RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14559
(405 letters)
>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11),
splicing regulatory glutamine/lysine-rich protein 1
(SREK1) and similar proteins. This subfamily
corresponds to the RRM domain of SRSF11 (SRp54 or p54),
SREK1 ( SFRS12 or SRrp86) and similar proteins, a group
of proteins containing regions rich in serine-arginine
dipeptides (SR protein family). These are involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SR proteins have been identified as crucial
regulators of alternative splicing. Different SR
proteins display different substrate specificity, have
distinct functions in alternative splicing of different
pre-mRNAs, and can even negatively regulate splicing.
All SR family members are characterized by the presence
of one or two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and the C-terminal regions
rich in serine and arginine dipeptides (SR domains).
The RRM domain is responsible for RNA binding and
specificity in both alternative and constitutive
splicing. In contrast, SR domains are thought to be
protein-protein interaction domains that are often
interchangeable. .
Length = 76
Score = 118 bits (298), Expect = 5e-33
Identities = 48/77 (62%), Positives = 64/77 (83%), Gaps = 1/77 (1%)
Query: 13 VVQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKCVGIS 72
VVQV N++PQAT +QM+TLFG+LGK+E+LRLYP D+ PV S++C+VK+ D + VG++
Sbjct: 1 VVQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDL-APVLSKVCFVKYEDPEDVGVA 59
Query: 73 QHLTNTVFIDRALVVTP 89
HLTNTVFIDRAL+V P
Sbjct: 60 LHLTNTVFIDRALIVVP 76
>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 = 108 bits (272), Expect = 3e-29
Identities = 36/85 (42%), Positives = 53/85 (62%)
Query: 163 EEIRRTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPA 222
EEIRRT+ N++ + + +L++FF + G V Y+R E +YA VEF++Q VI A
Sbjct: 1 EEIRRTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINA 60
Query: 223 LKLNGTNLKGKTLQMFHSTQSIQKP 247
LKLNG G+ L++ HS +I KP
Sbjct: 61 LKLNGAMFGGRPLKVNHSNNAIVKP 85
Score = 28.8 bits (65), Expect = 1.4
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKCVGISQ 73
+ V N+ P T DQ+ F G+V+ +R+ A D + P +R +V+F ++ V +
Sbjct: 7 IYVGNLDPTTTADQLLEFFSQAGEVKYVRM---AGDETQP--TRYAFVEFAEQTSVINAL 61
Query: 74 HLTNTVFIDRALVVT 88
L +F R L V
Sbjct: 62 KLNGAMFGGRPLKVN 76
>gnl|CDD|240962 cd12518, RRM_SRSF11, RNA recognition motif in
serine/arginine-rich splicing factor 11 (SRSF11) and
similar proteins. This subgroup corresponds to the RRM
of SRSF11, also termed arginine-rich 54 kDa nuclear
protein (SRp54 or p54), which belongs to a family of
proteins containing regions rich in serine-arginine
dipeptides (SR proteins family). It is involved in
bridge-complex formation and splicing by mediating
protein-protein interactions across either introns or
exons. SRSF11 has been identified as a tau exon 10
splicing repressor. It interacts with a purine-rich
element in exon 10, and suppresses exon 10 inclusion by
antagonizing Tra2beta, an SR-domain-containing protein
that enhances exon 10 inclusion. SRSF11 is a unique SR
family member and may regulate the alternative splicing
in a tissue- and substrate-dependent manner. It can
directly interact with the U2 auxiliary factor 65-kDa
subunit (U2AF65), a protein associated with the 3'
splice site. In addition, unlike the typical SR
proteins, SRSF11 associates with other SR proteins but
not with the U1 small nuclear ribonucleoprotein U1-70K
or the U2 auxiliary factor 35-kDa subunit (U2AF35).
SREK1 has unique properties in regulating alternative
splicing of different pre-mRNAs; it promotes the use of
the distal 5' splice site in E1A pre-mRNA alternative
splicing. It also inhibits cryptic splice site
selection on the beta-globin pre-mRNA containing
competing 5' splice sites. SREK1 contains an RNA
recognition motif (RRM), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and one
serine-arginine (SR)-rich domains (SR domains). .
