDPRDAEDAVRALDG 58
Query: 73 FPFYDKPMRIQYSK 86
+R++ S+
Sbjct: 59 RRICGNRVRVELSR 72
>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR
and similar proteins. This subgroup corresponds to the
RRM3 of nucleolysin TIAR, also termed TIA-1-related
protein, a cytotoxic granule-associated RNA-binding
protein that shows high sequence similarity with 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific
binding to uridylate-rich RNAs. .
Length = 73
Score = 33.8 bits (77), Expect = 0.011
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
VY I+S ++ + FS FGQIM+I + +G +F+ F SA +A+ S+ G
Sbjct: 3 VYCGGIASGLTEQLMRQTFSPFGQIMEI---RVFPEKGYSFIRFSTHESAAHAIVSVNG 58
>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM3 of p40-TIA-1, the
40-kDa isoform of T-cell-restricted intracellular
antigen-1 (TIA-1) and a cytotoxic granule-associated
RNA-binding protein mainly found in the granules of
cytotoxic lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and function as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a
glutamine-rich C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich
RNAs. .
Length = 74
Score = 33.9 bits (77), Expect = 0.011
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
VY ++S ++ + FS FGQIM++ + +G +FV F SA +A+ S+ G
Sbjct: 3 VYCGGVTSGLTEQLMRQTFSPFGQIMEV---RVFPDKGYSFVRFNSHESAAHAIVSVNG 58
>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 = 36.4 bits (84), Expect = 0.012
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV ++ ++ L IF FG I D+ + T + +G F+ F + A AL M
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248
Query: 71 QGFPFYDKPMRIQY 84
GF +P+++ Y
Sbjct: 249 NGFELAGRPIKVGY 262
Score = 27.2 bits (60), Expect = 9.7
Identities = 20/94 (21%), Positives = 42/94 (44%), Gaps = 6/94 (6%)
Query: 158 APMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAF 212
A AT + P L++ NL +E L +F F ++V+L + F
Sbjct: 173 AKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGF 232
Query: 213 VEFENEMQSAAAKLALHGFKITPTHAMKISFAKK 246
++F + ++ A ++GF++ +K+ +A+
Sbjct: 233 IQFHDAEEAKEALEVMNGFELA-GRPIKVGYAQD 265
>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 = 33.3 bits (77), Expect = 0.012
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVA---LKTLKMRGQAFVIFKEIASATNALRSM 70
VY+ H+ + L FSQFG + + KT K +G AFV F+ A +M
Sbjct: 2 VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61
Query: 71 QGFPFYDKPMRIQ 83
+ +++ ++ +
Sbjct: 62 NNYLLFERLLKCK 74
Score = 27.9 bits (63), Expect = 1.1
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENEMQSAAAKLA 227
++++ +LP E L F+QF +RL ++ AFVEFE+ AK+
Sbjct: 1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP---EVAKIV 57
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and
the RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 33.3 bits (77), Expect = 0.012
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 32 FSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
FS+FG I++I + A V F A A RS
Sbjct: 23 FSKFGTIVNI---QVNYNPESALVQFSTSEEAKKAYRS 57
>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 = 33.4 bits (77), Expect = 0.012
Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 6/69 (8%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKT--LKMRGQAFVIFKEIASATNALR--- 68
V+V+++ + + L +FS+ G+I D+ +K K +G A+V F+ S AL+
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLDR 61
Query: 69 -SMQGFPFY 76
++G P +
Sbjct: 62 ELIKGRPMF 70
Score = 28.8 bits (65), Expect = 0.64
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR----HDIAFVEFENEMQSAAAKLAL 228
+F++NL E L LF++ +VRLV N A+VEFENE +S L L
Sbjct: 2 VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENE-ESVQEALKL 59
>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the
peroxisome proliferator-activated receptor gamma
coactivator 1A (PGC-1alpha) family of regulated
coactivators. This subfamily corresponds to the RRM of
PGC-1alpha, PGC-1beta, and PGC-1-related coactivator
(PRC), which serve as mediators between environmental
or endogenous signals and the transcriptional machinery
governing mitochondrial biogenesis. They play an
important integrative role in the control of
respiratory gene expression through interacting with a
number of transcription factors, such as NRF-1, NRF-2,
ERR, CREB and YY1. All family members are multi-domain
proteins containing the N-terminal activation domain,
an LXXLL coactivator signature, a tetrapeptide motif
(DHDY) responsible for HCF binding, and an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In contrast
to PGC-1alpha and PRC, PGC-1beta possesses two
glutamic/aspartic acid-rich acidic domains, but lacks
most of the arginine/serine (SR)-rich domain that is
responsible for the regulation of RNA processing. .
Length = 89
Score = 33.8 bits (78), Expect = 0.013
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 8/58 (13%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ----AFVIFKEIASATNAL 67
+YV I + L F FG+I +I TL R FV ++ A A+
Sbjct: 5 IYVGKIPIDTTRSELRQRFQPFGEIEEI----TLHFRDDGDNYGFVTYRYACDAFRAI 58
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 33.3 bits (76), Expect = 0.013
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
LF+ NLP E +E + LF Q+ E ++ N FV +++ + A LH +K+
Sbjct: 3 LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN---YGFVHMDDKTAADEAIRNLHHYKL 59
Query: 234 TPTHAMKIS 242
H + I+
Sbjct: 60 ---HGVAIN 65
>gnl|CDD|241128 cd12684, RRM_cpo, RNA recognition motif in Drosophila couch potato
(cpo) coding RNA-binding protein and similar proteins.
This subfamily corresponds to the RRM of Cpo, an
RNA-binding protein encoded by Drosophila couch potato
(cpo) gene. Cpo contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). It may
control the processing of RNA molecules required for the
proper functioning of the peripheral nervous system
(PNS). .
Length = 83
Score = 33.9 bits (77), Expect = 0.013
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 8/80 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRL------VPNRHDIAFVEFENEMQSAAAKLA 227
LF++ LP + L +LF + G++ L + FV FE + AAK
Sbjct: 4 LFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSPVGFVTFETRAGAEAAKQD 63
Query: 228 LHGFKITPT--HAMKISFAK 245
L G + P +++ FAK
Sbjct: 64 LQGVRFDPDIPQTIRLEFAK 83
>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 = 33.7 bits (77), Expect = 0.014
Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 5/77 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YVT++ + L IF +G I+ L+ T RG AFV + + A A+ S+
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 71 QG--FPFYDKPMRIQYS 85
G P P+ ++Y+
Sbjct: 63 NGTIPPGSTMPLSVRYA 79
Score = 27.2 bits (60), Expect = 2.8
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
L++TNLP + +E L +F + + L+ ++ +AFV ++ ++ AA +L
Sbjct: 3 LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62
Query: 229 HGFKITPTHAMKIS 242
+G I P M +S
Sbjct: 63 NG-TIPPGSTMPLS 75
>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 = 33.4 bits (77), Expect = 0.014
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 14/69 (20%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTLKM--------RGQAFVIFKEIASATNALRSMQGFPFY 76
KK L +FS FGQ+ K++++ RG AFV F A NA+ +++ Y
Sbjct: 14 KKELRELFSPFGQV------KSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLY 67
Query: 77 DKPMRIQYS 85
+ + ++Y+
Sbjct: 68 GRHLVLEYA 76
Score = 33.0 bits (76), Expect = 0.017
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
L + N+P E ++ L LF+ F K VRL P + D AFVEF + ++ A AL
Sbjct: 3 LIVRNVPFEATKKELRELFSPFGQVKSVRL-PKKFDGSHRGFAFVEFVTKQEAQNAMEAL 61
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 35.9 bits (83), Expect = 0.015
Identities = 45/236 (19%), Positives = 90/236 (38%), Gaps = 35/236 (14%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRG--QAFVIFKEIASATNALRSMQGFPFYDK--PMRIQ 83
LY IF+ +G+++ IV T QA V F+ + SA +A ++ G Y+ ++I+
Sbjct: 113 LYQIFNPYGKVLRIV---TFTKNNVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIE 169
Query: 84 YSKTDS-DVISKIKGT-------------FMERPKKVRKQPAPVEDPAEAKKSKKKAAKE 129
Y+K +V + ++QPA + + ++
Sbjct: 170 YAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHG 229
Query: 130 QARLMQAQQQQM----QALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSE 185
A +M S +P +++ G P +L ++ L +E +
Sbjct: 230 GPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQE--K 287
Query: 186 MMLSMLFNQFPGF---KEVRLVPNRHDIAFVEFENEMQSAAA-----KLALHGFKI 233
+ LFN F + + V+ + N+ + A +E + Q+ A + L G +
Sbjct: 288 VNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPL 343
Score = 33.6 bits (77), Expect = 0.092
Identities = 40/229 (17%), Positives = 78/229 (34%), Gaps = 52/229 (22%)
Query: 27 SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
L+ +F +G + + +K K A + + A AL + G + KP+R+ SK
Sbjct: 292 RLFNLFCVYGNVERVKFMKNKK--ETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSK 349
Query: 87 TDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSV 146
+ + + K ++ R + +
Sbjct: 350 QQNVQPPRE-----------------GQLDDGLTSYKDYSSSRNHRFKKPGSANKNNI-- 390
Query: 147 QQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQ--FPGFKEVRLV 204
QPP+ L L+N+P SE L LF + K+ +
Sbjct: 391 ---------------------QPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFF 429
Query: 205 P---NRHDIAFVEFENEMQSAAAKLALHGFKITPTHA-----MKISFAK 245
P R + +E+E+ + A +AL+ ++ + +K+SF+
Sbjct: 430 PKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFST 478
Score = 28.6 bits (64), Expect = 3.6
Identities = 17/70 (24%), Positives = 26/70 (37%), Gaps = 10/70 (14%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY--DKPMRIQYS 85
L FG + ++ L + QA V F++ SA + P Y +P YS
Sbjct: 19 LVEALIPFGPVSYVMMLPG---KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS 75
Query: 86 -----KTDSD 90
K D +
Sbjct: 76 TSQEIKRDGN 85
>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1,
RRM2) in Arabidopsis thaliana CTC-interacting domain
protein CID8, CID9, CID10, CID11, CID12, CID 13 and
similar proteins. This subgroup corresponds to the RRM
domains found in A. thaliana CID8, CID9, CID10, CID11,
CID12, CID 13 and mainly their plant homologs. These
highly related RNA-binding proteins contain an
N-terminal PAM2 domain (PABP-interacting motif 2), two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a basic region that resembles a bipartite nuclear
localization signal. The biological role of this family
remains unclear.
Length = 77
Score = 33.5 bits (77), Expect = 0.015
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 175 FLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFENEMQSAAAKLALHGF 231
+ + SE L F+ VRL +R AFVEF + +SA + L L G
Sbjct: 4 HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFAD-AESALSALNLSG- 61
Query: 232 KITPTHAMKISFAK 245
+ H +++S +K
Sbjct: 62 TLLGGHPLRVSPSK 75
>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome
biogenesis protein 15 (Nop15p) and similar proteins.
This subgroup corresponds to the RRM of Nop15p, also
termed nucleolar protein 15, which is encoded by
YNL110C from Saccharomyces cerevisiae, and localizes to
the nucleoplasm and nucleolus. Nop15p has been
identified as a component of a pre-60S particle. It
interacts with RNA components of the early pre-60S
particles. Furthermore, Nop15p binds directly to a
pre-rRNA transcript in vitro and is required for
pre-rRNA processing. It functions as a ribosome
synthesis factor required for the 5' to 3' exonuclease
digestion that generates the 5' end of the major, short
form of the 5.8S rRNA as well as for processing of 27SB
to 7S pre-rRNA. Nop15p also play a specific role in
cell cycle progression. Nop15p contains an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 33.2 bits (76), Expect = 0.018
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 3/74 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VA--LKTLKMRGQAFVIFKEIASATNALRSM 70
+Y+ H+ L+K L FSQFG + ++ VA KT + F+ F A A +SM
Sbjct: 2 IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61
Query: 71 QGFPFYDKPMRIQY 84
+ K +++
Sbjct: 62 NNYLLMGKVLQVHV 75
Score = 27.1 bits (60), Expect = 2.7
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN------RHDIAFVEFENEMQSAAAKL 226
++++ +LP E L F+QF K VR+ + +H F++F N +A A
Sbjct: 1 VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKH-YGFIQFLNPEVAAIAAK 59
Query: 227 ALHGFKI 233
+++ + +
Sbjct: 60 SMNNYLL 66
>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 = 32.8 bits (75), Expect = 0.020
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ----AFVIFKEIASATNALRS 69
+YV ++ S +K L +F ++G+I DI LK R AFV F++ A +A+
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDI----ELKNRRGLVPFAFVRFEDPRDAEDAVFG 57
Query: 70 MQGFPFYDKPMRIQY 84
G+ F +R+++
Sbjct: 58 RNGYDFGQCRLRVEF 72
Score = 29.0 bits (65), Expect = 0.54
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI--AFVEFENEMQSAAAKLALHGF 231
+++ NLP + E L LF ++ +++ L R + AFV FE+ + A +G+
Sbjct: 2 IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNGY 61
>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 = 32.9 bits (76), Expect = 0.021
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 21 STDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
S D K+LY FS FG I+ + + +G FV F+ +A A+ + G DK
Sbjct: 13 SID-NKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDK 71
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 35.6 bits (83), Expect = 0.022
Identities = 15/74 (20%), Positives = 19/74 (25%), Gaps = 4/74 (5%)
Query: 102 RPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQP-PVSQPAPPAPM 160
P P P P A + A A Q P PA P P
Sbjct: 360 HPAAP--LPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPE 417
Query: 161 ATAGVPEQPPNQIL 174
T+ + Q+
Sbjct: 418 TTSQLL-AARQQLQ 430
Score = 27.1 bits (61), Expect = 9.1
Identities = 10/55 (18%), Positives = 20/55 (36%)
Query: 109 QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATA 163
P A + + ++L+ A+QQ +A + S+PA +
Sbjct: 398 AVPPPPASAPQQAPAVPLPETTSQLLAARQQLQRAQGATKAKKSEPAAASRARPV 452
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 32.6 bits (75), Expect = 0.022
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 6/64 (9%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV----PNRHDIAFVEFENEMQSAAAKLALH 229
L + +LP E SE L F G VR++ ++ AF F+NE ++ A LH
Sbjct: 2 LLVRHLPPELSEDDKEDLLKHF-GASSVRVMSRRGKLKN-TAFATFDNEQAASQALSRLH 59
Query: 230 GFKI 233
KI
Sbjct: 60 QLKI 63
>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 = 32.7 bits (74), Expect = 0.023
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
+IL++ NL ETSE + F QF PG V V D AFV F + + A L+G
Sbjct: 2 KILYVRNLMIETSEDTIKKTFGQFNPGC--VERVKKIRDYAFVHFTSREDAVHAMNNLNG 59
Query: 231 FKITPTHAMKISFAK 245
++ + ++++ AK
Sbjct: 60 TELEGS-CIEVTLAK 73
>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM2 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 71
Score = 32.6 bits (75), Expect = 0.024
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALR 68
V+V ++ ++ L FSQFG++ D+ K R AFV F + A +
Sbjct: 3 VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF--RAFAFVTFADPEVAQSLCG 55
>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in
serine/arginine-rich splicing factor 1 (SRSF1) and
similar proteins. This subgroup corresponds to the
RRM1 in three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 1 (SRSF1 or
ASF-1), serine/arginine-rich splicing factor 9 (SRSF9
or SRp30C), and plant pre-mRNA-splicing factor SF2
(SR1). SRSF1 is a shuttling SR protein involved in
constitutive and alternative splicing,
nonsense-mediated mRNA decay (NMD), mRNA export and
translation. It also functions as a splicing-factor
oncoprotein that regulates apoptosis and proliferation
to promote mammary epithelial cell transformation.
SRSF9 has been implicated in the activity of many
elements that control splice site selection, the
alternative splicing of the glucocorticoid receptor
beta in neutrophils and in the gonadotropin-releasing
hormone pre-mRNA. It can also interact with other
proteins implicated in alternative splicing, including
YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both,
SRSF1 and SRSF9, contain two N-terminal RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), and a C-terminal
RS domains rich in serine-arginine dipeptides. In
contrast, SF2 contains two N-terminal RRMs and a
C-terminal PSK domain rich in proline, serine and
lysine residues. .
Length = 72
Score = 32.4 bits (74), Expect = 0.028
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR----GQAFVIFKEIASATNALRS 69
+YV ++ ++ + +F ++G I I LK R AFV F++ A +A+R
Sbjct: 2 IYVGNLPGDIRERDIEDLFYKYGPIKAI----DLKNRRRGPPFAFVEFEDPRDAEDAVRG 57
Query: 70 MQGFPFYDKPMRIQY 84
G+ F +R+++
Sbjct: 58 RDGYDFDGYRLRVEF 72
Score = 29.7 bits (67), Expect = 0.28
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD--IAFVEFENE 218
+++ NLP + E + LF ++ K + L R AFVEFE+
Sbjct: 2 IYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDP 48
>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 = 32.4 bits (74), Expect = 0.028
Identities = 18/70 (25%), Positives = 38/70 (54%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VYV ++ ++ + +F ++G I+DI + G AF+ F++ A +A+R G+
Sbjct: 2 VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDGY 61
Query: 74 PFYDKPMRIQ 83
F + +R++
Sbjct: 62 DFDGQRLRVE 71
>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 = 32.8 bits (75), Expect = 0.029
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV----PNRHDIAFVEFENEMQSAAAKLALH 229
LF+ NL +E L F ++ ++V + + AFV+F N + AK+A+
Sbjct: 5 LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAMS 64
Query: 230 GFKITPTHAMKISFAK 245
G + + +KI + K
Sbjct: 65 G-QYIGRNQIKIGYGK 79
Score = 28.5 bits (64), Expect = 0.70
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 26 KSLYAIFSQFGQIMDIVALKTLKMRGQ----AFVIFKEIASATNALRSMQGFPFYDKPMR 81
+ L F ++G + D+ + RGQ AFV F + A A +M G ++
Sbjct: 17 EELRRAFERYGVVEDVDIKRP--PRGQGNAYAFVKFLNLDMAHRAKVAMSGQYIGRNQIK 74
Query: 82 IQYSK 86
I Y K
Sbjct: 75 IGYGK 79
>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 = 32.8 bits (75), Expect = 0.030
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFENE 218
P + LF+ NLP + +E L F +F EVR+ + FV F++
Sbjct: 1 PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDP 55
>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and
similar proteins. This subgroup corresponds to the RRM1
of nucleolysin TIAR, also termed TIA-1-related protein,
and a cytotoxic granule-associated RNA-binding protein
that shows high sequence similarity with 40-kDa isoform
of T-cell-restricted intracellular antigen-1
(p40-TIA-1). TIAR is mainly localized in the nucleus of
hematopoietic and nonhematopoietic cells. It is
translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. TIAR
possesses nucleolytic activity against cytolytic
lymphocyte (CTL) target cells. It can trigger DNA
fragmentation in permeabilized thymocytes, and thus may
function as an effector responsible for inducing
apoptosis. TIAR is composed of three N-terminal highly
homologous RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glutamine-rich C-terminal auxiliary
domain containing a lysosome-targeting motif. It
interacts with RNAs containing short stretches of
uridylates and its RRM2 can mediate the specific binding
to uridylate-rich RNAs. .
Length = 81
Score = 32.8 bits (74), Expect = 0.030
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVP---NRHDIAFVEFENEMQSAAAKLALHG 230
L++ NL + +E+++ LF+Q K +++ + FVEF +AAA A++G
Sbjct: 2 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 61
Query: 231 FKI 233
KI
Sbjct: 62 RKI 64
>gnl|CDD|240289 PTZ00144, PTZ00144, dihydrolipoamide succinyltransferase;
Provisional.
Length = 418
Score = 35.0 bits (81), Expect = 0.031
Identities = 17/81 (20%), Positives = 27/81 (33%), Gaps = 7/81 (8%)
Query: 115 DPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPA-----PMATAGVPEQP 169
D A + AA A+ + ++ +A + P + P P A + P
Sbjct: 119 DTGGAPPAAAPAAAAAAKAEKTTPEKPKAAAPTPEPPAASKPTPPAAAKPPEPAPAAKPP 178
Query: 170 PNQILFLTNLPEETSEMMLSM 190
P + P ET M M
Sbjct: 179 PTPV--ARADPRETRVPMSRM 197
>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast
negative growth regulatory protein NGR1, yeast protein
NAM8 and similar proteins. This subgroup corresponds
to the RRM2 of NGR1 and NAM8. NGR1, also termed
RNA-binding protein RBP1, is a putative
glucose-repressible protein that binds both, RNA and
single-stranded DNA (ssDNA), in yeast. It may function
in regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a glutamine-rich stretch that may
be involved in transcriptional activity. In addition,
NGR1 has an asparagine-rich region near the carboxyl
terminus which also harbors a methionine-rich region.
The family also includes protein NAM8, which is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. Like
NGR1, NAM8 contains two RRMs. .
Length = 80
Score = 32.5 bits (74), Expect = 0.032
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 50 RGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
RG FV F + AL MQG +PMRI +
Sbjct: 44 RGYGFVRFSDENDQQRALIEMQGVYCGGRPMRISTA 79
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 35.0 bits (81), Expect = 0.038
Identities = 16/65 (24%), Positives = 19/65 (29%), Gaps = 3/65 (4%)
Query: 109 QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQ---MQALSVQQPPVSQPAPPAPMATAGV 165
PAP P + A Q A + + PAPPA A A
Sbjct: 434 APAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAA 493
Query: 166 PEQPP 170
P P
Sbjct: 494 PAAPA 498
Score = 28.0 bits (63), Expect = 5.0
Identities = 15/72 (20%), Positives = 20/72 (27%)
Query: 103 PKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT 162
P P P P+ AA E A + + PA PA
Sbjct: 449 PAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADD 508
Query: 163 AGVPEQPPNQIL 174
A + +IL
Sbjct: 509 AATLRERWPEIL 520
>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 = 32.1 bits (73), Expect = 0.039
Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
V+V +I ++ L IFS+ G ++ + +T K +G F +K+ +A +A+R++
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 71 QGFPFYDKPMRI 82
G+ + +R+
Sbjct: 61 NGYELNGRQLRV 72
Score = 28.2 bits (63), Expect = 0.88
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+F+ N+P E +E L +F++ RLV +R F E++++ + +A L
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60
Query: 229 HGFKI 233
+G+++
Sbjct: 61 NGYEL 65
>gnl|CDD|241134 cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM3 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 = 97
Score = 32.5 bits (74), Expect = 0.039
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 13/94 (13%)
Query: 2 NIILAHICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIA 61
N++LA I N Y + L+ +FS FG + I A+ QA + + ++
Sbjct: 2 NVLLASI--ENMQYAVTVDV------LHTVFSAFGFVQKI-AIFEKNGGFQALIQYPDVP 52
Query: 62 SATNALRSMQGFPFYDK---PMRIQYSK-TDSDV 91
+A NA +++G YD + + YS+ TD +V
Sbjct: 53 TAVNAKEALEGHCIYDGGYCKLHLSYSRHTDLNV 86
>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 = 32.6 bits (75), Expect = 0.039
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 20/75 (26%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDI----VALKTLKMRG----------------Q 52
V+V ++ T KK L +F QFG I + V +K K+
Sbjct: 2 TVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVN 61
Query: 53 AFVIFKEIASATNAL 67
A+V+FKE SA AL
Sbjct: 62 AYVVFKEEESAEKAL 76
>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 = 0.042
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 6/43 (13%)
Query: 31 IFSQFGQIMDIVALK------TLKMRGQAFVIFKEIASATNAL 67
+ + FG++ I ++ + K +G AFV F+EI ATNAL
Sbjct: 15 LRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 34.7 bits (80), Expect = 0.043
Identities = 19/77 (24%), Positives = 26/77 (33%), Gaps = 5/77 (6%)
Query: 100 MERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPA---- 155
+ + AP P ++K + E+ Q+QQ L Q P P
Sbjct: 128 TAPKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLP-QPPQQVLPQGMPP 186
Query: 156 PPAPMATAGVPEQPPNQ 172
A G PEQPP
Sbjct: 187 RQAAFPQQGPPEQPPGY 203
Score = 33.6 bits (77), Expect = 0.096
Identities = 10/46 (21%), Positives = 10/46 (21%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLP 180
Q Q QQ P A P P P P
Sbjct: 254 QMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPP 299
Score = 29.0 bits (65), Expect = 2.9
Identities = 12/50 (24%), Positives = 14/50 (28%), Gaps = 5/50 (10%)
Query: 134 MQAQQQQMQALSVQQPPV-----SQPAPPAPMATAGVPEQPPNQILFLTN 178
QQQQ QPP P P P Q P + +
Sbjct: 261 QPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQ 310
Score = 27.8 bits (62), Expect = 6.1
Identities = 14/63 (22%), Positives = 16/63 (25%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQ 194
Q QP PAP A +P Q P Q L + Q
Sbjct: 202 GYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQ 261
Query: 195 FPG 197
P
Sbjct: 262 PPQ 264
>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 = 32.2 bits (73), Expect = 0.044
Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 5/83 (6%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLV-PNRHD---IAFVEFENEMQSA 222
+Q + LF+ NL SE+ L F+++ +EV + P R AF++F+N +
Sbjct: 4 DQRATRNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAH 63
Query: 223 AAKLALHGFKITPTHAMKISFAK 245
AK+A+ G ++ + +KI + K
Sbjct: 64 RAKVAMSG-RVIGRNPIKIGYGK 85
Score = 28.8 bits (64), Expect = 0.70
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQA--FVIFKEIASATNALRSMQGFPFY 76
+S +L+++ F ++G I ++V + + +G A F+ F+ + A A +M G
Sbjct: 20 VSEVELRRA----FDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAMSGRVIG 75
Query: 77 DKPMRIQYSK 86
P++I Y K
Sbjct: 76 RNPIKIGYGK 85
>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 = 31.6 bits (72), Expect = 0.045
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
K+ L+ IFS +G++ IV LK FV F S NA+ QG + + ++
Sbjct: 14 KEDLFRIFSTYGELAQIV-LK----NAYGFVQFDSPESCANAINCEQGKMIRGRKLHLEV 68
Query: 85 SKT 87
SK
Sbjct: 69 SKP 71
>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 = 31.7 bits (72), Expect = 0.047
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
L + NL S L +F + KE+R P + + FVEF + +A A A++G +I
Sbjct: 4 LVIFNLDPTVSSETLRSIFQVYGDVKELRETPCKREQRFVEFFDVRDAAKALRAMNGKEI 63
Score = 29.0 bits (65), Expect = 0.40
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 27 SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
+L +IF +G + ++ +T R Q FV F ++ A ALR+M G KP+ I+
Sbjct: 17 TLRSIFQVYGDVKEL--RETPCKREQRFVEFFDVRDAAKALRAMNGKEISGKPVVIE 71
>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein R (hnRNP R) and similar
proteins. This subfamily corresponds to the RRM2 in
hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF),
and dead end protein homolog 1 (DND1). hnRNP R is a
ubiquitously expressed nuclear RNA-binding protein that
specifically bind mRNAs with a preference for poly(U)
stretches. It has been implicated in mRNA processing and
mRNA transport, and also acts as a regulator to modify
binding to ribosomes and RNA translation. hnRNP Q is
also a ubiquitously expressed nuclear RNA-binding
protein. It has been identified as a component of the
spliceosome complex, as well as a component of the
apobec-1 editosome, and has been implicated in the
regulation of specific mRNA transport. ACF is an
RNA-binding subunit of a core complex that interacts
with apoB mRNA to facilitate C to U RNA editing. It may
also act as an apoB mRNA recognition factor and
chaperone and play a key role in cell growth and
differentiation. DND1 is essential for maintaining
viable germ cells in vertebrates. It interacts with the
3'-untranslated region (3'-UTR) of multiple messenger
RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated
repression of mRNA. This family also includes two
functionally unknown RNA-binding proteins, RBM46 and
RBM47. All members in this family, except for DND1,
contain three conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains); DND1 harbors only two RRMs.
.
Length = 82
Score = 31.9 bits (73), Expect = 0.047
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 171 NQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHD------IAFVEFENEMQSAA 223
N LF+ +P+ T E +L G +V + + D AFVE+E+ +A
Sbjct: 1 NCRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAM 60
Query: 224 AKLAL 228
A+ L
Sbjct: 61 ARRKL 65
>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
3 in multiple RNA-binding domain-containing protein 1
(MRD1). This subfamily corresponds to the RRM4 of RBM19
and the RRM3 of MRD1. RBM19, also termed RNA-binding
domain-1 (RBD-1), is a nucleolar protein conserved in
eukaryotes involved in ribosome biogenesis by processing
rRNA and is essential for preimplantation development.
It has a unique domain organization containing 6
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). MRD1 is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well conserved in
yeast and its homologues exist in all eukaryotes. MRD1
is present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 72
Score = 31.8 bits (73), Expect = 0.053
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFEN--EMQSAAAKLALHG 230
++ + NLP T+E L LF +F + L P+R IA VEF + + A LA
Sbjct: 2 VILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSR-TIALVEFLEPSDARKAFKSLAYKR 60
Query: 231 FKITP 235
FK P
Sbjct: 61 FKHVP 65
>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin.
This subfamily corresponds to the RRM2 of ubiquitously
expressed protein nucleolin, also termed protein C23, a
multifunctional major nucleolar phosphoprotein that has
been implicated in various metabolic processes, such as
ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines.RRM2, together with RRM1, binds
specifically to RNA stem-loops containing the sequence
(U/G)CCCG(A/G) in the loop. .
Length = 77
Score = 31.7 bits (72), Expect = 0.056
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
LF+ NLP + L +F ++RL + IA++EF+ E ++ A
Sbjct: 6 LFVKNLPYNITVDELKEVFEDA---VDIRLPSGKDGSSKGIAYIEFKTEAEAEKALEEKQ 62
Query: 230 GFKI 233
G ++
Sbjct: 63 GAEV 66
Score = 26.3 bits (58), Expect = 4.5
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
++V ++ L +F I + + K +G A++ FK A A AL QG
Sbjct: 6 LFVKNLPYNITVDELKEVFEDAVDIR-LPSGKDGSSKGIAYIEFKTEAEAEKALEEKQG 63
>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 = 31.6 bits (72), Expect = 0.059
Identities = 12/71 (16%), Positives = 30/71 (42%), Gaps = 1/71 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
VY ++ + +F G + + L ++ AF+ F+ + +A A+ ++ G
Sbjct: 2 VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR-TVQPHAFITFENLEAAQLAIETLNGA 60
Query: 74 PFYDKPMRIQY 84
+++Q
Sbjct: 61 SVDGNCIKVQR 71
>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 = 31.4 bits (72), Expect = 0.063
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
VYV ++ ++ L+ +F Q G ++++ K T +G FV F A A++ M
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60
Query: 71 QGFPFYDKPMRI 82
Y KP+R+
Sbjct: 61 NMIKLYGKPIRV 72
Score = 25.6 bits (57), Expect = 6.9
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRL----VPNRHD-IAFVEFENE 218
+++ NL E+ +E +L LF Q V + V H FVEF +E
Sbjct: 1 VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSE 50
>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 = 31.5 bits (71), Expect = 0.063
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF 231
++LF+ NL +E +L F QF + V+ + D AF+ F+ + A ++G
Sbjct: 2 KVLFVRNLANTVTEEILEKAFGQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGK 58
Query: 232 KITPTHAMKISFAK 245
++ + ++I FAK
Sbjct: 59 ELEGEN-IEIVFAK 71
Score = 28.8 bits (64), Expect = 0.53
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
++V ++++T ++ L F QFG++ + K++ AF+ F E A A+ M G
Sbjct: 4 LFVRNLANTVTEEILEKAFGQFGKLE-----RVKKLKDYAFIHFDERDGAVKAMEEMNGK 58
Query: 74 PFYDKPMRIQYSK 86
+ + I ++K
Sbjct: 59 ELEGENIEIVFAK 71
>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 = 31.6 bits (72), Expect = 0.063
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
S+Y F ++G+I + + + +G +V F +A AL ++ G +P+R+
Sbjct: 14 SIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPVRL 72
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0 is a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. hnRNP A/B has also been
identified as an APOBEC1-binding protein that interacts
with apolipoprotein B (apoB) mRNA transcripts around
the editing site and thus plays an important role in
apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All members in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 74
Score = 31.4 bits (71), Expect = 0.065
Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 18/83 (21%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKEIASATNALRS 69
++V +S KK L FS+FG+++D +K T + RG FV+FK+ AS
Sbjct: 1 MFVGGLSWDTTKKDLKEYFSKFGEVVD-CTIKIDPVTGRSRGFGFVLFKDAASV------ 53
Query: 70 MQGFPFYDKPMRIQYSKTDSDVI 92
+K + + K D VI
Sbjct: 54 -------EKVLDQKEHKLDGRVI 69
>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 = 31.5 bits (72), Expect = 0.066
Identities = 21/62 (33%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ NLP T+E L LF F EV L ++ AFV F + A L
Sbjct: 2 LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61
Query: 229 HG 230
G
Sbjct: 62 DG 63
>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 = 31.5 bits (72), Expect = 0.067
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEF------ENEMQSAAAKLA 227
L++ L E +E L F QF + + +VP + AFV F E + KL
Sbjct: 4 LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQ-CAFVTFTTREAAEKAAERLFNKLI 62
Query: 228 LHGFKIT 234
++G ++
Sbjct: 63 INGRRLK 69
>gnl|CDD|240865 cd12419, RRM_Ssp2_like, RNA recognition motif in yeast
sporulation-specific protein 2 (Ssp2) and similar
protein. This subfamily corresponds to the RRM of the
lineage specific yeast sporulation-specific protein 2
(Ssp2) and similar proteins. Ssp2 is encoded by a
sporulation-specific gene necessary for outer spore
wall assembly in the yeast Saccharomyces cerevisiae. It
localizes to the spore wall and may play an important
role after meiosis II and during spore wall formation.
Ssp2 contains one RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 80
Score = 31.6 bits (72), Expect = 0.068
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 18 HISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ--GFPF 75
+ S + L F+ FG+I+DI + + K+ + F +I SA A +++ G
Sbjct: 1 VLPSDFDVEELKDDFTVFGEIVDISPIISRKL--CVSIFFADIRSAIRAKETLEDKGSSL 58
Query: 76 YDK 78
+K
Sbjct: 59 NNK 61
>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 = 31.7 bits (72), Expect = 0.071
Identities = 17/49 (34%), Positives = 30/49 (61%), Gaps = 3/49 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKE 59
++V +S +++L FSQ+G+++D V +K T + RG FV FK+
Sbjct: 2 LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50
>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 = 31.3 bits (71), Expect = 0.074
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
+YVT + + L F ++G+++ DI +T + R AFV ++ A +A M
Sbjct: 2 LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEMH 61
Query: 72 GFPFYDKP--MRIQYSK 86
G F D + +Q++K
Sbjct: 62 GRRFPDTGDTLHVQWAK 78
>gnl|CDD|241145 cd12701, RRM4_PTBP1, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM4 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence shows that
the RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 76
Score = 31.2 bits (70), Expect = 0.077
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPG-FKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
L L+N+P SE L MLF+ G K + +A ++ + ++ + + LH
Sbjct: 2 LHLSNIPPSVSEEDLKMLFSSNGGTVKGFKFFQKDRKMALIQMGSVEEAIQSLIDLHNHD 61
Query: 233 ITPTHAMKISFAK 245
+ H +++SF+K
Sbjct: 62 LGENHHLRVSFSK 74
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 33.9 bits (78), Expect = 0.077
Identities = 14/62 (22%), Positives = 17/62 (27%)
Query: 111 APVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPP 170
A PAE K + A A AQ A + + P A P P
Sbjct: 370 AEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAP 429
Query: 171 NQ 172
Sbjct: 430 AA 431
Score = 30.8 bits (70), Expect = 0.60
Identities = 18/66 (27%), Positives = 20/66 (30%), Gaps = 1/66 (1%)
Query: 106 VRKQPAPVEDPA-EAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG 164
PAPV PA A + AA L A Q +V P P P A
Sbjct: 419 AAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPA 478
Query: 165 VPEQPP 170
P
Sbjct: 479 PAAAPA 484
Score = 28.9 bits (65), Expect = 2.7
Identities = 18/64 (28%), Positives = 21/64 (32%), Gaps = 2/64 (3%)
Query: 108 KQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE 167
K PA E A A +AA A A + P + PAP A A A
Sbjct: 379 KTPARPEAAAPAAAPVAQAA--AAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAA 436
Query: 168 QPPN 171
P
Sbjct: 437 APAA 440
>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 = 30.9 bits (70), Expect = 0.079
Identities = 16/72 (22%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
++V ++ ++ L A+F +G ++ A+ MR AFV + A+A A+ + G
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLS-CAV----MRQFAFVHLRGEAAADRAIEELNGR 57
Query: 74 PFYDKPMRIQYS 85
+ + + +++S
Sbjct: 58 ELHGRKLVVEHS 69
Score = 28.2 bits (63), Expect = 0.93
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
+F+ N+ E+TS+ L LF + ++ AFV E + A L+G
Sbjct: 3 IFVGNVDEDTSQEELRALFEAYGAVLSCAVM---RQFAFVHLRGEAAADRAIEELNG 56
>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 = 31.5 bits (72), Expect = 0.087
Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENE 218
PP +LF+ L T++ L ++F++F K ++ ++ AF+EFE +
Sbjct: 1 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETK 55
Score = 27.2 bits (61), Expect = 2.6
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 26 KSLYAIFSQFGQIM--DIVA-LKTLKMRGQAFVIFKEIASATNALRSMQG 72
+ L IFS+FG+I +++ KT AF+ F+ A M
Sbjct: 18 EDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDN 67
>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1
isoform p40 (p40-TIA-1) and similar proteins. This
subgroup corresponds to the RRM1 of TIA-1, the 40-kDa
isoform of T-cell-restricted intracellular antigen-1
(TIA-1) and a cytotoxic granule-associated RNA-binding
protein mainly found in the granules of cytotoxic
lymphocytes. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis, and functions as the granule
component responsible for inducing apoptosis in
cytolytic lymphocyte (CTL) targets. It is composed of
three N-terminal highly homologous RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 interacts with RNAs
containing short stretches of uridylates and its RRM2
can mediate the specific binding to uridylate-rich RNAs.
.
Length = 74
Score = 31.2 bits (70), Expect = 0.092
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 3/63 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPN---RHDIAFVEFENEMQSAAAKLALHG 230
L++ NL + +E ++ LF+Q K +++ + FVEF +AA+ A++G
Sbjct: 2 LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASLAAMNG 61
Query: 231 FKI 233
KI
Sbjct: 62 RKI 64
>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 = 30.8 bits (69), Expect = 0.10
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
++V +ISS+ + L A F ++G ++ DIV + AFV + A A+R +
Sbjct: 3 LHVGNISSSCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLD 55
Query: 72 GFPFYDKPMRIQ 83
F K M +Q
Sbjct: 56 NTEFQGKRMHVQ 67
>gnl|CDD|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis
thaliana arginine/serine-rich-splicing factor RSp31 and
similar proteins from plants. This subfamily
corresponds to the RRM1in a family that represents a
novel group of arginine/serine (RS) or serine/arginine
(SR) splicing factors existing in plants, such as A.
thaliana RSp31, RSp35, RSp41 and similar proteins. Like
vertebrate RS splicing factors, these proteins function
as plant splicing factors and play crucial roles in
constitutive and alternative splicing in plants. They
all contain two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), at their N-terminus, and
an RS domain at their C-terminus.