Length = 80
Score = 102 bits (256), Expect = 3e-27
Identities = 46/81 (56%), Positives = 63/81 (77%), Gaps = 1/81 (1%)
Query: 13 VVQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKCVGIS 72
V+QV N++P A+ +QM+TLFG+LGK+++LRL+P D +PV SR+C+VKF D +S
Sbjct: 1 VIQVTNVSPSASSEQMRTLFGFLGKIDELRLFP-PDDSPLPVTSRVCFVKFHDPDSAVVS 59
Query: 73 QHLTNTVFIDRALVVTPYNSG 93
QHLTNTVF+DRAL+V PY G
Sbjct: 60 QHLTNTVFVDRALIVVPYAEG 80
>gnl|CDD|240963 cd12519, RRM1_SREK1, RNA recognition motif 1 in splicing
regulatory glutamine/lysine-rich protein 1 (SREK1) and
similar proteins. This subgroup corresponds to the
RRM1 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), and 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 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 generally
contains two 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; 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 = 80
Score = 93.5 bits (232), Expect = 1e-23
Identities = 42/81 (51%), Positives = 59/81 (72%), Gaps = 1/81 (1%)
Query: 13 VVQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKCVGIS 72
V+QV N++ T DQM+TLFG+LG +E+LRLYP + + S++CY+K+ + VG++
Sbjct: 1 VIQVTNLSAAVTSDQMRTLFGFLGDIEELRLYP-PDNAPLAFSSKVCYIKYREPSSVGVA 59
Query: 73 QHLTNTVFIDRALVVTPYNSG 93
QHLTNTVFIDRAL+V P G
Sbjct: 60 QHLTNTVFIDRALIVVPCAEG 80
>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II
polyadenylate-binding proteins. This subfamily
corresponds to the RRM of type II polyadenylate-binding
proteins (PABPs), including polyadenylate-binding
protein 2 (PABP-2 or PABPN1), embryonic
polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and
similar proteins. PABPs are highly conserved proteins
that bind to the poly(A) tail present at the 3' ends of
most eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. ePABP-2 is
predominantly located in the cytoplasm and PABP-2 is
located in the nucleus. In contrast to the type I PABPs
containing four copies of RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), the type II PABPs contains
a single highly-conserved RRM. This subfamily also
includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C)
gene encoding cytoplasmic mRNA-binding protein Rbp29
that binds preferentially to poly(A). Although not
essential for cell viability, Rbp29 plays a role in
modulating the expression of cytoplasmic mRNA. Like
other type II PABPs, Rbp29 contains one RRM only. .
Length = 73
Score = 54.6 bits (132), Expect = 8e-10
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRF-CTRENDTNK-YALVEFSDQACVIPALKLNGTNL 230
N++ +P+EL + F+ GT+N I C + K +A +EF D++ V AL LN +
Sbjct: 6 NVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNESEF 65
Query: 231 KGKTLQMF 238
+G+ +++
Sbjct: 66 RGRQIKVT 73
>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 = 51.5 bits (124), Expect = 8e-09
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSDQACVIPALK-LNGTNL 230
N+ + ++L + F K G + +R ++ +K +A VEF AL+ LNG L
Sbjct: 5 NLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKEL 64
Query: 231 KGKTLQ 236
G+ L+
Sbjct: 65 DGRKLK 70
Score = 35.0 bits (81), Expect = 0.006
Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 11/78 (14%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFD----EKCV 69
+ V N+ P T + ++ LF G++E +R+ S +V+F EK +
Sbjct: 1 LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKS----KGFAFVEFESPEDAEKAL 56
Query: 70 GISQHLTNTVFIDRALVV 87
+ L R L V
Sbjct: 57 ---EALNGKELDGRKLKV 71
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 51.0 bits (123), Expect = 1e-08
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALK-LNGTNLK 231
N+ SV+ ++L +FF G V +R ++ +A VEF+ ALK LNG L
Sbjct: 5 NLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLD 64
Query: 232 GKTLQ 236
G+TL+
Sbjct: 65 GRTLR 69
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 50.3 bits (121), Expect = 2e-08
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPALK-LNGT 228
N+ + +EL + F K G V +R R+ +T K +A VEF + AL+ LNG
Sbjct: 6 NLPPDTTEEELRELFSKFGKVESVRLV-RDKETGKSKGFAFVEFESEEDAEKALEALNGK 64
Query: 229 NLKGKTL 235
L G+ L
Sbjct: 65 ELDGRPL 71
Score = 34.1 bits (79), Expect = 0.012
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 16 VANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFD----EKCVGI 71
V N+ P T ++++ LF GKVE +R + RD +V+F EK +