Length = 72
Score = 30.9 bits (70), Expect = 0.10
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 13/77 (16%)
Query: 12 NFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
NF Y S ++++ +F ++G++ D V +K+ G AFV ++ A +A+R +
Sbjct: 7 NFEYDARQS--EIER----LFGKYGRV-DRVDMKS----GFAFVYMEDERDAEDAIRGLD 55
Query: 72 GFPF--YDKPMRIQYSK 86
F F + +R++++K
Sbjct: 56 NFEFGRQRRRLRVEWAK 72
>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 = 30.7 bits (69), Expect = 0.12
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 11/61 (18%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKM-------RGQAFVIFKEIASATNA 66
++V +S KK L F++FG++ D T+KM RG F++FK+ +S
Sbjct: 2 MFVGGLSWDTSKKDLKDYFTKFGEVTDC----TIKMDPNTGRSRGFGFILFKDASSVEKV 57
Query: 67 L 67
L
Sbjct: 58 L 58
>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 = 31.2 bits (70), Expect = 0.12
Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
+IL++ NL T+E + FN PG V V D AFV F N + A AL+G
Sbjct: 9 KILYVRNLMLSTTEETIEKEFNSIKPG--AVERVKKIRDYAFVHFSNREDAVDAMNALNG 66
Query: 231 FKITPTHAMKISFAK 245
K+ ++++ AK
Sbjct: 67 -KVIDGSPIEVTLAK 80
>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 = 30.8 bits (69), Expect = 0.12
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
V+V +S + A F+ FG+I D +K T K +G FV F A NA++ M
Sbjct: 4 VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63
Query: 71 QG 72
G
Sbjct: 64 GG 65
>gnl|CDD|241133 cd12689, RRM1_hnRNPL_like, RNA recognition motif 1 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM1 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 80
Score = 30.8 bits (70), Expect = 0.12
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 18 HISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY- 76
++ DL ++L S+FG I + + + QA V F++I+ A + Q P Y
Sbjct: 13 GVTEADLVEAL----SEFGPISYVTMMPKKR---QALVEFEDISDAKACVNHAQQNPVYI 65
Query: 77 -DKPMRIQYSKT 87
+ YS +
Sbjct: 66 AGRQAYFNYSTS 77
Score = 29.3 bits (66), Expect = 0.44
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFEN 217
P+ ++ + LP+ +E L ++F V ++P + A VEFE+
Sbjct: 1 PSPVVHVRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQ-ALVEFED 47
>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing
factor SLT11 and similar proteins. This subfamily
corresponds to the RRM of SLT11, also known as
extracellular mutant protein 2, or synthetic lethality
with U2 protein 11, and is a splicing factor required
for spliceosome assembly in yeast. It contains a
conserved RNA recognition motif (RRM), also known as RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
SLT11 can facilitate the cooperative formation of U2/U6
helix II in association with stem II in the yeast
spliceosome by utilizing its RNA-annealing and -binding
activities. .
Length = 86
Score = 30.8 bits (70), Expect = 0.13
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 3/70 (4%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEM--QSAAAKLALHGF 231
FL + ++ E + F QF K V +V +R FV FE + AA ++ +G
Sbjct: 5 FFLFGVEDDLPEYKIRDYFEQFGKSKSV-IVNHRAKCGFVRFETREAAEKFAAAISENGL 63
Query: 232 KITPTHAMKI 241
+ +
Sbjct: 64 NAGLSRGGLL 73
>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 = 30.6 bits (70), Expect = 0.14
Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 18/73 (24%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR--------GQAFVIFKEIASATNALRSM 70
++ DL++ +F + G+ +K +K+ G A V+F++ A A++
Sbjct: 12 VTEEDLEE----LFGRVGE------VKKVKINYDRSGRSEGTADVVFEKREDAERAIKQF 61
Query: 71 QGFPFYDKPMRIQ 83
G +PM+++
Sbjct: 62 NGVLLDGQPMQVE 74
Score = 27.2 bits (61), Expect = 2.4
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
L ++NL + +E L LF + K+V++ +R A V FE + A +
Sbjct: 3 LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62
Query: 230 GFKI 233
G +
Sbjct: 63 GVLL 66
>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila
melanogaster Bruno protein and similar proteins. This
subgroup corresponds to the RRM3 of Bruno protein, a
Drosophila RNA recognition motif (RRM)-containing
protein that plays a central role in regulation of Oskar
(Osk) expression. It mediates repression by binding to
regulatory Bruno response elements (BREs) in the Osk
mRNA 3' UTR. The full-length Bruno protein contains
three RRMs, two located in the N-terminal half of the
protein and the third near the C-terminus, separated by
a linker region. .
Length = 79
Score = 30.7 bits (69), Expect = 0.14
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAA 223
P LF+ +LP+E ++ L+ F F ++ ++ FV ++N + A
Sbjct: 2 PEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQA 61
Query: 224 AKLALHGFKI 233
A A++GF+I
Sbjct: 62 AIQAMNGFQI 71
>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP
Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6
and similar proteins. This subfamily corresponds to
the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of
which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that display dual nuclear and cytoplasmic
localizations and have been implicated in the
regulation of pre-mRNA splicing and in the control of
mRNA translation and deadenylation. CELF-3, expressed
in brain and testis only, is also known as bruno-like
protein 1 (BRUNOL-1), or CAG repeat protein 4, or
CUG-BP- and ETR-3-like factor 3, or embryonic lethal
abnormal vision (ELAV)-type RNA-binding protein 1
(ETR-1), or expanded repeat domain protein CAG/CTG 4,
or trinucleotide repeat-containing gene 4 protein
(TNRC4). It plays an important role in the pathogenesis
of tauopathies. CELF-3 contains three highly conserved
RNA recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the
protein.The effect of CELF-3 on tau splicing is
mediated mainly by the RNA-binding activity of RRM2.
The divergent linker region might mediate the
interaction of CELF-3 with other proteins regulating
its activity or involved in target recognition. CELF-4,
highly expressed throughout the brain and in glandular
tissues, moderately expressed in heart, skeletal
muscle, and liver, is also known as bruno-like protein
4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like
CELF-3, CELF-4 also contain three highly conserved
RRMs. The splicing activation or repression activity of
CELF-4 on some specific substrates is mediated by its
RRM1/RRM2. On the other hand, both RRM1 and RRM2 of
CELF-4 can activate cardiac troponin T (cTNT) exon 5
inclusion. CELF-5, expressed in brain, is also known as
bruno-like protein 5 (BRUNOL-5), or CUG-BP- and
ETR-3-like factor 5. Although its biological role
remains unclear, CELF-5 shares same domain architecture
with CELF-3. CELF-6, strongly expressed in kidney,
brain, and testis, is also known as bruno-like protein
6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It
activates exon inclusion of a cardiac troponin T
minigene in transient transfection assays in an
muscle-specific splicing enhancer (MSE)-dependent
manner and can activate inclusion via multiple copies
of a single element, MSE2. CELF-6 also promotes
skipping of exon 11 of insulin receptor, a known target
of CELF activity that is expressed in kidney. In
additiona to three highly conserved RRMs, CELF-6 also
possesses numerous potential phosphorylation sites, a
potential nuclear localization signal (NLS) at the C
terminus, and an alanine-rich region within the
divergent linker region. .
Length = 87
Score = 30.8 bits (70), Expect = 0.14
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 26 KSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASA---TNALRSMQGFPFYDKP 79
K L +F QFG+I ++ LK T +G AF+ + SA +AL + P ++P
Sbjct: 20 KDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSALHEQKTLPGMNRP 79
Query: 80 MRIQ 83
++++
Sbjct: 80 IQVK 83
Score = 26.6 bits (59), Expect = 4.5
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ +P E L LF QF E+ ++ +++ AF+ + + A+ AL
Sbjct: 8 LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67
Query: 229 HGFKITP 235
H K P
Sbjct: 68 HEQKTLP 74
>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 = 30.8 bits (69), Expect = 0.14
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL---KMRGQAFVIFKEIASATNALRSM 70
V+V +S + + + F+ FG+I D +K + K +G FV F A NA+ M
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63
Query: 71 QG 72
G
Sbjct: 64 GG 65
>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 = 30.3 bits (69), Expect = 0.14
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNAL 67
TN VY+ + + L + FG+I+ I+ KT K +G FV F +A A+
Sbjct: 1 TN-VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAI 59
Query: 68 RSMQG 72
+ G
Sbjct: 60 EGLNG 64
>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 = 30.7 bits (69), Expect = 0.15
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T +K L +FSQ+G+I+ L+ T RG F+ F + A A++ +
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 71 QG 72
G
Sbjct: 63 NG 64
Score = 26.1 bits (57), Expect = 5.4
Identities = 14/64 (21%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
L+++ LP+ ++ L LF+Q+ R++ ++ + F+ F+ +++ A L
Sbjct: 3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62
Query: 229 HGFK 232
+G K
Sbjct: 63 NGQK 66
>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 = 30.3 bits (69), Expect = 0.15
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 14/71 (19%)
Query: 19 ISSTDLKKSLYAIFSQFGQI------MDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
+S D+K+ +F++FG + D ++ + G A V+F+ A A A++ G
Sbjct: 12 VSDDDIKE----LFAEFGALKKAAVHYD----RSGRSLGTADVVFERRADALKAMKQYNG 63
Query: 73 FPFYDKPMRIQ 83
P +PM+IQ
Sbjct: 64 VPLDGRPMKIQ 74
>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 = 30.3 bits (68), Expect = 0.15
Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 5/50 (10%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK----TLKMRGQAFVIFKE 59
+++ +S KK L FS+FG+++D LK T + RG FV+FKE
Sbjct: 1 MFIGGLSWDTTKKDLKDYFSKFGEVVD-CTLKLDPITGRSRGFGFVLFKE 49
>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 = 30.6 bits (70), Expect = 0.15
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 211 AFVEFENEMQSAAAKLALHG 230
FVEF + + A+LAL G
Sbjct: 59 VFVEFADVEDAQKAQLALAG 78
>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 = 30.6 bits (70), Expect = 0.16
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 11 TNFVYVTHISS--TDLKKSLYAIFSQFGQIMDIVALK--TLKMRGQAFVIFKEIASATNA 66
TN VYV ++ D K L +F ++G+I +K K +G FV F+ +A A
Sbjct: 2 TN-VYVKNLGEDMDDEK--LKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKA 58
Query: 67 LRSMQGFPFYDKPM 80
+ + G K +
Sbjct: 59 VEELNGKEVNGKKL 72
Score = 27.2 bits (61), Expect = 2.6
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 4/61 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLALH 229
+++ NL E+ + L LF ++ +++ + FV FEN + A L+
Sbjct: 4 VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63
Query: 230 G 230
G
Sbjct: 64 G 64
>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 = 30.6 bits (69), Expect = 0.17
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 31 IFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSM 70
+F+ FG I + L+ + RG AFV F A NA+++M
Sbjct: 21 MFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAM 62
>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate
Hu-antigen R (HuR). This subgroup corresponds to the
RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1),
the ubiquitously expressed Hu family member. It has a
variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. HuR has an anti-apoptotic function
during early cell stress response. It binds to mRNAs
and enhances the expression of several anti-apoptotic
proteins, such as p21waf1, p53, and prothymosin alpha.
HuR also has pro-apoptotic function by promoting
apoptosis when cell death is unavoidable. Furthermore,
HuR may be important in muscle differentiation,
adipogenesis, suppression of inflammatory response and
modulation of gene expression in response to chronic
ethanol exposure and amino acid starvation. Like other
Hu proteins, HuR contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 84
Score = 30.4 bits (68), Expect = 0.17
Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+Y++ + T +K + +FS+FG+I++ +V T RG AF+ F + + A A+ S
Sbjct: 3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62
Query: 71 QGF--PFYDKPMRIQYS 85
G P +P+ ++++
Sbjct: 63 NGHKPPGSSEPITVKFA 79
>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like
proteins. This subgroup corresponds to the RRM2 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and is highly conserved
between plants and fungi. To date, the intracellular
localization, RNA target(s), cellular interactions and
phosphorylation states of Mei2-like proteins in plants
remain unclear. .
Length = 71
Score = 30.2 bits (68), Expect = 0.17
Identities = 18/56 (32%), Positives = 27/56 (48%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALH 229
L + NL S L +F + KE+R PN+ F+EF + + AA AL+
Sbjct: 4 LVVFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALN 59
Score = 30.2 bits (68), Expect = 0.20
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSM 70
+S+ DL + IF +G+I +I +T R F+ F ++ SA AL+++
Sbjct: 13 VSNDDLHQ----IFGAYGEIKEI--RETPNKRHHKFIEFYDVRSAEAALKAL 58
>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 = 30.3 bits (68), Expect = 0.19
Identities = 19/78 (24%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
++V +I+ + L F ++G I+D+ + T + RG A+V F+++ A +AL ++
Sbjct: 3 LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62
Query: 71 QGFPFYDKPMRIQYSKTD 88
+ + IQ+++ D
Sbjct: 63 DRKWICGRQIEIQFAQGD 80
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 32.3 bits (74), Expect = 0.20
Identities = 24/109 (22%), Positives = 39/109 (35%), Gaps = 11/109 (10%)
Query: 75 FYDKPMRIQYSKTD----SDVISKIKGTFMERPKKVRKQP-------APVEDPAEAKKSK 123
F D+P++ SK D + + +G R +V P A P +
Sbjct: 36 FRDRPLKRMKSKRDDDSYDEDVEDDEGVGEVRVHRVNHAPANAQEHEAARPSPQHQYQPP 95
Query: 124 KKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
+A+ + + Q + Q+ +P P P A PEQP Q
Sbjct: 96 YASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPEQPLQQ 144
Score = 30.0 bits (68), Expect = 1.0
Identities = 12/68 (17%), Positives = 19/68 (27%), Gaps = 4/68 (5%)
Query: 109 QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQA----LSVQQPPVSQPAPPAPMATAG 164
P P + + + + + L Q Q+ + P Q PA A
Sbjct: 118 APRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAP 177
Query: 165 VPEQPPNQ 172
PE
Sbjct: 178 QPEPVAEP 185
Score = 28.8 bits (65), Expect = 2.5
Identities = 10/55 (18%), Positives = 14/55 (25%)
Query: 109 QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATA 163
P PA+ + Q + Q QQ + P AP
Sbjct: 114 PPQHAPRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAF 168
>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related
protein 7 (LARP7) and similar proteins. This subfamily
corresponds to the RRM1 of LARP7, also termed La
ribonucleoprotein domain family member 7, or
P-TEFb-interaction protein for 7SK stability (PIP7S),
an oligopyrimidine-binding protein that binds to the
highly conserved 3'-terminal U-rich stretch (3'
-UUU-OH) of 7SK RNA. LARP7 is a stable component of the
7SK small nuclear ribonucleoprotein (7SK snRNP). It
intimately associates with all the nuclear 7SK and is
required for 7SK stability. LARP7 also acts as a
negative transcriptional regulator of cellular and
viral polymerase II genes, acting by means of the 7SK
snRNP system. It plays an essential role in the
inhibition of positive transcription elongation factor
b (P-TEFb)-dependent transcription, which has been
linked to the global control of cell growth and
tumorigenesis. LARP7 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), at
the N-terminal region, which mediates binding to the
U-rich 3' terminus of 7SK RNA. LARP7 also carries
another putative RRM domain at its C-terminus. .
Length = 80
Score = 30.0 bits (68), Expect = 0.20
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL----KTLKMRGQAFVIFKEIASATNALRS 69
VYV + + L A+FS++G ++ V+L T ++G AF+ F+ A A +
Sbjct: 2 VYVECLPKNATHEWLKAVFSKYGTVV-YVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60
Query: 70 MQGFP 74
+ P
Sbjct: 61 LNNPP 65
>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein
45 (RBM45) and similar proteins. This subfamily
corresponds to the RRM3 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 75
Score = 30.0 bits (68), Expect = 0.20
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 188 LSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALHGFKITPTHAMKIS 242
L LF+ PG + L + + A+V + N + AK L+GF+ P + +K+
Sbjct: 16 LHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNGFEYPPGNRLKVK 75
>gnl|CDD|236154 PRK08119, PRK08119, flagellar motor switch protein; Validated.
Length = 382
Score = 32.1 bits (74), Expect = 0.21
Identities = 12/68 (17%), Positives = 21/68 (30%)
Query: 106 VRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV 165
++ PA + + A + QA Q+ + QP QPA +
Sbjct: 233 EVEEEEAQASPAAEPATAQAAPAPKQEQQQAPPQRQEPEKEAQPVNVQPAQFQSFDPPPL 292
Query: 166 PEQPPNQI 173
P +
Sbjct: 293 ATTEPRNL 300
Score = 28.7 bits (65), Expect = 2.8
Identities = 12/65 (18%), Positives = 23/65 (35%)
Query: 108 KQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE 167
++ E+ A+A + + A + A + +QQQ + +QP P
Sbjct: 230 EEEEVEEEEAQASPAAEPATAQAAPAPKQEQQQAPPQRQEPEKEAQPVNVQPAQFQSFDP 289
Query: 168 QPPNQ 172
P
Sbjct: 290 PPLAT 294
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM1 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 29.9 bits (68), Expect = 0.21
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 10/64 (15%)
Query: 8 ICVTNF-VYVTHISSTDLKKSLYAIFSQFGQIMD--IVALKTLKMRGQAFVIFKEIASAT 64
I V N YVT + L F G++ D ++ + K R FV FK A
Sbjct: 3 IIVKNLPKYVT-------EDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQ 55
Query: 65 NALR 68
A++
Sbjct: 56 QAVK 59
>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA
(uracil-5-)-methyltransferase homolog A (TRMT2A) and
similar proteins. This subfamily corresponds to the RRM
of TRMT2A, also known as HpaII tiny fragments locus 9c
protein (HTF9C), a novel cell cycle regulated protein.
It is an independent biologic factor expressed in tumors
associated with clinical outcome in HER2 expressing
breast cancer. The function of TRMT2A remains unclear
although by sequence homology it has a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), related to RNA
methyltransferases. .
Length = 79
Score = 30.3 bits (69), Expect = 0.21
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 190 MLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
L Q +++L+ R D AFV F +E + A L GFK
Sbjct: 25 FLKKQLFKPHKIKLLK-RQDFAFVTFRSEEERQKALEILDGFKW 67
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT
motif responsible for docking many substrates to
calcineurin, and an unrecognized C-terminal TxxP motif
of unknown function. .
Length = 75
Score = 29.9 bits (68), Expect = 0.21
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 21 STDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPM 80
+ +LK +L ++FS +G+I V L + +A V+F A A + G F +
Sbjct: 13 NAELKAALESLFSSYGEIATFVYLPSF---RRARVVFSSPEEAALARIELHGTVFEGSVL 69
Query: 81 RI 82
R+
Sbjct: 70 RV 71
Score = 28.3 bits (64), Expect = 0.81
Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 25/85 (29%)
Query: 174 LFLTNLPEE------TSEMMLSML--------FNQFPGFKEVRLVPNRHDIAFVEFENEM 219
L +TN+P E + S+ F P F+ R V F +
Sbjct: 1 LIVTNVPSEVFTNAELKAALESLFSSYGEIATFVYLPSFRRAR----------VVFSSPE 50
Query: 220 QSAAAKLALHGFKITPTHAMKISFA 244
++A A++ LHG +++ F
Sbjct: 51 EAALARIELHGTVF-EGSVLRVYFG 74
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM5 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 30.2 bits (68), Expect = 0.22
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRI 82
KK + +FS +GQ+ + K RG AFV F A NA+ +++ + + +
Sbjct: 14 KKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALKDTHLLGRRLVL 73
Query: 83 QYS 85
QY+
Sbjct: 74 QYA 76
Score = 29.4 bits (66), Expect = 0.40
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+ + NLP E ++ + LF+ + K VR VP + D AFVEF ++ A AL
Sbjct: 3 ILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMNAL 61
Query: 229 HGFKITPTH 237
+
Sbjct: 62 KDTHLLGRR 70
>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 = 30.3 bits (68), Expect = 0.22
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRL-VPNRHDIAFVEFENEMQSAA 223
P+++L L NLP E +E L L F + V + AFVEF + Q+ A
Sbjct: 1 PSKVLHLRNLPWECTEEELIELCKPFGKIVNTKCNVGANRNQAFVEFADLNQAIA 55
>gnl|CDD|241226 cd12782, RRM2_PTBP1, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM2 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there
is an unusual and conserved interdomain interaction
between RRM3 and RRM4. It is widely held that only RRMs
3 and 4 are involved in RNA binding and RRM2 mediates
PTB homodimer formation. However, new evidence shows
that the RRMs 1 and 2 also contribute substantially to
RNA binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 100
Score = 30.5 bits (68), Expect = 0.23
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYS 85
L+ IFS+FG ++ I+ T + QA + + + SA +A S+ G Y+ +RI +S
Sbjct: 21 LHQIFSKFGTVLKIITF-TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 79
Query: 86 KTDS 89
K S
Sbjct: 80 KLTS 83
>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 = 29.7 bits (67), Expect = 0.23
Identities = 21/57 (36%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 178 NLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAA--KLALHGFK 232
N P T+ L LF V L+P IA VEF N Q+ A LA FK
Sbjct: 7 NFPYGTTAEELRDLFEPHGKLTRV-LMPPAGTIAIVEFANPQQARLAFKALAYRRFK 62
>gnl|CDD|241140 cd12696, RRM3_PTBP2, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM3 of PTBP2, also known as
neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein (PTB)
and perhaps specific to the vertebrates. Unlike PTB,
PTBP2 is enriched in the brain and in some neural cell
lines. It binds more stably to the downstream control
sequence (DCS) RNA than PTB does but is a weaker
repressor of splicing in vitro. PTBP2 also greatly
enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 107
Score = 30.4 bits (68), Expect = 0.25
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 169 PPNQILFLTNLPEE-TSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
N +L ++NL EE + L LF + + V+++ N+ D A ++ + QS A
Sbjct: 11 GGNTVLLVSNLNEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSH 70
Query: 228 LHGFKI 233
L+G K+
Sbjct: 71 LNGQKM 76
>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins.
This subgroup corresponds to the RRM2 of CELF-1 (also
termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA
translation and deadenylation. CELF-1 is strongly
expressed in all adult and fetal tissues tested. Human
CELF-1 is a nuclear and cytoplasmic RNA-binding protein
that regulates multiple aspects of nuclear and
cytoplasmic mRNA processing, with implications for
onset of type 1 myotonic dystrophy (DM1), a
neuromuscular disease associated with an unstable CUG
triplet expansion in the 3'-UTR (3'-untranslated
region) of the DMPK (myotonic dystrophy protein kinase)
gene; it preferentially targets UGU-rich mRNA elements.
It has been shown to bind to a Bruno response element,
a cis-element involved in translational control of
oskar mRNA in Drosophila, and share sequence similarity
to Bruno, the Drosophila protein that mediates this
process. The Xenopus homolog embryo deadenylation
element-binding protein (EDEN-BP) mediates
sequence-specific deadenylation of Eg5 mRNA. It binds
specifically to the EDEN motif in the 3'-untranslated
regions of maternal mRNAs and targets these mRNAs for
deadenylation and translational repression. CELF-1
contains three highly conserved RNA recognition motifs
(RRMs), also known as RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains): two consecutive RRMs
(RRM1 and RRM2) situated in the N-terminal region
followed by a linker region and the third RRM (RRM3)
close to the C-terminus of the protein. The two
N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including
alternative splicing, RNA editing, stability and
translation. CELF-2 shares high sequence identity with
CELF-1, but shows different binding specificity; it
preferentially binds to sequences with UG repeats and
UGUU motifs. It has been shown to bind to a Bruno
response element, a cis-element involved in
translational control of oskar mRNA in Drosophila, and
share sequence similarity to Bruno, the Drosophila
protein that mediates this process. It also binds to
the 3'-UTR of cyclooxygenase-2 messages, affecting both
translation and mRNA stability, and binds to apoB mRNA,
regulating its C to U editing. CELF-2 also contains
three highly conserved RRMs. It binds to RNA via the
first two RRMs, which are also important for
localization in the cytoplasm. The splicing activation
or repression activity of CELF-2 on some specific
substrates is mediated by RRM1/RRM2. Both, RRM1 and
RRM2 of CELF-2, can activate cardiac troponin T (cTNT)
exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 81
Score = 30.0 bits (67), Expect = 0.25
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLK--MRGQAFVIFKEIASATNALRSMQ 71
+++ +S + + +FS FGQI + L+ RG AFV F A A A+++M
Sbjct: 4 LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63
>gnl|CDD|183859 PRK13103, secA, preprotein translocase subunit SecA; Reviewed.
Length = 913
Score = 32.2 bits (73), Expect = 0.25
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 114 EDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQI 173
EDPAE + ++ A+E A MQ Q + L +QP + + +A A P + ++
Sbjct: 834 EDPAEEEARLRREAEELASRMQFQHAEAPGL--EQPQLGEEEEEPAVAVASAPVRNEQKL 891
>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 = 29.6 bits (67), Expect = 0.25
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
VY+ + ++ + F +G+I +I LK G FV F++ A +A+ + G
Sbjct: 2 VYIGRLPYRARERDVERFFKGYGRIREI----NLK-NGFGFVEFEDPRDADDAVYELNG 55
>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 = 31.9 bits (72), Expect = 0.25
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNAL 67
TN +YVT++ T L IF ++GQI+ L+ T RG AFV F + A A+
Sbjct: 194 TN-LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAI 252
Query: 68 RSM 70
++
Sbjct: 253 SAL 255
>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 = 29.7 bits (67), Expect = 0.25
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+YV ++ K + +F ++G I DI LK + AFV F++ A +A+ G+
Sbjct: 2 IYVGNLPPDIRTKDIEDLFYKYGAIRDI-DLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60
Query: 74 PFYDKPMRIQYSK 86
+ +R+++ +
Sbjct: 61 DYDGYRLRVEFPR 73
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other EJC
components (such as Magoh, Aly/REF, RNPS1, Srm160, and
Upf3), plays critical roles in postsplicing processing,
including nuclear export and cytoplasmic localization of
the mRNA, and the nonsense-mediated mRNA decay (NMD)
surveillance process. RBM8 binds to mRNA 20-24
nucleotides upstream of a spliced exon-exon junction. It
is also involved in spliced mRNA nuclear export, and the
process of nonsense-mediated decay of mRNAs with
premature stop codons. RBM8 forms a specific heterodimer
complex with the EJC protein Magoh which then associates
with Aly/REF, RNPS1, DEK, and SRm160 on the spliced
mRNA, and inhibits ATP turnover by eIF4AIII, thereby
trapping the EJC core onto RNA. RBM8 contains an
N-terminal putative bipartite nuclear localization
signal, one RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
in the central region, and a C-terminal serine-arginine
rich region (SR domain) and glycine-arginine rich region
(RG domain). .
Length = 88
Score = 29.9 bits (68), Expect = 0.26
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLA 227
I+F+T + EE E + F +F K + L +R A +E+E + ++ AA
Sbjct: 8 IIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67
Query: 228 LHGFKITPTHAMKISFA 244
L+G ++ + + +A
Sbjct: 68 LNGKELL-GQTISVDWA 83
>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 = 29.5 bits (67), Expect = 0.26
Identities = 15/72 (20%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQ 71
++V ++ + L A+F ++G + D+V + FV +E A +A++++
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVV-------KNYGFVHMEEEEDAEDAIKALN 54
Query: 72 GFPFYDKPMRIQ 83
G+ F K + ++
Sbjct: 55 GYEFMGKRINVE 66
Score = 27.2 bits (61), Expect = 2.0
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
LF+ NLP+ T+ L LF ++ E +V N FV E E + A AL+G++
Sbjct: 2 LFVGNLPDATTSEELRALFEKYGTVTECDVVKN---YGFVHMEEEEDAEDAIKALNGYEF 58
>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 = 30.0 bits (67), Expect = 0.27
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 26 KSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQ 83
K L +FS G ++ DI+ K K RG V F++ A A+ G +D+PM ++
Sbjct: 15 KKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHVK 74
>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 = 29.8 bits (67), Expect = 0.28
Identities = 22/80 (27%), Positives = 45/80 (56%), Gaps = 11/80 (13%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI-VALKTLKM-RGQAFVIF--KEIASAT----N 65
++V ++ +K + +FS +G++ DI + +K RG AFV + KE+A A N
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61
Query: 66 ALRSMQGFPFYDKPMRIQYS 85
+ +M+G D+P+ ++++
Sbjct: 62 GVYTMRG---CDQPLIVRFA 78
Score = 26.0 bits (57), Expect = 5.9
Identities = 13/61 (21%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI----AFVEFENEMQSAAAKLALH 229
LF+ L ++ +E + +F+ + +++ ++ + AFV++ ++ + AA AL+
Sbjct: 2 LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61
Query: 230 G 230
G
Sbjct: 62 G 62
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate
Hu-antigen B (HuB). This subgroup corresponds to the
RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2),
or ELAV-like neuronal protein 1, or nervous
system-specific RNA-binding protein Hel-N1 (Hel-N1),
one of the neuronal members of the Hu family. The
neuronal Hu proteins play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. It is up-regulated during neuronal
differentiation of embryonic carcinoma P19 cells. Like
other Hu proteins, HuB contains three RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may
cooperate in binding to an AU-rich RNA element (ARE).
RRM3 may help to maintain the stability of the
RNA-protein complex, and might also bind to poly(A)
tails or be involved in protein-protein interactions. .
Length = 90
Score = 30.1 bits (67), Expect = 0.28
Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T +K L +FSQ+G+I+ +V T RG F+ F + A A++ +
Sbjct: 8 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67
Query: 71 QGF--PFYDKPMRIQYSKTDS 89
G P +P+ ++++ S
Sbjct: 68 NGQKPPGATEPITVKFANNPS 88
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate
Hu-antigen D (HuD). This subgroup corresponds to the
RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4),
or paraneoplastic encephalomyelitis antigen HuD, one of
the neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function,
such as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator
of mRNA expression in neurons by interacting with
AU-rich RNA element (ARE) and stabilizing multiple
transcripts. Moreover, HuD regulates the nuclear
processing/stability of N-myc pre-mRNA in neuroblastoma
cells and also regulates the neurite elongation and
morphological differentiation. HuD specifically binds
poly(A) RNA. Like other Hu proteins, HuD contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 81
Score = 29.7 bits (66), Expect = 0.30
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T +K L +FSQ+G+I+ +V T RG F+ F + A A++ +
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64
Query: 71 QG 72
G
Sbjct: 65 NG 66
Score = 26.2 bits (57), Expect = 6.5
Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
L+++ LP+ ++ L LF+Q+ R++ ++ + F+ F+ +++ A L
Sbjct: 5 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64
Query: 229 HGFKIT-PTHAMKISFA 244
+G K + + + FA
Sbjct: 65 NGQKPSGAAEPITVKFA 81
>gnl|CDD|240969 cd12525, RRM1_MEI2_fungi, RNA recognition motif 1 in fungal
Mei2-like proteins. This subgroup corresponds to the
RRM1 of fungal Mei2-like proteins. The Mei2 protein is
an essential component of the switch from mitotic to
meiotic growth in the fission yeast Schizosaccharomyces
pombe. It is an RNA-binding protein that contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
the nucleus, S. pombe Mei2 stimulates meiosis upon
binding a specific non-coding RNA through its C-terminal
RRM motif. .
Length = 72
Score = 29.7 bits (67), Expect = 0.30
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFK 199
L +T +P++ S L +F + K
Sbjct: 4 LKVTGVPKDVSTSNLKEIFEKMGDVK 29
>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 = 29.7 bits (67), Expect = 0.30
Identities = 24/78 (30%), Positives = 33/78 (42%), Gaps = 8/78 (10%)
Query: 8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQI--MDIVALKTLKMRGQAFVIFKEIASATN 65
I V N Y KK L +F G++ DI K K RG V F+ A
Sbjct: 1 IFVANLDY-----KVGWKK-LKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQ 54
Query: 66 ALRSMQGFPFYDKPMRIQ 83
A+ G +D+PMR++
Sbjct: 55 AISMFNGQMLFDRPMRVK 72
>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP
DL) and similar proteins. This subgroup corresponds to
the RRM1 of hnRNP DL (or hnRNP D-like), also termed
AU-rich element RNA-binding factor, or JKT41-binding
protein (protein laAUF1 or JKTBP), which is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
hnRNP DL binds single-stranded DNA (ssDNA) or
double-stranded DNA (dsDNA) in a non-sequencespecific
manner, and interacts with poly(G) and poly(A)
tenaciously. It contains two putative two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 76
Score = 29.6 bits (66), Expect = 0.31
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNAL 67
+++ +S KK L S+FG+++D T + RG FV+FK+ AS L
Sbjct: 2 MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVL 58
>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 = 29.5 bits (67), Expect = 0.33
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 2/68 (2%)
Query: 15 YVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKM--RGQAFVIFKEIASATNALRSMQG 72
YV ++ + + L FS FG I + K +G FV F AT A+ M G
Sbjct: 5 YVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNG 64
Query: 73 FPFYDKPM 80
KP+
Sbjct: 65 RIIGGKPL 72
>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast
pre-mRNA-splicing factor Cwc2 and similar proteins.
This subfamily corresponds to the RRM of yeast protein
Cwc2, also termed Complexed with CEF1 protein 2, or
PRP19-associated complex protein 40 (Ntc40), or
synthetic lethal with CLF1 protein 3, one of the
components of the Prp19-associated complex [nineteen
complex (NTC)] that can bind to RNA. NTC is composed of
the scaffold protein Prp19 and a number of associated
splicing factors, and plays a crucial role in intron
removal during premature mRNA splicing in eukaryotes.
Cwc2 functions as an RNA-binding protein that can bind
both small nuclear RNAs (snRNAs) and pre-mRNA in vitro.
It interacts directly with the U6 snRNA to link the NTC
to the spliceosome during pre-mRNA splicing. In the
N-terminal half, Cwc2 contains a CCCH-type zinc finger
(ZnF domain), a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and an intervening loop,
also termed RNA-binding loop or RB loop, between ZnF
and RRM, all of which are necessary and sufficient for
RNA binding. The ZnF is also responsible for mediating
protein-protein interaction. The C-terminal flexible
region of Cwc2 interacts with the WD40 domain of Prp19.
Length = 78
Score = 29.5 bits (67), Expect = 0.33
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 14 VYVTHISSTDLKKSLYAI----FSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
+YV I + K + I F ++G I DI + L +G AFV +K ASA A +
Sbjct: 4 LYVGGIKAGSALKQIEEILRRHFGEWGDIEDI---RVLPSKGIAFVRYKYRASAEFAKEA 60
Query: 70 MQG 72
M
Sbjct: 61 MAD 63
Score = 29.5 bits (67), Expect = 0.36
Identities = 9/30 (30%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 201 VRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
+R++P++ IAFV ++ + AK A+
Sbjct: 35 IRVLPSKG-IAFVRYKYRASAEFAKEAMAD 63
>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 = 0.34
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 6/75 (8%)
Query: 174 LFLTNLPEETSEM-MLSMLFNQF--PGFKEVRLVPNR--HDIAFVEFENEMQSAAAKLAL 228
LF+ LP+ ++ +L LF+Q P F ++ + PN AFVE+ + A+ AL
Sbjct: 5 LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQAL 64
Query: 229 HGFKITPTHAMKISF 243
+G + + +++SF
Sbjct: 65 NGHSLQGSP-IRVSF 78
>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 = 31.8 bits (72), Expect = 0.35
Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 7/95 (7%)
Query: 143 ALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVR 202
+S + P + + + V + +++ NLP E + L F K
Sbjct: 269 EVSQKNPDDNAKNVEKLVNSTTVLDSKDR--IYIGNLPLYLGEDQIKELLESFGDLKAFN 326
Query: 203 LVPNRHD-----IAFVEFENEMQSAAAKLALHGFK 232
L+ + AF E+++ + A AL+G
Sbjct: 327 LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKD 361
Score = 27.6 bits (61), Expect = 8.4
Identities = 19/92 (20%), Positives = 41/92 (44%), Gaps = 10/92 (10%)
Query: 8 ICVTNFVYVTHI----SSTDLKKSLYAIFSQFGQIMDIVALKTLKMR------GQAFVIF 57
+ +TN V + ++ + + FS++G +++IV + R G+ F+ +
Sbjct: 412 VQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEY 471
Query: 58 KEIASATNALRSMQGFPFYDKPMRIQYSKTDS 89
++ SA A+ M G F D+ + + D
Sbjct: 472 ADVRSAEKAMEGMNGRKFNDRVVVAAFYGEDC 503
>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 = 29.2 bits (65), Expect = 0.35
Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 5/59 (8%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
++V ++++T ++ L FS+FG++ + K++ AFV F+E +A A+ M G
Sbjct: 4 LFVRNLATTVTEEILEKSFSEFGKLE-----RVKKLKDYAFVHFEERDAAVRAMDEMNG 57
Score = 28.1 bits (62), Expect = 1.0
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF 231
++LF+ NL +E +L F++F + V+ + D AFV FE + A ++G
Sbjct: 2 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKL---KDYAFVHFEERDAAVRAMDEMNGK 58
Query: 232 KI 233
+I
Sbjct: 59 EI 60
>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 = 29.4 bits (66), Expect = 0.35
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 5/53 (9%)
Query: 170 PNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIA----FVEFENE 218
PN+I F+ + +T+E L F+Q+ KEV++V +R ++ FV FE +
Sbjct: 2 PNRI-FVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQ 53
>gnl|CDD|235777 PRK06302, PRK06302, acetyl-CoA carboxylase biotin carboxyl carrier
protein subunit; Validated.
Length = 155
Score = 30.5 bits (70), Expect = 0.35
Identities = 10/45 (22%), Positives = 13/45 (28%), Gaps = 1/45 (2%)
Query: 128 KEQARLMQAQQQQMQALSVQQPPVSQPAP-PAPMATAGVPEQPPN 171
+ A + QQ A V P + A AP A
Sbjct: 34 RAAAAPVAPVAQQAAAAPVAAAPAAAAAAAAAPAAAPAAAAAEAE 78
>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin.
This subfamily corresponds to the RRM4 of ubiquitously
expressed protein nucleolin, also termed protein C23, is
a multifunctional major nucleolar phosphoprotein that
has been implicated in various metabolic processes, such
as ribosome biogenesis, cytokinesis, nucleogenesis, cell
proliferation and growth, cytoplasmic-nucleolar
transport of ribosomal components, transcriptional
repression, replication, signal transduction, inducing
chromatin decondensation, etc. Nucleolin exhibits
intrinsic self-cleaving, DNA helicase, RNA helicase and
DNA-dependent ATPase activities. It can be
phosphorylated by many protein kinases, such as the
major mitotic kinase Cdc2, casein kinase 2 (CK2), and
protein kinase C-zeta. Nucleolin shares similar domain
architecture with gar2 from Schizosaccharomyces pombe
and NSR1 from Saccharomyces cerevisiae. The highly
phosphorylated N-terminal domain of nucleolin is made up
of highly acidic regions separated from each other by
basic sequences, and contains multiple phosphorylation
sites. The central domain of nucleolin contains four
closely adjacent N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), which suggests that
nucleolin is potentially able to interact with multiple
RNA targets. The C-terminal RGG (or GAR) domain of
nucleolin is rich in glycine, arginine and phenylalanine
residues, and contains high levels of
NG,NG-dimethylarginines. .
Length = 78
Score = 29.6 bits (66), Expect = 0.38
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKL 226
+ LF+ L E+T+E L F G R+V +R FV+F +E + AAK
Sbjct: 1 KTLFVKGLSEDTTEETLK---ESFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKE 57
Query: 227 AL 228
A+
Sbjct: 58 AM 59
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 31.8 bits (72), Expect = 0.40
Identities = 18/65 (27%), Positives = 21/65 (32%), Gaps = 3/65 (4%)
Query: 107 RKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVP 166
R P P ++S + AA AR Q A V P S P P A P
Sbjct: 372 RHHPKRASLPTRKRRSARHAATPFARGPGGDDQTRPAAPV---PASVPTPAPTPVPASAP 428
Query: 167 EQPPN 171
P
Sbjct: 429 PPPAT 433
Score = 30.7 bits (69), Expect = 0.80
Identities = 16/78 (20%), Positives = 24/78 (30%), Gaps = 4/78 (5%)
Query: 106 VRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV 165
VR++P A+ + + AR ++ + A PP PP P A
Sbjct: 2862 VRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFA----LPPDQPERPPQPQAPPPP 2917
Query: 166 PEQPPNQILFLTNLPEET 183
QP P
Sbjct: 2918 QPQPQPPPPPQPQPPPPP 2935
Score = 28.4 bits (63), Expect = 4.3
Identities = 15/66 (22%), Positives = 20/66 (30%), Gaps = 4/66 (6%)
Query: 105 KVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG 164
VR+ P + + E+ QA PP QP PP P
Sbjct: 2882 PVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPP----P 2937
Query: 165 VPEQPP 170
P+ P
Sbjct: 2938 RPQPPL 2943
Score = 28.4 bits (63), Expect = 4.4
Identities = 16/61 (26%), Positives = 24/61 (39%)
Query: 110 PAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQP 169
P + PA A S+ + + + A + PP + PA P P T+ P P
Sbjct: 2780 PRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAP 2839
Query: 170 P 170
P
Sbjct: 2840 P 2840
Score = 28.0 bits (62), Expect = 6.5
Identities = 12/72 (16%), Positives = 18/72 (25%), Gaps = 1/72 (1%)
Query: 100 MERPKKVRK-QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPA 158
+ RP R + + + + +A Q PP QP
Sbjct: 2886 LARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAP 2945
Query: 159 PMATAGVPEQPP 170
AG E
Sbjct: 2946 TTDPAGAGEPSG 2957
>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar
protein 4 (Nop4p) and similar proteins. This subgroup
corresponds to the RRM3 of Nop4p (also known as Nop77p),
encoded by YPL043W from Saccharomyces cerevisiae. It is
an essential nucleolar protein involved in processing
and maturation of 27S pre-rRNA and biogenesis of 60S
ribosomal subunits. Nop4p has four RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 107
Score = 29.9 bits (67), Expect = 0.41
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAA 224
LF+ NLP + +E L+ F++F + V ++ FV F+++ A
Sbjct: 4 LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59
>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate
RNA-binding protein 46 (RBM46). This subgroup
corresponds to the RRM3 of RBM46, also termed
cancer/testis antigen 68 (CT68), is a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP R)
and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
Its biological function remains unclear. Like hnRNP R
and hnRNP Q, RBM46 contains two well defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 74
Score = 29.2 bits (65), Expect = 0.44
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHG 230
++L++ NL T+E + FN+F PG V V D AFV F N + AA ++G
Sbjct: 2 KVLYVRNLMISTTEETIKAEFNKFKPGV--VERVKKLRDYAFVHFFNREDAVAAMSVMNG 59
Query: 231 FKITPTHAMKISFAK 245
K +++++ AK
Sbjct: 60 -KCIDGASIEVTLAK 73
>gnl|CDD|240795 cd12349, RRM2_SHARP, RNA recognition motif 2 in
SMART/HDAC1-associated repressor protein (SHARP) and
similar proteins. This subfamily corresponds to the
RRM2 of SHARP, also termed Msx2-interacting protein
(MINT), or SPEN homolog, an estrogen-inducible
transcriptional repressor that interacts directly with
the nuclear receptor corepressor SMRT, histone
deacetylases (HDACs) and components of the NuRD
complex. SHARP recruits HDAC activity and binds to the
steroid receptor RNA coactivator SRA through four
conserved N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), further suppressing
SRA-potentiated steroid receptor transcription
activity. Thus, SHARP has the capacity to modulate both
liganded and nonliganded nuclear receptors. SHARP also
has been identified as a component of transcriptional
repression complexes in Notch/RBP-Jkappa signaling
pathways. In addition to the N-terminal RRMs, SHARP
possesses a C-terminal SPOC domain (Spen paralog and
ortholog C-terminal domain), which is highly conserved
among Spen proteins. .
Length = 74
Score = 29.2 bits (66), Expect = 0.46
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 13/81 (16%)
Query: 8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQ-----AFVIFKEIAS 62
I V N S T LK L+ F + G++ ++K+ G A V F++
Sbjct: 2 IIVKNLP--LRSSDTSLKDGLFHEFKKHGKV------TSVKVHGTGSERYAIVFFRKPED 53
Query: 63 ATNALRSMQGFPFYDKPMRIQ 83
A AL +G F+ + +
Sbjct: 54 AEKALEVSKGKLFFGAEIEVT 74
>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. This subfamily corresponds to
the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs
represent a novel class of plant-specific RNA-binding
proteins that may play a unique role in the polarized
mRNA transport to the vicinity of the cell plate. The
family members consist of multiple functional domains,
including a lysine-rich domain (KRD domain) that
contains three nuclear localization motifs (KKKR/NK),
two RNA recognition motifs (RRMs), and three CCHC-type
zinc fingers. PHIP1 is a peripheral membrane protein
and is localized at the cell plate during cytokinesis
in plants. In addition to phragmoplastin, PHIP1
interacts with two Arabidopsis small GTP-binding
proteins, Rop1 and Ran2. However, PHIP1 interacted only
with the GTP-bound form of Rop1 but not the GDP-bound
form. It also binds specifically to Ran2 mRNA. .
Length = 72
Score = 28.9 bits (65), Expect = 0.46
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL----KMRGQAFVIFKEIASATNALRS 69
VYV I + + + FS G+I + + L T + RG AF+ FK +A AL +
Sbjct: 1 VYVGGIPYYSTEDEIRSYFSYCGEIEE-LDLMTFPDTGRFRGIAFITFKTEEAAKRAL-A 58
Query: 70 MQGFPFYDKPMRIQ 83
+ G + ++++
Sbjct: 59 LDGEDMGGRFLKVE 72
>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation
initiation factor 3 subunit B (eIF-3B) and similar
proteins. This subfamily corresponds to the RRM domain
in eukaryotic translation initiation factor 3 (eIF-3), a
large multisubunit complex that plays a central role in
the initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3
subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or
eIF-3 p116, is the major scaffolding subunit of eIF-3.
It interacts with eIF-3 subunits A, G, I, and J. eIF-3B
contains an N-terminal RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is involved in the
interaction with eIF-3J. The interaction between eIF-3B
and eIF-3J is crucial for the eIF-3 recruitment to the
40 S ribosomal subunit. eIF-3B also binds directly to
domain III of the internal ribosome-entry site (IRES)
element of hepatitis-C virus (HCV) RNA through its
N-terminal RRM, which may play a critical role in both
cap-dependent and cap-independent translation.
Additional research has shown that eIF-3B may function
as an oncogene in glioma cells and can be served as a
potential therapeutic target for anti-glioma therapy.
This family also includes the yeast homolog of eIF-3
subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that
interacts with the yeast homologs of eIF-3 subunits
A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In
yeast, eIF-3B (PRT1) contains an N-terminal RRM that is
directly involved in the interaction with eIF-3A (TIF32)
and eIF-3J (HCR1). In contrast to its human homolog,
yeast eIF-3B (PRT1) may have potential to bind its total
RNA through its RRM domain. .
Length = 84
Score = 29.1 bits (66), Expect = 0.47
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 211 AFVEFENEMQSAAAKLALHGFKITPTHAMKI 241
AFVEF ++ A AL+G+K+ H +
Sbjct: 53 AFVEFATPEEAKEAVKALNGYKLDKKHTFAV 83
Score = 26.4 bits (59), Expect = 5.3
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 24 LKKSLYAIFSQFGQIMDIVAL-----KTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK 78
LKK L IFS+FG IV + +T K +G AFV F A A++++ G+ DK
Sbjct: 20 LKKVLRKIFSKFGVG-KIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKL-DK 77
>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42
(RBM42) and similar proteins. This subfamily
corresponds to the RRM of RBM42 which has been
identified as a heterogeneous nuclear ribonucleoprotein
K (hnRNP K)-binding protein. It also directly binds the
3' untranslated region of p21 mRNA that is one of the
target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are
components of stress granules (SGs). Under nonstress
conditions, RBM42 predominantly localizes within the
nucleus and co-localizes with hnRNP K. Under stress
conditions, hnRNP K and RBM42 form cytoplasmic foci
where the SG marker TIAR localizes, and may play a role
in the maintenance of cellular ATP level by protecting
their target mRNAs. RBM42 contains an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 83
Score = 29.1 bits (66), Expect = 0.48
Identities = 11/43 (25%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 167 EQPPNQI-LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRH 208
E P N +F+ +L E ++ +L+ F+++P F++ ++V ++
Sbjct: 1 EWPENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKR 43
>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 = 29.2 bits (66), Expect = 0.48
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 50 RGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
+G FV F + AL M G +PMR+ +
Sbjct: 44 KGYGFVRFGDEDERDRALTEMNGVYCSSRPMRVSPA 79
>gnl|CDD|241227 cd12783, RRM2_PTBP2, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM2 of PTBP2, also known
as neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein
(PTB) and perhaps specific to the vertebrates. Unlike
PTB, PTBP2 is enriched in the brain and in some neural
cell lines. It binds more stably to the downstream
control sequence (DCS) RNA than PTB does but is a
weaker repressor of splicing in vitro. PTBP2 also
greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 101
Score = 29.6 bits (66), Expect = 0.52
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYS 85
L+ IFS+FG ++ I+ T + QA + + + +A A ++ G Y+ +RI +S
Sbjct: 20 LHQIFSKFGTVLKIITF-TKNNQFQALLQYGDPVNAQQAKLALDGQNIYNACCTLRIDFS 78
Query: 86 K 86
K
Sbjct: 79 K 79
>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF
35 kDa subunit B (U2AF35B). This subgroup corresponds
to the RRM of U2AF35B, also termed zinc finger CCCH
domain-containing protein 60 (C3H60), which is one of
the small subunits of U2 small nuclear ribonucleoprotein
(snRNP) auxiliary factor (U2AF). It has been implicated
in the recruitment of U2 snRNP to pre-mRNAs and is a
highly conserved heterodimer composed of large and small
subunits. Members in this family are mainly found in
plant. They show high sequence homology to vertebrates
U2AF35 that directly binds to the 3' splice site of the
conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. U2AF35B contains two
N-terminal zinc fingers, a central RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich domain. In contrast to U2AF35,
U2AF35B has a plant-specific conserved C-terminal region
containing SERE motif(s), which may have an important
function specific to higher plants. .
Length = 103
Score = 29.6 bits (67), Expect = 0.52
Identities = 14/38 (36%), Positives = 25/38 (65%), Gaps = 2/38 (5%)
Query: 49 MRGQAFVIFKEIASATNALRSMQGFPFYD-KPMRIQYS 85
M G +V F++ A AL+++QG FYD +P+ +++S
Sbjct: 66 MVGNVYVKFRDEEHAAAALKALQG-RFYDGRPIIVEFS 102
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 31.1 bits (70), Expect = 0.59
Identities = 17/77 (22%), Positives = 24/77 (31%), Gaps = 16/77 (20%)
Query: 109 QPAPVEDPAEAKKSKKKAAKE-------------QARLMQAQQQQMQALSVQQPPVSQPA 155
P+P P KK+ + + AR + QQPPV A
Sbjct: 381 APSPAGSPDVKKKAPEPDLPQPDRHPGPAKPEAPGARPAELPSPASAPTPEQQPPV---A 437
Query: 156 PPAPMATAGVPEQPPNQ 172
AP+ + P N
Sbjct: 438 RSAPLPPSPQASAPRNV 454
>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106). This
family of proteins are found in large numbers in the
Trichomonas vaginalis proteome. The function of this
protein is unknown.
Length = 422
Score = 30.8 bits (69), Expect = 0.60
Identities = 12/38 (31%), Positives = 13/38 (34%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
+ QQ QQP V PA P QP Q
Sbjct: 202 KPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQ 239
Score = 30.4 bits (68), Expect = 0.78
Identities = 16/58 (27%), Positives = 22/58 (37%)
Query: 107 RKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAG 164
R P P + P +++ + A+ Q Q QQ QQP PA P G
Sbjct: 198 RHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQG 255
Score = 28.1 bits (62), Expect = 5.2
Identities = 23/78 (29%), Positives = 28/78 (35%), Gaps = 8/78 (10%)
Query: 103 PKKVRKQPAP------VEDPAEAKKSKKKAAKEQARLMQAQQQQMQ--ALSVQQPPVSQP 154
P R+ PAP + K ++ AQQ +Q A QQ P QP
Sbjct: 174 PNPPREAPAPGLPKTFTSSHGHRHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQP 233
Query: 155 APPAPMATAGVPEQPPNQ 172
PA T P Q P Q
Sbjct: 234 VQPAQQPTPQNPAQQPPQ 251
>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 = 28.8 bits (65), Expect = 0.60
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 25 KKSLYAIFSQFGQIMDIVALKTLK---MRGQAFVIFKEIASATNALR 68
+ L +F FG I D V LK K R FV +K A AL+
Sbjct: 14 EDKLRKLFEAFGTITD-VQLKYTKDGKFRKFGFVGYKTEEEAQKALK 59
>gnl|CDD|241147 cd12703, RRM4_ROD1, RNA recognition motif 4 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM4 of ROD1 coding protein Rod1, 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 that negatively regulates the
onset of differentiation. ROD1 is predominantly
expressed in hematopoietic cells or organs. It might
play a role controlling differentiation in mammals. Rod1
contains four repeats of RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and does have RNA binding
activities. .
Length = 81
Score = 28.9 bits (64), Expect = 0.61
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 169 PPNQILFLTNLPEETSEMMLSMLF-NQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLA 227
PP+ L L+N+P +E L LF + K + +A ++ + ++ A +
Sbjct: 1 PPSATLHLSNIPPSVTEDDLKGLFLSSGCSVKAFKFFQKDRKMALIQLGSVEEAIEALIE 60
Query: 228 LHGFKITPTHAMKISFAK 245
LH + H +++SF+K
Sbjct: 61 LHNHDLGENHHLRVSFSK 78
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 30.7 bits (70), Expect = 0.67
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 7/53 (13%)
Query: 114 EDPAEAKKSKKKAAKEQARL-------MQAQQQQMQALSVQQPPVSQPAPPAP 159
PAE KK +KK K + + A+++ A + P + P
Sbjct: 406 LSPAERKKLRKKQRKAEKKAEKEEAEKAAAKKKAEAAAKKAKGPDGETKKVDP 458
>gnl|CDD|201881 pfam01597, GCV_H, Glycine cleavage H-protein. This is a family of
glycine cleavage H-proteins, part of the glycine
cleavage multienzyme complex (GCV) found in bacteria and
the mitochondria of eukaryotes. GCV catalyzes the
catabolism of glycine in eukaryotes. A lipoyl group is
attached to a completely conserved lysine residue. The H
protein shuttles the methylamine group of glycine from
the P protein to the T protein.
Length = 122
Score = 29.6 bits (67), Expect = 0.68
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 76 YDKPMRIQYS-KTDSDVISKIKGTFMERPKKVRKQPAPV-EDPAEAK---KSKKKAAKEQ 130
+ + S K S+V + + G +E +K+ P + +DP E K K +E
Sbjct: 47 KGESLGAVESVKAASEVYAPVSGEVVEVNEKLEDNPGLINKDPYEDGWIAKLKPSNLEEL 106
Query: 131 ARLMQAQQ 138
LM A+Q
Sbjct: 107 ESLMTAEQ 114
>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 = 28.7 bits (64), Expect = 0.69
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
LF+ +LP+E + L +F F ++ +R FV F+N + AA A+
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66
Query: 229 HGFKI 233
+GF+I
Sbjct: 67 NGFQI 71
Score = 26.7 bits (59), Expect = 3.2
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+++ H+ L +F FG ++ V T + + FV F ASA A+++M
Sbjct: 7 LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66
Query: 71 QGFPFYDKPMRIQ 83
GF K +++Q
Sbjct: 67 NGFQIGMKRLKVQ 79
>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 = 28.3 bits (63), Expect = 0.70
Identities = 14/59 (23%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQG 72
++V ++S+T L +F +FG++++ +K AFV + A A+ ++ G
Sbjct: 3 IFVGNVSATCTSDELRGLFEEFGRVVECDKVK-----DYAFVHMEREEEALAAIEALNG 56
>gnl|CDD|218774 pfam05843, Suf, Suppressor of forked protein (Suf). This family
consists of several eukaryotic suppressor of forked
(Suf) like proteins. The Drosophila melanogaster
Suppressor of forked [Su(f)] protein shares homology
with the yeast RNA14 protein and the 77-kDa subunit of
human cleavage stimulation factor, which are proteins
involved in mRNA 3' end formation. This suggests a role
for Su(f) in mRNA 3' end formation in Drosophila. The
su(f) gene produces three transcripts; two of them are
polyadenylated at the end of the transcription unit, and
one is a truncated transcript, polyadenylated in intron
4. It is thought that su(f) plays a role in the
regulation of poly(A) site utilisation and an important
role of the GU-rich sequence for this regulation to
occur.
Length = 271
Score = 30.3 bits (69), Expect = 0.70
Identities = 31/108 (28%), Positives = 37/108 (34%), Gaps = 22/108 (20%)
Query: 84 YSKTDSDVISK---IKGTFMERPKKVRKQ--------PAPVEDPAEAKKSKKKAAKEQAR 132
YS D D I K ERPK P+ED +KK K +Q R
Sbjct: 150 YSFLDFDPIKKRELGSPGSQERPKATLNPVTQATNSKKRPLEDDDSSKKPDKSRRLDQQR 209
Query: 133 LMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLP 180
+ QA QQ QPAP PP + L+ LP
Sbjct: 210 RSPSTNPAPQASGPQQQQQGQPAP-----------LPPEIVALLSVLP 246
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 30.9 bits (70), Expect = 0.71
Identities = 13/65 (20%), Positives = 19/65 (29%), Gaps = 4/65 (6%)
Query: 110 PAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAP----MATAGV 165
P P PA+ + + + A + PV + A P P V
Sbjct: 362 PVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPV 421
Query: 166 PEQPP 170
P P
Sbjct: 422 PHTPE 426
Score = 27.9 bits (62), Expect = 5.5
Identities = 15/67 (22%), Positives = 22/67 (32%)
Query: 103 PKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT 162
P VR PAP P A + + + ++ P + AP A
Sbjct: 376 PSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAA 435
Query: 163 AGVPEQP 169
V E+P
Sbjct: 436 IPVDEKP 442
>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate
Hu-antigen C (HuC). This subgroup corresponds to the
RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3),
or paraneoplastic cerebellar degeneration-associated
antigen, or paraneoplastic limbic encephalitis antigen
21 (PLE21), one of the neuronal members of the Hu
family. The neuronal Hu proteins play important roles
in neuronal differentiation, plasticity and memory.
Like other Hu proteins, HuC contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an AU-rich
RNA element (ARE). The AU-rich element binding of HuC
can be inhibited by flavonoids. RRM3 may help to
maintain the stability of the RNA-protein complex, and
might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 28.8 bits (64), Expect = 0.74
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T +K + +FSQ+G+I+ +V T RG F+ F + A A++ +
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63
Query: 71 QG 72
G
Sbjct: 64 NG 65
Score = 26.5 bits (58), Expect = 4.6
Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFENEMQSAAAKLAL 228
L+++ LP+ S+ + LF+Q+ R++ ++ + F+ F+ +++ A L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63
Query: 229 HGFK-ITPTHAMKISFA 244
+G K + + + FA
Sbjct: 64 NGQKPLGAAEPITVKFA 80
>gnl|CDD|165309 PHA03008, PHA03008, hypothetical protein; Provisional.
Length = 234
Score = 30.3 bits (68), Expect = 0.74
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAF 212
I F++N+ ++ + F++F F E+ VP DI F
Sbjct: 23 IAFISNITHIHDHNIIKIFFDKFDDFDEIIFVPGDIDILF 62
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 28.7 bits (65), Expect = 0.75
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 212 FVEFENEMQSAAAKLALHG 230
FVEF + ++ A AL+G
Sbjct: 53 FVEFSDADEAIKAVRALNG 71
Score = 26.4 bits (59), Expect = 4.7
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 8 ICVTNFVYVTHISSTDLKKSLYAIFSQFGQIMDIV----ALKTLKMRGQAFVIFKEIASA 63
+ + N V I DLK + ++G++++++ A + FV F + A
Sbjct: 4 LVLRNMVTPGEIDE-DLKDEIEEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEA 62
Query: 64 TNALRSMQG 72
A+R++ G
Sbjct: 63 IKAVRALNG 71
>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein
Vip1 and similar proteins. This subfamily corresponds
to Vip1, an RNA-binding protein encoded by gene vip1
from fission yeast Schizosaccharomyces pombe. Its
biological role remains unclear. Vip1 contains an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 68
Score = 28.3 bits (63), Expect = 0.81
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNAL 67
VYV++IS +K + FS G+I ++ L A + F++ ++A AL
Sbjct: 1 VYVSNISPKTTEKQISDFFSFCGKISNL-DLTNDGESQTATITFEKPSAAKTAL 53
>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 = 28.5 bits (63), Expect = 0.83
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 27 SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF--YDKPMRIQY 84
SL A+ +F + I + +K A++ ++ + +A A M+GFP D+ +R+ +
Sbjct: 15 SLAALAREFDRFGSIRTIDYVKGDSFAYIQYESLDAAQAACAQMRGFPLGGPDRRLRVDF 74
Query: 85 SK 86
+K
Sbjct: 75 AK 76
>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 = 0.83
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 19 ISSTDLK---KSLYAIFSQFGQI--MDIVALKTLKMRGQAFVIFKEIASATNALRSMQGF 73
+++ D K K L +FS G + DI K K RG V F++ A A+ G
Sbjct: 5 VANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFNGQ 64
Query: 74 PFYDKPMRIQ 83
+D+PM ++
Sbjct: 65 FLFDRPMHVK 74
>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate
paraspeckle protein 1 (PSP1). This subgroup corresponds
to the RRM1 of PSPC1, also termed paraspeckle component
1 (PSPC1), a novel nucleolar factor that accumulates
within a new nucleoplasmic compartment, termed
paraspeckles, and diffusely distributes in the
nucleoplasm. It is ubiquitously expressed and highly
conserved in vertebrates. Its cellular function remains
unknown currently, however, PSPC1 forms a novel
heterodimer with the nuclear protein p54nrb, also known
as non-POU domain-containing octamer-binding protein
(NonO), which localizes to paraspeckles in an
RNA-dependent manner. PSPC1 contains two conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), at the
N-terminus. .
Length = 71
Score = 28.4 bits (63), Expect = 0.88
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
LF+ NLP + +E LF ++ EV + +R F+ E+ + AK L G I
Sbjct: 4 LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR-GFGFIRLESRTLAEIAKAELDG-TI 61
Query: 234 TPTHAMKISF 243
++I F
Sbjct: 62 LKNRPLRIRF 71
>gnl|CDD|223009 PHA03211, PHA03211, serine/threonine kinase US3; Provisional.
Length = 461
Score = 30.2 bits (68), Expect = 0.94
Identities = 23/89 (25%), Positives = 34/89 (38%), Gaps = 13/89 (14%)
Query: 97 GTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAP 156
TF P+ V P P DP S A E ARL Q Q+ + S ++ P
Sbjct: 36 ETFYNPPRGVCFPPPPEHDPP----SPHGARDEAARLCQIQELLAEMRSSEEYP-----D 86
Query: 157 PAPMATAGVPEQPPNQILFLTNLPEETSE 185
A + P+ + + P+E +E
Sbjct: 87 SGAEAEDDDDDDAPDDVAY----PDEYAE 111
>gnl|CDD|237082 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional.
Length = 400
Score = 30.2 bits (68), Expect = 0.97
Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 1/79 (1%)
Query: 89 SDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQ 148
D + +I GT + + APV P+EA + K A+ A L A +
Sbjct: 217 GDTVKRIDGTEVPLLAPWQGDAAPVP-PSEAARPKSADAETNAALKTPATAPKAAAKNAK 275
Query: 149 PPVSQPAPPAPMATAGVPE 167
P +QP A E
Sbjct: 276 APEAQPVSGTAAAEPAPKE 294
>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM1 of RBM47, a putative
RNA-binding protein that shows high sequence homology
with heterogeneous nuclear ribonucleoprotein R (hnRNP
R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP
Q). Its biological function remains unclear. Like hnRNP
R and hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 78
Score = 28.4 bits (63), Expect = 1.0
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQ 71
V+V I + L +F G+I ++ + K RG AFV++ + A A+R +
Sbjct: 4 VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63
Query: 72 GFPFYDKPMRI 82
+ +P R+
Sbjct: 64 NYEI--RPGRL 72
>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 = 28.3 bits (64), Expect = 1.1
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 44 LKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
K L M G FV FK +A AL+ +QG + ++ S
Sbjct: 42 GKLLSM-GYGFVEFKSKEAAQKALKRLQGTVLDGHALELKLS 82
>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52
motif-containing protein 1 (RDM1) and similar proteins.
This subfamily corresponds to the RRM of RDM1, also
termed RAD52 homolog B, a novel factor involved in the
cellular response to the anti-cancer drug cisplatin in
vertebrates. RDM1 contains a small RD motif that shares
with the recombination and repair protein RAD52, and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). The
RD motif is responsible for the acidic pH-dependent
DNA-binding properties of RDM1. It interacts with ss-
and dsDNA, and may act as a DNA-damage recognition
factor by recognizing the distortions of the double
helix caused by cisplatin-DNA adducts in vitro. In
addition, due to the presence of RRM, RDM1 can bind to
RNA as well as DNA. .
Length = 81
Score = 28.1 bits (63), Expect = 1.1
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 14 VYVTHISSTDLKK----SLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRS 69
+YV IS ++ SL + FSQFG + + + F F + SA A R+
Sbjct: 3 LYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVFPNAAVATPGFYAFVKFYSARAASRA 62
Query: 70 MQGFP----FYDKPMRIQY 84
+ F P+++++
Sbjct: 63 QKACNGKWLFQGSPLKVRF 81
>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 = 28.1 bits (63), Expect = 1.1
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFE 216
ILF+ NLP +T+ L F VRL+ ++ AFVEF+
Sbjct: 2 ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFD 50
>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding
protein 45 (RBM45) and similar proteins. This
subfamily corresponds to the RRM1 of RBM45, also termed
developmentally-regulated RNA-binding protein 1 (DRB1),
a new member of RNA recognition motif (RRM)-type neural
RNA-binding proteins, which expresses under
spatiotemporal control. It is encoded by gene drb1 that
is expressed in neurons, not in glial cells. RBM45
predominantly localizes in cytoplasm of cultured cells
and specifically binds to poly(C) RNA. It could play an
important role during neurogenesis. RBM45 carries four
RRMs, also known as RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 81
Score = 28.1 bits (63), Expect = 1.2
Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 32 FSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQG 72
F+ FG+I DI +K T + +G A+V F + +SA A+ M G
Sbjct: 23 FAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNG 66
Score = 26.9 bits (60), Expect = 3.1
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 169 PPNQILFLT---NLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQ 220
PPN LF+ ++ E+ L F F +++ +V ++ +A+V+F
Sbjct: 1 PPNSRLFIVCGKSVTEDD----LREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASS 56
Query: 221 SAAAKLALHG 230
+A A ++G
Sbjct: 57 AARAMEEMNG 66
>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 = 28.1 bits (62), Expect = 1.2
Identities = 17/78 (21%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDI---VALKTLKMRGQAFVIFKEIASATNALRSM 70
++V +++ + L F ++G I+D+ + T + RG A++ F+++ A +AL ++
Sbjct: 3 LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62
Query: 71 QGFPFYDKPMRIQYSKTD 88
+ + IQ+++ D
Sbjct: 63 NRKWVCGRQIEIQFAQGD 80
>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 = 28.4 bits (64), Expect = 1.2
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 28 LYAIFSQFGQIMDIVALKTL--KMRGQAFVIFKEIASATNALRSMQGFPFYDKPMRIQYS 85
++ S+FG+I D+V L + G +V F+ A AL+++ G + +P+ + S
Sbjct: 42 VFLELSRFGEIEDLVVCDNLGDHLLGNVYVKFETEEDAEAALQALNGRYYAGRPLYPELS 101
>gnl|CDD|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional.
Length = 256
Score = 29.6 bits (67), Expect = 1.2
Identities = 20/58 (34%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 132 RLMQAQQQQMQALSVQQPPVSQP----APPAPMATAGVPEQPPNQILFLTNLPEETSE 185
QAQQQQ A + Q PV+ P AP P A V QP + P+ +E
Sbjct: 121 IQQQAQQQQPPATTAQPQPVTPPRQTTAPVQPQTPAPVRTQPAAPVTQAVEAPKVEAE 178
Score = 27.7 bits (62), Expect = 4.7
Identities = 13/36 (36%), Positives = 13/36 (36%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPP 170
Q QQQ Q QP P TA V Q P
Sbjct: 120 QIQQQAQQQQPPATTAQPQPVTPPRQTTAPVQPQTP 155
>gnl|CDD|236555 PRK09537, pylS, pyrolysyl-tRNA synthetase; Reviewed.
Length = 417
Score = 29.8 bits (67), Expect = 1.3
Identities = 37/143 (25%), Positives = 60/143 (41%), Gaps = 11/143 (7%)
Query: 87 TDSDVISKIKGTFMERPK-KVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALS 145
+D D+ + TF ++ + KV+ AP + KS +A K + AQ + +
Sbjct: 75 SDEDINRFLTKTFEDKTQVKVKVVSAPTKKKKAMPKSVVRAPKPLENPVPAQAESSGSKP 134
Query: 146 VQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEV--RL 203
V PVS P AP P P+Q L L ++ L+ ++ P FKE+ L
Sbjct: 135 VPSIPVSTPEVKAP-----APALTPSQKDRLETLLSPKDKISLN---SEKPKFKELESEL 186
Query: 204 VPNRHDIAFVEFENEMQSAAAKL 226
V R + +E + + KL
Sbjct: 187 VSRRKNDLKQMYEEDREDYLGKL 209
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 29.9 bits (68), Expect = 1.3
Identities = 8/62 (12%), Positives = 16/62 (25%)
Query: 109 QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQ 168
PA P + +K+ A+ + + +A P + A
Sbjct: 78 APAAEPAPWLVEHAKRLTAQREQLVARAAAPAAPEAQAPAAPAERAAAENAARRLARAAA 137
Query: 169 PP 170
Sbjct: 138 AA 139
>gnl|CDD|218621 pfam05518, Totivirus_coat, Totivirus coat protein.
Length = 753
Score = 30.2 bits (68), Expect = 1.3
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 9/80 (11%)
Query: 102 RPKKVRKQPAPVEDPAEAKKSKKKAAKE--QARLMQAQQQQMQALSVQQPPVSQPAPPAP 159
RP + + EDP E ++++ + A+ QAR +S PPV + A P P
Sbjct: 589 RPTGLASGASNAEDP-EVRRARTRGARALAQARTFGRATVGEMIIS-GFPPVFKTALPRP 646
Query: 160 -----MATAGVPEQPPNQIL 174
G P +
Sbjct: 647 DYNRGGEAGGPGVPGPVPVG 666
>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 = 28.2 bits (62), Expect = 1.4
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 33 SQFGQIMDIVALKTL--KMRGQA----FVIFKEIASATNALRSMQGFPFYDKPMRIQYSK 86
S FG I +I + K + K+ GQ+ FV + + A A+ ++ G K +++ Y++
Sbjct: 22 SLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYAR 81
Query: 87 TDS 89
S
Sbjct: 82 PSS 84
>gnl|CDD|237541 PRK13881, PRK13881, conjugal transfer protein TrbI; Provisional.
Length = 472
Score = 29.7 bits (67), Expect = 1.4
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 104 KKVRKQPAPVEDPAEAKKSKKKAAKEQAR-----LMQAQQQQMQALSVQQPPVSQPAPPA 158
+ KQ AP + P E + AKE A L++ L V + P + P
Sbjct: 51 DRAAKQNAPAQGPKEKAGNTSMFAKEIAGDQTGGLIEPASP----LKVPEMPTGPASAPL 106
Query: 159 PMATAGVPEQPP 170
P+A P+ PP
Sbjct: 107 PIARPDNPDAPP 118
>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 = 27.6 bits (62), Expect = 1.4
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSM 70
+YV+ + T ++ L A+FS +G+I+ L T RG F+ F + A A++++
Sbjct: 3 LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62
Query: 71 QG 72
G
Sbjct: 63 NG 64
>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of
uncharacterized plant proteins similar to fission yeast
Vip1. This subfamily corresponds to the Vip1-like,
uncharacterized proteins found in plants. Although
their biological roles remain unclear, these proteins
show high sequence similarity to the fission yeast
Vip1. Like Vip1 protein, members in this family contain
an N-terminal RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). .
Length = 69
Score = 27.4 bits (61), Expect = 1.4
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNAL 67
V VT++S ++ +Y FS G I + ++ + A+V FK+ + AL
Sbjct: 1 VEVTNLSPKATERDIYDFFSFSGDIEYVEIQRSGEQSQTAYVTFKDPQAQETAL 54
>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 = 27.8 bits (62), Expect = 1.5
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD---IAFVEFENEMQSAAAKLALHG 230
L ++N+P + L +F QF +V ++ N FV F N + A+ LHG
Sbjct: 3 LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHG 62
>gnl|CDD|241228 cd12784, RRM2_ROD1, RNA recognition motif 2 in vertebrate
regulator of differentiation 1 (Rod1). This subgroup
corresponds to the RRM2 of ROD1 coding protein Rod1, 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 and negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It might play a role controlling
differentiation in mammals. Rod1 contains four repeats
of RNA recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and
does have RNA binding activities. .
Length = 103
Score = 28.0 bits (62), Expect = 1.7
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFYDK--PMRIQYS 85
L+ IFS+FG ++ I+ T + QA + + + +A +A ++ G Y+ +RI +S
Sbjct: 22 LHQIFSKFGTVLKIITF-TKNNQFQALLQYADPMNAHHAKMALDGQNIYNACCTLRIDFS 80
Query: 86 KTDS 89
K S
Sbjct: 81 KLTS 84
>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 = 27.2 bits (61), Expect = 1.7
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 23 DLKKSLYAIFSQFGQIM--DIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPF 75
DLK +F + G ++ D+ + +G V+F+ A A+ G+
Sbjct: 14 DLKD----LFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFNGYDL 64
>gnl|CDD|197876 smart00792, Agouti, Agouti protein. The agouti protein regulates
pigmentation in the mouse hair follicle producing a
black hair with a subapical yellow band. A highly
homologous protein agouti signal protein (ASIP) is
present in humans and is expressed at highest levels in
adipose tissue where it may play a role in energy
homeostasis and possibly human pigmentation.
Length = 124
Score = 28.3 bits (63), Expect = 1.8
Identities = 13/58 (22%), Positives = 25/58 (43%)
Query: 113 VEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPP 170
V KK KK +A+E + + ++++ +V +P P + + QPP
Sbjct: 45 VSIVGLNKKPKKISAEEAEKKLLQKKEKKALTNVLRPEPRSPRRCVRLRDSCKGPQPP 102
>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a
role in the biomineralisation of teeth. They seem to
regulate formation of crystallites during the secretory
stage of tooth enamel development and are thought to
play a major role in the structural organisation and
mineralisation of developing enamel. The extracellular
matrix of the developing enamel comprises two major
classes of protein: the hydrophobic amelogenins and the
acidic enamelins. Circular dichroism studies of porcine
amelogenin have shown that the protein consists of 3
discrete folding units: the N-terminal region appears to
contain beta-strand structures, while the C-terminal
region displays characteristics of a random coil
conformation. Subsequent studies on the bovine protein
have indicated the amelogenin structure to contain a
repetitive beta-turn segment and a "beta-spiral" between
Gln112 and Leu138, which sequester a (Pro, Leu, Gln)
rich region. The beta-spiral offers a probable site for
interactions with Ca2+ ions. Muatations in the human
amelogenin gene (AMGX) cause X-linked hypoplastic
amelogenesis imperfecta, a disease characterised by
defective enamel. A 9bp deletion in exon 2 of AMGX
results in the loss of codons for Ile5, Leu6, Phe7 and
Ala8, and replacement by a new threonine codon,
disrupting the 16-residue (Met1-Ala16) amelogenin signal
peptide.
Length = 165
Score = 28.6 bits (64), Expect = 1.9
Identities = 12/46 (26%), Positives = 14/46 (30%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLP 180
Q Q Q L QP P +P QPP +F
Sbjct: 96 AQQPFQPQPLQPPQPQQPMQPQPPVHPIPPLPPQPPLPPMFPMQPL 141
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 29.7 bits (66), Expect = 2.0
Identities = 14/31 (45%), Positives = 15/31 (48%)
Query: 130 QARLMQAQQQQMQALSVQQPPVSQPAPPAPM 160
QA+ AL QQPP QP PPAP
Sbjct: 312 QAQPHSHTPPSQSALQPQQPPREQPLPPAPS 342
>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 = 27.0 bits (60), Expect = 2.2
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIF 57
++V +S+ + + FSQFG++ D + + +T + RG FV F
Sbjct: 2 IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48
>gnl|CDD|235334 PRK05035, PRK05035, electron transport complex protein RnfC;
Provisional.
Length = 695
Score = 29.1 bits (66), Expect = 2.5
Identities = 15/60 (25%), Positives = 27/60 (45%)
Query: 104 KKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATA 163
+ R+ A+ KK+ AA +A+ +A QQ A + ++ + A A +A A
Sbjct: 530 ARARQAEKQAAAAADPKKAAVAAAIARAKAKKAAQQAANAEAEEEVDPKKAAVAAAIARA 589
>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast
asparagine-rich protein (ARP) and similar proteins.
This subfamily corresponds to the RRM of ARP, also
termed NRP1, encoded by Saccharomyces cerevisiae
YDL167C. Although its exact biological function remains
unclear, ARP contains an RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), two Ran-binding protein zinc
fingers (zf-RanBP), and an asparagine-rich region. It
may possess RNA-binding and zinc ion binding activities.
Additional research had indicated that ARP may function
as a factor involved in the stress response. .
Length = 88
Score = 27.4 bits (61), Expect = 2.6
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 12/72 (16%)
Query: 172 QILFLTNLPEETSEMMLSMLFNQFPG-------FK---EVRLVPNRHDI-AFVEFENEMQ 220
++L+++NLP +T+++ L F Q+ K E V ++ I F F++ +
Sbjct: 1 KVLYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEE 60
Query: 221 SAAAKLALHGFK 232
+ A LAL+G
Sbjct: 61 AMEA-LALNGRC 71
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 26.8 bits (60), Expect = 2.6
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 12/44 (27%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFE 216
+L + + E+TS L F +F ++A+V+F
Sbjct: 3 VLHFSGVGEQTSREDLKEAFEEF------------GEVAWVDFA 34
>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subfamily corresponds to the
RRM4 of MRD1which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). MRD1 is essential for
the initial processing at the A0-A2 cleavage sites in
the 35 S pre-rRNA. It contains 5 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), which may
play an important structural role in organizing specific
rRNA processing events. .
Length = 84
Score = 27.1 bits (60), Expect = 2.6
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 11/83 (13%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLV----PNRH------DIAFVEFENEMQSAA 223
LF+ NL T+ L+ F GF R+ P R FV F+ + Q+ A
Sbjct: 3 LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62
Query: 224 AKLALHGFKITPTHAMKISFAKK 246
A A+ GF + H + + F+ +
Sbjct: 63 ALKAMDGFVLD-GHTLVVKFSHR 84
Score = 26.7 bits (59), Expect = 4.1
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 45 KTLKMRGQAFVIFKEIASATNALRSMQGF 73
+TL M G FV FK A AL++M GF
Sbjct: 43 QTLSM-GFGFVGFKTKEQAQAALKAMDGF 70
>gnl|CDD|236365 PRK09041, motB, flagellar motor protein MotB; Validated.
Length = 317
Score = 28.8 bits (65), Expect = 2.6
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 128 KEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPP 170
K + ++ + ALS Q PVS PA A VP P
Sbjct: 272 KAEEAILHENAES-VALSAQNEPVSALEAPAAAPAASVPAAPA 313
>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 = 26.9 bits (59), Expect = 2.6
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAF--VIFKEIASATNALRSMQ 71
++V ++ ++ LY +F Q G + + K + + ++F V FK S A+ +
Sbjct: 4 LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63
Query: 72 GFPFYDKPMRIQ 83
G Y +P+++
Sbjct: 64 GIRLYGRPIKVH 75
>gnl|CDD|237081 PRK12372, PRK12372, ribonuclease III; Reviewed.
Length = 413
Score = 28.7 bits (64), Expect = 2.7
Identities = 17/82 (20%), Positives = 28/82 (34%), Gaps = 12/82 (14%)
Query: 101 ERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQ-------AQQQQMQALSVQQP---- 149
ER K + PA+ + +KAA++ A Q + S +P
Sbjct: 315 ERAAKPAAADKAADKPADRPDAAEKAAEKPAEAAPRAADKPAGQAADPASSSADKPGASA 374
Query: 150 -PVSQPAPPAPMATAGVPEQPP 170
++ A A A + PP
Sbjct: 375 DAAARTPARARDAAAPDADTPP 396
>gnl|CDD|220871 pfam10759, DUF2587, Protein of unknown function (DUF2587). This is
a bacterial family of proteins with no known function.
Length = 168
Score = 28.2 bits (63), Expect = 2.8
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 3/49 (6%)
Query: 126 AAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQIL 174
A++ A Q +Q + +AL P V P P G P Q L
Sbjct: 123 FAQQMAARAQLEQMRRRALP---PGVGIAPPGQPQGARGGPPPGTGQYL 168
>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding
protein 43 (TDP-43) and similar proteins. This
subfamily corresponds to the RRM1 of TDP-43 (also
termed TARDBP), a ubiquitously expressed pathogenic
protein whose normal function and abnormal aggregation
are directly linked to the genetic disease cystic
fibrosis, and two neurodegenerative disorders:
frontotemporal lobar degeneration (FTLD) and
amyotrophic lateral sclerosis (ALS). TDP-43 binds both
DNA and RNA, and has been implicated in transcriptional
repression, pre-mRNA splicing and translational
regulation. TDP-43 is a dimeric protein with two RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a C-terminal glycine-rich domain. The RRMs are
responsible for DNA and RNA binding; they bind to TAR
DNA and RNA sequences with UG-repeats. The glycine-rich
domain can interact with the hnRNP family proteins to
form the hnRNP-rich complex involved in splicing
inhibition. It is also essential for the cystic
fibrosis transmembrane conductance regulator (CFTR)
exon 9-skipping activity. .
Length = 77
Score = 27.0 bits (60), Expect = 2.8
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 19 ISSTDLKKSLYAIFSQFGQIMDIVA---LKTLKMRGQAFVIFKEIASATNAL 67
+ DLK Y FS FG+++ + KT + +G FV F + L
Sbjct: 11 TTEQDLKD--Y--FSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58
>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 = 26.9 bits (60), Expect = 2.9
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
++V + ++ FSQFG+++D + T + RG FV F SA + S
Sbjct: 2 IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60
Query: 71 QGFPFYDKPMRIQ 83
K + ++
Sbjct: 61 GMLELGGKQVEVK 73
>gnl|CDD|236507 PRK09424, pntA, NAD(P) transhydrogenase subunit alpha; Provisional.
Length = 509
Score = 28.6 bits (65), Expect = 2.9
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 149 PPVSQPAPPAPMATAGVPEQPP 170
PP+ A PA A A ++
Sbjct: 371 PPIQVSAAPAAAAAAPAAKEEE 392
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation factor
3 (eIF3). In yeast it is called Hcr1. The Saccharomyces
cerevisiae protein eIF3j (HCR1) has been shown to be
required for processing of 20S pre-rRNA and binds to 18S
rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 28.5 bits (64), Expect = 2.9
Identities = 9/40 (22%), Positives = 23/40 (57%)
Query: 101 ERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQ 140
E ++ ++ A V A+AKK+ K +E+ + + ++++
Sbjct: 40 EEDEEKEEEKAKVAAKAKAKKALKAKIEEKEKAKREKEEK 79
>gnl|CDD|165431 PHA03160, PHA03160, hypothetical protein; Provisional.
Length = 499
Score = 28.9 bits (64), Expect = 3.0
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 6/36 (16%)
Query: 136 AQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPN 171
+QQ MQ L VQQ P+ P P P QPP+
Sbjct: 419 SQQLPMQPLHVQQAPMQAPHVAPP------PMQPPH 448
>gnl|CDD|240888 cd12442, RRM_RBM48, RNA recognition motif in RNA-binding protein
48 (RBM48) and similar proteins. This subfamily
corresponds to the RRM of RBM48, a putative RNA-binding
protein of unknown function. It contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). .
Length = 100
Score = 27.3 bits (61), Expect = 3.0
Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMR--GQAFVI-FKEIASATNALRS 69
++ V + + ++K L +F+ +G I + L + ++I F+ I SA A R
Sbjct: 12 YLLVQGVPALGVEKELLELFALYGTIEEYRLLDEYPCEEFTEVYLIKFETIQSARFAKRK 71
Query: 70 MQGFPFYDKPMRIQY 84
+ F+ + + Y
Sbjct: 72 LDERSFFGGLLHVCY 86
>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39) and similar proteins.
This subfamily corresponds to the RRM1 of RNA-binding
protein 39 (RBM39), RNA-binding protein 23 (RBM23) and
similar proteins. RBM39 (also termed HCC1) is a nuclear
autoantigen that contains an N-terminal arginine/serine
rich (RS) motif and three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). An octapeptide sequence
called the RS-ERK motif is repeated six times in the RS
region of RBM39. Although the cellular function of RBM23
remains unclear, it shows high sequence homology to
RBM39 and contains two RRMs. It may possibly function as
a pre-mRNA splicing factor. .
Length = 73
Score = 26.8 bits (60), Expect = 3.1
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 175 FLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLALH 229
F+ L + E L F++ ++VR++ +R+ +A+VEF +E +S L L
Sbjct: 3 FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDE-ESVPLALGLT 61
Query: 230 G 230
G
Sbjct: 62 G 62
Score = 26.0 bits (58), Expect = 6.2
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMD---IVALKTLKMRGQAFVIFKEIASATNALRSM 70
V+V +S ++ LY FS+ G++ D I + + +G A+V F + S AL +
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GL 60
Query: 71 QGFPFYDKPMRIQ 83
G +P+ +Q
Sbjct: 61 TGQRLLGQPIMVQ 73
>gnl|CDD|215618 PLN03184, PLN03184, chloroplast Hsp70; Provisional.
Length = 673
Score = 28.7 bits (64), Expect = 3.3
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 108 KQPAPVEDPAEAKKSKKKAA------KEQARLMQAQQQQMQAL--SVQQPPVSQPAPPAP 159
K PA V++ EAK + K A ++ M A Q++ + S+ P + A PAP
Sbjct: 588 KVPADVKEKVEAKLKELKDAIASGSTQKMKDAMAALNQEVMQIGQSLYNQPGAGGAGPAP 647
Query: 160 MATAG 164
AG
Sbjct: 648 GGEAG 652
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 28.5 bits (64), Expect = 3.4
Identities = 10/52 (19%), Positives = 19/52 (36%), Gaps = 4/52 (7%)
Query: 110 PAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMA 161
+ + K SKK A K A+ + +++ + S P+A
Sbjct: 2 SQEAVEESGEKISKKAAKKAAAKAEKLRREATAKAAAA----SLEDEDDPLA 49
>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM1 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 81
Score = 26.8 bits (60), Expect = 3.4
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 28 LYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNALRSMQG 72
+Y+ F++ G++ + ++ T K G FV F +A AL+S+ G
Sbjct: 16 IYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63
>gnl|CDD|222655 pfam14291, DUF4371, Domain of unknown function (DUF4371).
Length = 179
Score = 28.0 bits (63), Expect = 3.4
Identities = 10/42 (23%), Positives = 21/42 (50%), Gaps = 7/42 (16%)
Query: 13 FVYVTHISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAF 54
V+V +S LK ++ ++ ++ G + K+RGQ +
Sbjct: 133 VVHVEETTSLTLKSAIDSLLAKHGLSLS-------KVRGQGY 167
>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like
family member CELF-1, CELF-2 and similar proteins. This
subgroup corresponds to the RRM3 of CELF-1 (also termed
BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also
termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both
of which belong to the CUGBP1 and ETR-3-like factors
(CELF) or BRUNOL (Bruno-like) family of RNA-binding
proteins that have been implicated in the regulation of
pre-mRNA splicing and in the control of mRNA translation
and deadenylation. CELF-1 is strongly expressed in all
adult and fetal tissues tested. Human CELF-1 is a
nuclear and cytoplasmic RNA-binding protein that
regulates multiple aspects of nuclear and cytoplasmic
mRNA processing, with implications for onset of type 1
myotonic dystrophy (DM1), a neuromuscular disease
associated with an unstable CUG triplet expansion in the
3'-UTR (3'-untranslated region) of the DMPK (myotonic
dystrophy protein kinase) gene; it preferentially
targets UGU-rich mRNA elements. It has been shown to
bind to a Bruno response element, a cis-element involved
in translational control of oskar mRNA in Drosophila,
and share sequence similarity to Bruno, the Drosophila
protein that mediates this process. The Xenopus homolog
embryo deadenylation element-binding protein (EDEN-BP)
mediates sequence-specific deadenylation of Eg5 mRNA. It
specifically binds to the EDEN motif in the
3'-untranslated regions of maternal mRNAs and targets
these mRNAs for deadenylation and translational
repression. CELF-1 contain three highly conserved RNA
recognition motifs (RRMs), also known as RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains):
two consecutive RRMs (RRM1 and RRM2) situated in the
N-terminal region followed by a linker region and the
third RRM (RRM3) close to the C-terminus of the protein.
The two N-terminal RRMs of EDEN-BP are necessary for the
interaction with EDEN as well as a part of the linker
region (between RRM2 and RRM3). Oligomerization of
EDEN-BP is required for specific mRNA deadenylation and
binding. CELF-2 is expressed in all tissues at some
level, but highest in brain, heart, and thymus. It has
been implicated in the regulation of nuclear and
cytoplasmic RNA processing events, including alternative
splicing, RNA editing, stability and translation. CELF-2
shares high sequence identity with CELF-1, but shows
different binding specificity; it binds preferentially
to sequences with UG repeats and UGUU motifs. It has
been shown to bind to a Bruno response element, a
cis-element involved in translational control of oskar
mRNA in Drosophila, and share sequence similarity to
Bruno, the Drosophila protein that mediates this
process. It also binds to the 3'-UTR of cyclooxygenase-2
messages, affecting both translation and mRNA stability,
and binds to apoB mRNA, regulating its C to U editing.
CELF-2 also contain three highly conserved RRMs. It
binds to RNA via the first two RRMs, which are important
for localization in the cytoplasm. The splicing
activation or repression activity of CELF-2 on some
specific substrates is mediated by RRM1/RRM2. Both, RRM1
and RRM2 of CELF-2, can activate cardiac troponin T
(cTNT) exon 5 inclusion. In addition, CELF-2 possesses a
typical arginine and lysine-rich nuclear localization
signal (NLS) in the C-terminus, within RRM3. .
Length = 92
Score = 26.9 bits (59), Expect = 3.5
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 167 EQPPNQILFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQS 221
E P LF+ +LP+E + L +F F ++ ++ FV ++N + +
Sbjct: 3 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 62
Query: 222 AAAKLALHGFKI 233
AA A++GF+I
Sbjct: 63 QAAIQAMNGFQI 74
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 28.9 bits (64), Expect = 3.5
Identities = 15/70 (21%), Positives = 19/70 (27%)
Query: 103 PKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMAT 162
QP P ++ + Q Q Q P+ QP P
Sbjct: 349 VDVPPAQPTVAWQPVPGPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYY 408
Query: 163 AGVPEQPPNQ 172
A EQP Q
Sbjct: 409 APAAEQPAQQ 418
>gnl|CDD|177556 PHA03195, PHA03195, tegument protein VP11/12; Provisional.
Length = 746
Score = 28.8 bits (64), Expect = 3.5
Identities = 10/67 (14%), Positives = 15/67 (22%)
Query: 123 KKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFLTNLPEE 182
+ + Q P PAPP P + LP
Sbjct: 415 RTGSCPPQGATFGRNPSGFPGQFCCPPQGPLPAPPNSKTRGTFRRPRPGSVRGSRQLPAS 474
Query: 183 TSEMMLS 189
++S
Sbjct: 475 PPSNIVS 481
>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 = 26.6 bits (59), Expect = 3.6
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 6/61 (9%)
Query: 31 IFSQFGQIMDIVALKTLKMR------GQAFVIFKEIASATNALRSMQGFPFYDKPMRIQY 84
I S F I +I + K ++ + G FV + + A A+ ++ G +K +++ Y
Sbjct: 18 IRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVSY 77
Query: 85 S 85
+
Sbjct: 78 A 78
>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 = 26.4 bits (59), Expect = 3.6
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 5/65 (7%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEFENEMQSAAAKLAL 228
+F+ LP SE + L F K LV + AF E+ + + A L
Sbjct: 3 IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62
Query: 229 HGFKI 233
+G ++
Sbjct: 63 NGMQL 67
>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 = 26.6 bits (59), Expect = 3.9
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHD-----IAFVEF 215
LF+ NL +E L LF+++ EV L ++ AFV +
Sbjct: 5 LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 51
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 28.2 bits (63), Expect = 4.1
Identities = 9/38 (23%), Positives = 11/38 (28%)
Query: 135 QAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
A Q+ + QP Q A V PP
Sbjct: 397 AASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAA 434
>gnl|CDD|240997 cd12553, RRM1_RBM15, RNA recognition motif 1 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM1 of RBM15, also termed
one-twenty two protein 1 (OTT1), conserved in
eukaryotes, a novel mRNA export factor and component of
the NXF1 pathway. It binds to NXF1 and serves as
receptor for the RNA export element RTE. It also
possesses mRNA export activity and can facilitate the
access of DEAD-box protein DBP5 to mRNA at the nuclear
pore complex (NPC). RBM15 belongs to the Spen (split
end) protein family, which contains three N-terminal
RNA recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal SPOC (Spen paralog and ortholog
C-terminal) domain. This family also includes a
RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is
N-terminally fused to megakaryoblastic leukemia 1
protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties.
Length = 78
Score = 26.5 bits (58), Expect = 4.2
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 17 THISSTDLKKSLYAIFSQFGQIMDIVALKTLKMRGQAFVIFKEIASATNALRSMQGFPFY 76
+ +S ++ L+ F +FG + V + L AFV F+ A A + Y
Sbjct: 11 SQLSDEAVEDGLFHEFKKFGDVS--VKISRLGDERVAFVNFRRPEDARAAKHARGRLVLY 68
Query: 77 DKPMRIQ 83
D+P++I+
Sbjct: 69 DRPLKIE 75
>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found
in heterogeneous nuclear ribonucleoprotein (hnRNP) H
protein family, epithelial splicing regulatory proteins
(ESRPs), Drosophila RNA-binding protein Fusilli,
RNA-binding protein 12 (RBM12) and similar proteins.
The family includes RRM domains in the hnRNP H protein
family, G-rich sequence factor 1 (GRSF-1), ESRPs (also
termed RBM35), Drosophila Fusilli, RBM12 (also termed
SWAN), RBM12B, RBM19 (also termed RBD-1) and similar
proteins. The hnRNP H protein family includes hnRNP H
(also termed mcs94-1), hnRNP H2 (also termed FTP-3 or
hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9),
which represent a group of nuclear RNA binding proteins
that are involved in pre-mRNA processing. GRSF-1 is a
cytoplasmic poly(A)+ mRNA binding protein which
interacts with RNA in a G-rich element-dependent manner.
It may function in RNA packaging, stabilization of RNA
secondary structure, or other macromolecular
interactions. ESRP1 (also termed RBM35A) and ESRP2 (also
termed RBM35B) are epithelial-specific RNA binding
proteins that promote splicing of the epithelial variant
of fibroblast growth factor receptor 2 (FGFR2), ENAH
(also termed hMena), CD44 and CTNND1 (also termed
p120-Catenin) transcripts. Fusilli shows high sequence
homology to ESRPs. It can regulate endogenous FGFR2
splicing and functions as a splicing factor. The
biological roles of both, RBM12 and RBM12B, remain
unclear. RBM19 is a nucleolar protein conserved in
eukaryotes. It is involved in ribosome biogenesis by
processing rRNA. In addition, it is essential for
preimplantation development. Members in this family
contain 2~6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 73
Score = 26.4 bits (59), Expect = 4.3
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 173 ILFLTNLPEETSEMMLSMLFNQF-PGFKEVRLVPNRHD----IAFVEFENEMQSAAAKLA 227
++ L LP +E + F+ + +V + A+VEF + + A L
Sbjct: 1 VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRA-LR 59
Query: 228 LHGFKI 233
H K+
Sbjct: 60 KHNNKM 65
>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 = 4.3
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFKI 233
LF+ P + +L +F +F G +V LVP + + + ++ + + A LHG ++
Sbjct: 2 LFIVCNPSPPPDYILEDVFCRFGGLIDVYLVPGK-NYGYAKYADRESAERAITTLHGKEV 60
>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 = 26.2 bits (57), Expect = 4.7
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 27 SLYAIFSQFGQIMDIVALK---TLKMRGQAFVIFKEIASATNAL 67
SL FS+FG+I + + ++ T + RG FV F + AS L
Sbjct: 15 SLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVL 58
>gnl|CDD|241139 cd12695, RRM3_PTBP1, RNA recognition motif 3 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM3 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there is
an unusual and conserved interdomain interaction between
RRM3 and RRM4. It is widely held that only RRMs 3 and 4
are involved in RNA binding and RRM2 mediates PTB
homodimer formation. However, new evidence show that the
RRMs 1 and 2 also contribute substantially to RNA
binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 93
Score = 26.5 bits (58), Expect = 4.7
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 173 ILFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGF 231
+L ++NL PE + L +LF + + V+++ N+ + A V+ + Q+ A L+G
Sbjct: 1 VLLVSNLNPERVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQ 60
Query: 232 KI 233
K+
Sbjct: 61 KL 62
>gnl|CDD|223066 PHA03379, PHA03379, EBNA-3A; Provisional.
Length = 935
Score = 28.1 bits (62), Expect = 5.1
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 100 MERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAP 159
ME P + +Q P ++ A +A + A Q Q L +QQP +SQ AP AP
Sbjct: 622 MEYPLEPEQQMFPGSPFSQV------ADVMRAGGVPAMQPQYFDLPLQQP-ISQGAPLAP 674
Query: 160 M--ATAGVPEQPPNQ 172
+ + VP P Q
Sbjct: 675 LRASMGPVPPVPATQ 689
Score = 27.7 bits (61), Expect = 7.5
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 131 ARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQ 168
ARL Q ++ VQ P ++Q +P PM PEQ
Sbjct: 593 ARLRAEAQPYQASVEVQPPQLTQVSPQQPMEYPLEPEQ 630
>gnl|CDD|225711 COG3170, FimV, Tfp pilus assembly protein FimV [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 755
Score = 28.0 bits (62), Expect = 5.1
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 6/78 (7%)
Query: 101 ERPKKVRKQPAPVEDPAEAKKSKKKAAKE-QARLMQAQQQQMQALSVQQP----PVSQPA 155
E K R + PA+ K + A + +QAQ + Q + Q +Q A
Sbjct: 273 EPSKADRVGKPVAKAPAKVAKERALAELPARVAELQAQLNKAQHE-LAQKAAPLAAAQAA 331
Query: 156 PPAPMATAGVPEQPPNQI 173
AP TA P P Q+
Sbjct: 332 LDAPAETATAPSAPAPQV 349
>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 = 26.2 bits (58), Expect = 5.2
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 11 TNFVYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKE 59
T ++V + + L FSQFG + ++V + + + RG F+ F+
Sbjct: 2 TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFES 53
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 28.0 bits (62), Expect = 5.4
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 88 DSDVISKIKGTFMERPKKVRK--QPAPVEDPAEAKKSKKKAAKEQA 131
+ V S I+ K VR+ + A A KK KKA ++A
Sbjct: 960 ATAVASGIEKVAEAVRKTVRRSVKKAAATRAAMKKKVAKKAPAKKA 1005
>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 = 26.0 bits (57), Expect = 6.1
Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFGQIMDIVAL---KTLKMRGQAFVIFKEIASATNALRSM 70
++V +++ + ++ L FS I V + +T + RG FV F + A AL +
Sbjct: 2 LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61
Query: 71 QGFPFYDKPMRIQYSK 86
+ + + +R+ ++
Sbjct: 62 KNKKLHGRILRLDIAE 77
>gnl|CDD|182003 PRK09628, oorB, 2-oxoglutarate-acceptor oxidoreductase subunit
OorB; Reviewed.
Length = 277
Score = 27.4 bits (61), Expect = 6.2
Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 13/87 (14%)
Query: 2 NIILAHICVTNFVYVTHISSTD--LKKSLYAIFSQFGQI---MDIVALKTLKMRGQAFVI 56
NI L I + NF+Y S T K ++ + +Q+G I D A K G +FV
Sbjct: 113 NIDLNFILINNFIYGLTNSQTSPTTPKGMWTVTAQYGNIDPTFD--ACKLATAAGASFVA 170
Query: 57 FKEIASATNALR------SMQGFPFYD 77
+ + + S +GF F+D
Sbjct: 171 RESVIDPQKLEKLLVKGFSHKGFSFFD 197
>gnl|CDD|236394 PRK09169, PRK09169, hypothetical protein; Validated.
Length = 2316
Score = 27.8 bits (62), Expect = 6.3
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 127 AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATA 163
A+E A L+ AQ + + A P + P P A A
Sbjct: 1678 AREAAELLHAQLEALAAAPANTPSPAAPPPALSAALA 1714
>gnl|CDD|222579 pfam14179, YppG, YppG-like protein. The YppG-like protein family
includes the B. subtilis YppG protein, which is
functionally uncharacterized. This family of proteins is
found in bacteria. Proteins in this family are typically
between 115 and 181 amino acids in length. There are two
completely conserved residues (F and G) that may be
functionally important.
Length = 110
Score = 26.6 bits (59), Expect = 6.5
Identities = 10/40 (25%), Positives = 11/40 (27%)
Query: 133 LMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
Q Q PP Q P P+Q P Q
Sbjct: 20 YQQQPYHQQMPPPPYSPPQQQQGHFMPPQPQPYPKQSPQQ 59
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 27.4 bits (61), Expect = 6.5
Identities = 14/72 (19%), Positives = 17/72 (23%), Gaps = 1/72 (1%)
Query: 109 QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQ 168
P PV + QA QQQ P AG Q
Sbjct: 55 APPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTG-SPAANPPATFALPAGPAGPTIQ 113
Query: 169 PPNQILFLTNLP 180
L+ +P
Sbjct: 114 TEPGQLYPVQVP 125
>gnl|CDD|227911 COG5624, TAF61, Transcription initiation factor TFIID, subunit
TAF12 (also component of histone acetyltransferase SAGA)
[Transcription].
Length = 505
Score = 27.7 bits (61), Expect = 6.7
Identities = 23/99 (23%), Positives = 30/99 (30%), Gaps = 26/99 (26%)
Query: 128 KEQARLMQAQQQQMQALSVQQ---------------PPVSQPAPPAPMATAGVPEQPPNQ 172
+ R Q QQ Q Q LS QQ PP G E+ P
Sbjct: 229 RLVDRYPQFQQGQKQVLSPQQRFLHGMERYEASGMPPPAEWAGSNGLHVLPGRREEVPRG 288
Query: 173 ILFLTNLPEE----------TSEMMLSMLFNQFPGFKEV 201
I F PE + M + ++FPG +
Sbjct: 289 I-FRCPSPESSRGEPTHLDYRNGMANNAQRSRFPGTCSI 326
>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 = 27.7 bits (61), Expect = 6.7
Identities = 38/189 (20%), Positives = 65/189 (34%), Gaps = 32/189 (16%)
Query: 12 NFVYVTHI----SSTDLKKSLYAIFSQFGQIMDIV---ALKTLKMRGQAFVIFKEIASAT 64
N +YV + S TD+K ++F FG+I+ A +G F+ + + S +
Sbjct: 205 NRIYVASVHPDLSETDIK----SVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS 260
Query: 65 NALRSMQGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKK 124
A+ SM F + +R+ T D + + P V PA A A +K
Sbjct: 261 EAIASMNLFDLGGQYLRVGKCVTPPDALLQ--------PATVSAIPAAAAVAAAAATAKI 312
Query: 125 KA-------------AKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPN 171
A A+ A + + +V + P+ A P
Sbjct: 313 MAAEAVAGAAVLGPRAQSPATPSSSLPTDIGNKAVVSSAKKEAEEVPPLPQAAPAVVKPG 372
Query: 172 QILFLTNLP 180
+ T +P
Sbjct: 373 PMEIPTPVP 381
>gnl|CDD|234352 TIGR03779, Bac_Flav_CT_M, Bacteroides conjugative transposon TraM
protein. Members of this protein family are designated
TraM and are found in a proposed transfer region of a
class of conjugative transposon found in the Bacteroides
lineage [Cellular processes, DNA transformation].
Length = 410
Score = 27.8 bits (62), Expect = 6.8
Identities = 23/128 (17%), Positives = 48/128 (37%), Gaps = 7/128 (5%)
Query: 59 EIASATNALRSM--QGFPFYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDP 116
I S+ A R + + FY+ P + + +++ +++ + P E
Sbjct: 118 PIRSSAAAYRDINRELGSFYEYP----KTDEEKELLREVEELESRLATEPSPAPELEEQL 173
Query: 117 AEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQILFL 176
A +KS + AAK R + ++ ++P V QP +QP + F+
Sbjct: 174 ALMEKSYELAAKYMPRGQERLPVAPESKKGKKPSV-QPVRAVEEKAVSSLQQPMSDAEFV 232
Query: 177 TNLPEETS 184
+ +
Sbjct: 233 AEYSKPRN 240
>gnl|CDD|221431 pfam12127, YdfA_immunity, SigmaW regulon antibacterial. This
protein is found in bacteria. Proteins in this family
are about 330 amino acids in length. The operon from
which this protein is derived confers immunity for the
host species to a broad range of antibacterial
compounds, unlike the specific immunity proteins that
are linked to and co-regulated with their
antibiotic-synthesis proteins.
Length = 318
Score = 27.3 bits (61), Expect = 6.9
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 115 DPAEAKKSKKKAAKEQARLMQ-AQQQQMQAL 144
D AEA K +A E+ R M A++Q+M+A
Sbjct: 233 DQAEADKRIAQAKAEERRAMAVAREQEMKAK 263
>gnl|CDD|215544 PLN03029, PLN03029, type-a response regulator protein; Provisional.
Length = 222
Score = 27.3 bits (60), Expect = 7.0
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 16/83 (19%)
Query: 75 FYDKPMRIQYSKTDSDVISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLM 134
F+ KP+++ SD+ +++K M+ K +KQ + K++ +E
Sbjct: 128 FFLKPVQL------SDL-NRLKPHMMKTKSKNQKQ---------ENQEKQEKLEESEIQS 171
Query: 135 QAQQQQMQALSVQQPPVSQPAPP 157
+ Q+Q Q Q P QP P
Sbjct: 172 EKQEQPSQQPQSQPQPQQQPQQP 194
>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA
stem-loop-interacting RNA-binding protein (SLIRP) and
similar proteins. This subfamily corresponds to the
RRM of SLIRP, a widely expressed small steroid receptor
RNA activator (SRA) binding protein, which binds to
STR7, a functional substructure of SRA. SLIRP is
localized predominantly to the mitochondria and plays a
key role in modulating several nuclear receptor (NR)
pathways. It functions as a co-repressor to repress
SRA-mediated nuclear receptor coactivation. It
modulates SHARP- and SKIP-mediated co-regulation of NR
activity. SLIRP contains an RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), which is required for
SLIRP's corepression activities. .
Length = 73
Score = 25.7 bits (57), Expect = 7.4
Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 6/58 (10%)
Query: 14 VYVTHISSTDLKKSLYAIFSQFG---QIMDIVALKTLKMRGQAFVIFK---EIASATN 65
++V ++ T K L FSQFG +T +G FV F + +A
Sbjct: 2 LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQ 59
>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 = 25.6 bits (56), Expect = 7.5
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 174 LFLTNLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLAL 228
LF+ NLP + +E + LF ++ E+ + ++ F+ E + AK L
Sbjct: 4 LFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKDK-GFGFIRLETRTLAEIAKAEL 57
>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer
membranes [Cell envelope biogenesis, outer membrane].
Length = 244
Score = 27.1 bits (60), Expect = 7.7
Identities = 16/77 (20%), Positives = 24/77 (31%), Gaps = 4/77 (5%)
Query: 100 MERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQP--PVSQPAPP 157
E+PK +K P P K K K + + + A + P P P+
Sbjct: 85 KEKPKPEKKPKKPKPKPKPKPKPKPKVKPQPKP--KKPPSKTAAKAPAAPNQPARPPSAA 142
Query: 158 APMATAGVPEQPPNQIL 174
+ A P L
Sbjct: 143 SASGAATGPSASYLSGL 159
>gnl|CDD|240710 cd12264, RRM_AKAP17A, RNA recognition motif found in A-kinase
anchor protein 17A (AKAP-17A) and similar proteins.
This subfamily corresponds to the RRM domain of
AKAP-17A, also termed 721P, or splicing factor,
arginine/serine-rich 17A (SFRS17A). It was originally
reported as the pseudoautosomal or X inactivation escape
gene 7 (XE7) and as B-lymphocyte antigen precursor. It
has been suggested that AKAP-17A is an alternative
splicing factor and an SR-related splicing protein that
interacts with the classical SR protein ASF/SF2 and the
SR-related factor ZNF265. Additional studies have
indicated that AKAP-17A is a dual-specific protein
kinase A anchoring protein (AKAP) that can bind both
type I and type II protein kinase A (PKA) with high
affinity and co-localizes with the catalytic subunit of
PKA in nuclear speckles as well as the splicing factor
SC35 in splicing factor compartments. It is involved in
regulation of pre-mRNA splicing possibly by docking a
pool of PKA in splicing factor compartments. AKAP-17A
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
.
Length = 121
Score = 26.5 bits (59), Expect = 8.0
Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 25/90 (27%)
Query: 28 LYAIFSQFGQI--MDIVALKTL--KMRG--------------QAFVIFKEIASATNALRS 69
L +FS+FG+I +DI L +M + +V ++E A+ +
Sbjct: 31 LRTVFSKFGEIRNVDIPMLDPYRKEMDDRGSDTFSFGSHLHFEVYVQYEEYDGFVKAMDA 90
Query: 70 MQGFPFYDKPMRIQYSKTDSDVISKIKGTF 99
++G M++QY + + IK F
Sbjct: 91 LRG-------MKLQYKGDGKALAANIKVDF 113
>gnl|CDD|240987 cd12543, RRM2_PAR14, RNA recognition motif 2 in vertebrate poly
[ADP-ribose] polymerase 14 (PARP-14). This subgroup
corresponds to the RRM2 of PARP-14, also termed
aggressive lymphoma protein 2, a member of the B
aggressive lymphoma (BAL) family of
macrodomain-containing PARPs. It is expressed in B
lymphocytes and interacts with the IL-4-induced
transcription factor Stat6. It plays a fundamental role
in the regulation of IL-4-induced B-cell protection
against apoptosis after irradiation or growth factor
withdrawal. It mediates IL-4 effects on the levels of
gene products that regulate cell survival,
proliferation, and lymphomagenesis. PARP-14 acts as a
transcriptional switch for Stat6-dependent gene
activation. In the presence of IL-4, PARP-14 activates
transcription by facilitating the binding of Stat6 to
the promoter and release of HDACs from the promoter with
an IL-4 signal. In contrast, in the absence of a signal,
PARP-14 acts as a transcriptional repressor by
recruiting HDACs. Absence of PARP-14 protects against
Myc-induced developmental block and lymphoma. Thus,
PARP-14 may play an important role in Myc-induced
oncogenesis. Additional research indicates that PARP-14
is also a binding partner with phosphoglucose isomerase
(PGI)/ autocrine motility factor (AMF). It can inhibit
PGI/AMF ubiquitination, thus contributing to its
stabilization and secretion. PARP-14 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), three tandem macro domains, and C-terminal
region with sequence homology to PARP catalytic domain.
.
Length = 74
Score = 25.5 bits (56), Expect = 8.1
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 2/43 (4%)
Query: 178 NLPEETSEMMLSMLFNQFPGFKEVRLVPNRHDI--AFVEFENE 218
NLP + L + F G EV V + A + F++
Sbjct: 8 NLPPNANSDYLELYFENPNGGGEVANVEFFPEESSAIITFKDG 50
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 27.2 bits (61), Expect = 8.2
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 92 ISKIKGTFMERPKKVRKQPAPVEDPAEAKKSKKKAAKE 129
I +IK + + PKK R++ P + + K+ KK ++
Sbjct: 372 IEEIKEKYPKPPKKKREEKKPQKRKKKKKRKKKGKKRK 409
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 27.5 bits (61), Expect = 8.2
Identities = 16/69 (23%), Positives = 20/69 (28%), Gaps = 1/69 (1%)
Query: 103 PKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQP-PVSQPAPPAPMA 161
P A A A + A + A QA + P P + PA A A
Sbjct: 406 PAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPA 465
Query: 162 TAGVPEQPP 170
AG
Sbjct: 466 AAGPRPVAA 474
Score = 27.1 bits (60), Expect = 9.6
Identities = 18/81 (22%), Positives = 25/81 (30%), Gaps = 5/81 (6%)
Query: 107 RKQPAPVEDPAEAKKSKKKAAKEQARL-----MQAQQQQMQALSVQQPPVSQPAPPAPMA 161
R+ PAP A + S + A A + A + + A PA A
Sbjct: 425 RRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAA 484
Query: 162 TAGVPEQPPNQILFLTNLPEE 182
A P + LP E
Sbjct: 485 PAAAPAPADDDPPPWEELPPE 505
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 27.3 bits (60), Expect = 8.5
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 103 PKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQP-PVSQPAP-PAPM 160
P+ K APV P K S ++ R+ A + + A++++QP V + AP AP+
Sbjct: 73 PQAPTKPAAPVHAPL--KLSANANMSQRQRVASAAEDMIAAMALRQPVSVPRQAPAAAPV 130
Query: 161 ATAGVP 166
A +P
Sbjct: 131 RAASIP 136
>gnl|CDD|241142 cd12698, RRM3_PTBPH3, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subgroup corresponds to the RRM3 of PTBPH3.
Although its biological roles remain unclear, PTBPH3
shows significant sequence similarity to polypyrimidine
tract binding protein (PTB) that is an important
negative regulator of alternative splicing in mammalian
cells and also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. Like
PTB, PTBPH3 contains four RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 25.6 bits (56), Expect = 8.6
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 174 LFLTNL-PEETSEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFENEMQSAAAKLALHGFK 232
L ++NL PE+ L LF+ + ++L+ N+ D A ++ + Q A+LA++ K
Sbjct: 4 LLVSNLNPEKIDADKLFNLFSNYGNIVRIKLLHNKPDHALIQMGDGFQ---AELAVNYLK 60
Query: 233 ITPTHA--MKISFAK 245
M+++F+K
Sbjct: 61 GAMLFGKRMEVNFSK 75
>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the
p54nrb/PSF/PSP1 family. This subfamily corresponds to
the RRM2 of the p54nrb/PSF/PSP1 family, including 54
kDa nuclear RNA- and DNA-binding protein (p54nrb or
NonO or NMT55), polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF or POMp100),
paraspeckle protein 1 (PSP1 or PSPC1), which are
ubiquitously expressed and are conserved in
vertebrates. p54nrb is a multi-functional protein
involved in numerous nuclear processes including
transcriptional regulation, splicing, DNA unwinding,
nuclear retention of hyperedited double-stranded RNA,
viral RNA processing, control of cell proliferation,
and circadian rhythm maintenance. PSF is also a
multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSP1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSP1 remains unknown currently. The family also
includes some p54nrb/PSF/PSP1 homologs from
invertebrate species, such as the Drosophila
melanogaster gene no-ontransient A (nonA) encoding
puff-specific protein Bj6 (also termed NONA) and
Chironomus tentans hrp65 gene encoding protein Hrp65.
D. melanogaster NONA is involved in eye development and
behavior and may play a role in circadian rhythm
maintenance, similar to vertebrate p54nrb. C. tentans
Hrp65 is a component of nuclear fibers associated with
ribonucleoprotein particles in transit from the gene to
the nuclear pore. All family members contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction module. PSF has an
additional large N-terminal domain that differentiates
it from other family members. .
Length = 80
Score = 25.7 bits (57), Expect = 8.7
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 28 LYAIFSQFGQIMDIVALKTLKMRGQA----FVIFKEIASATNALR 68
L FSQFG++ A+ + RG++ V F A A++
Sbjct: 16 LEQAFSQFGEVER--AVVIVDDRGRSTGEGIVEFSRKPGAQAAIK 58
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 27.4 bits (61), Expect = 9.2
Identities = 14/69 (20%), Positives = 20/69 (28%), Gaps = 2/69 (2%)
Query: 106 VRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGV 165
R PA + PA + + + +A S PAPP
Sbjct: 650 SRAPPASLSKPASSPDASQTSASFDLDPDFELATHQSVPEAALASGSAPAPPPVPDPYDR 709
Query: 166 P--EQPPNQ 172
P E+ P
Sbjct: 710 PPWEEAPEV 718
>gnl|CDD|233787 TIGR02223, ftsN, cell division protein FtsN. FtsN is a poorly
conserved protein active in cell division in a number of
Proteobacteria. The N-terminal 30 residue region tends
to by Lys/Arg-rich, and is followed by a
membrane-spanning region. This is followed by an acidic
low-complexity region of variable length and a
well-conserved C-terminal domain of two tandem regions
matched by pfam05036 (Sporulation related repeat), found
in several cell division and sporulation proteins. The
role of FtsN as a suppressor for other cell division
mutations is poorly understood; it may involve cell wall
hydrolysis [Cellular processes, Cell division].
Length = 298
Score = 27.0 bits (59), Expect = 9.3
Identities = 14/59 (23%), Positives = 22/59 (37%)
Query: 109 QPAPVEDPAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPE 167
Q PVE A K K+ K++A Q + Q + ++ P + A E
Sbjct: 167 QKTPVETEKIASKVKEAKQKQKALPKQTAETQSNSKPIETAPKADKADKTKPKPKEKAE 225
>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional.
Length = 428
Score = 27.0 bits (60), Expect = 9.5
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 117 AEAKKSKKKAAKEQARLMQAQQQQMQALSVQQ 148
AE K+++++ A ++A L + Q QQ L QQ
Sbjct: 173 AELKQTREELAAQKAELEEKQSQQKTLLYEQQ 204
>gnl|CDD|177871 PLN02226, PLN02226, 2-oxoglutarate dehydrogenase E2 component.
Length = 463
Score = 27.0 bits (59), Expect = 9.9
Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 116 PAEAKKSKKKAAKEQARLMQAQQQQMQALSVQQPPVSQPAPPAPMATAGVPEQPPNQ 172
P++ K + K Q+ ++++ V + P + +PP P +A P+ PP +
Sbjct: 177 PSQ-KIPETTDPKPSPPAEDKQKPKVESAPVAEKPKAPSSPPPPKQSAKEPQLPPKE 232
>gnl|CDD|205480 pfam13300, DUF4078, Domain of unknown function (DUF4078). This
family is found from fungi to humans, but its exact
function is not known.
Length = 88
Score = 25.7 bits (57), Expect = 9.9
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 100 MERPKKVRKQPAPVEDPAEAKKSKKKAAKEQARLMQAQQ 138
ME +K R++ E +K K+K A E R + ++
Sbjct: 49 MEELEKAREETERERKEREERKEKRKRAIE-ERRKKIEE 86
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.130 0.365
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,312,648
Number of extensions: 1151456
Number of successful extensions: 3805
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3361
Number of HSP's successfully gapped: 593
Length of query: 246
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 152
Effective length of database: 6,768,326
Effective search space: 1028785552
Effective search space used: 1028785552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.3 bits)