Sbjct: 4 VGNLPPDTTEEELRELFSKFGKVESVR---LVRDKETGKSKGFAFVEFESEEDAEKAL-- 58
Query: 72 SQHLTNTVFIDRALVV 87
+ L R L V
Sbjct: 59 -EALNGKELDGRPLKV 73
>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 = 50.4 bits (121), Expect = 2e-08
Identities = 26/74 (35%), Positives = 40/74 (54%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLN 226
RT+ I+ S+S +L +FF G V +R C + ++A VEF+D + AL L+
Sbjct: 1 RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALNLS 60
Query: 227 GTNLKGKTLQMFHS 240
GT L G L++ S
Sbjct: 61 GTLLGGHPLRVSPS 74
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 49.5 bits (119), Expect = 4e-08
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSDQACVIPALK-LNGTNL 230
N+ + ++L D F K G + IR E +K +A VEF D+ AL+ LNG L
Sbjct: 5 NLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKEL 64
Query: 231 KGKTL 235
G+ L
Sbjct: 65 GGREL 69
Score = 30.6 bits (70), Expect = 0.17
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 16 VANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDE 66
V N+ P T + ++ LF G +E +R+ S +V+F DE
Sbjct: 3 VGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRS----KGFAFVEFEDE 49
>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 = 46.8 bits (112), Expect = 4e-07
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPALK 224
T+ + + V ++L +FF K G V +R R+ ++ + A VEF D+ V AL
Sbjct: 1 TVFVMQLSLKVRERDLYEFFSKAGKVRDVR-IIRDRNSRRSKGVAYVEFYDEESVPLALG 59
Query: 225 LNGTNLKG 232
L G L G
Sbjct: 60 LTGQRLLG 67
Score = 28.3 bits (64), Expect = 1.4
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSR-ICYVKFFDEKCVGIS 72
V V ++ + + F GKV D+R I RD +S+ + YV+F+DE+ V ++
Sbjct: 2 VFVMQLSLKVRERDLYEFFSKAGKVRDVR---IIRD-RNSRRSKGVAYVEFYDEESVPLA 57
Query: 73 QHLTNTVFIDRALVV 87
LT + + ++V
Sbjct: 58 LGLTGQRLLGQPIMV 72
>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 = 47.0 bits (112), Expect = 5e-07
Identities = 25/80 (31%), Positives = 42/80 (52%)
Query: 165 IRRTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALK 224
IRRT+ +I++ V+ ++L F G V R C N ++A +EF+D+ AL
Sbjct: 1 IRRTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAALS 60
Query: 225 LNGTNLKGKTLQMFHSTQSI 244
L+GT L +++ S +I
Sbjct: 61 LSGTMLGFYPVRVLPSKTAI 80
Score = 30.5 bits (69), Expect = 0.31
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 12 KVVQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKCVGI 71
+ V V++I Q T +Q+ LF G+V D R + D + + R +++F DE+
Sbjct: 3 RTVYVSDIDQQVTEEQLAALFSNCGQVVDCR---VCGDPNSVL--RFAFIEFTDEEGARA 57
Query: 72 SQHLTNTVFIDRALVVTP 89
+ L+ T+ + V P
Sbjct: 58 ALSLSGTMLGFYPVRVLP 75
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 48.8 bits (115), Expect = 2e-06
Identities = 33/184 (17%), Positives = 73/184 (39%), Gaps = 9/184 (4%)
Query: 82 DRALVVTPYNSGEIPDEQRALEIAAQQQGPNSGEPKLPAHVTNQIEGVPPNQVISTHDPV 141
+ L E ++ LE+ +++ P ++++ + ++ +D
Sbjct: 28 ELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDGE 87
Query: 142 LVQHGLPQYPPLPITYDTKKIEEIR---RTLVAINIEESVSPQELVDFFQKVGTVNYIRF 198
+ + K ++ + TL N+ V+ ++L + F+K G V +R
Sbjct: 88 RGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRL 147
Query: 199 CTRENDTNK---YALVEFSDQACVIPALK-LNGTNLKGKTLQMFHSTQSIQKPEAKSNEA 254
R+ +T K +A VEF + A++ LNG L+G+ L+ Q +P ++ +
Sbjct: 148 V-RDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLR-VQKAQPASQPRSELSNN 205
Query: 255 AQRE 258
Sbjct: 206 LDAS 209
Score = 31.8 bits (71), Expect = 0.54
Identities = 21/128 (16%), Positives = 42/128 (32%), Gaps = 6/128 (4%)
Query: 8 PVKTKVVQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEK 67
+ + V N+ T + ++ LF G V+ +R + RD +V+F E+
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVR---LVRDRETGKSRGFAFVEFESEE 168
Query: 68 CVGIS-QHLTNTVFIDRALVV--TPYNSGEIPDEQRALEIAAQQQGPNSGEPKLPAHVTN 124
+ + L R L V S + L+ + ++ L
Sbjct: 169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNL 228
Query: 125 QIEGVPPN 132
+ +P
Sbjct: 229 YVGNLPLK 236
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 49.1 bits (117), Expect = 2e-06
Identities = 31/108 (28%), Positives = 50/108 (46%), Gaps = 15/108 (13%)
Query: 151 PPLPITYDTKKIEEIRRTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK--- 207
P+T E RT+ + + ++L +FF KVG V ++ C ++ ++ +
Sbjct: 78 TKEPLTEA----ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQ-CIKDRNSRRSKG 132
Query: 208 YALVEFSDQACVIPALKLNGTNLKGKTLQMFHSTQSIQKPEAKSNEAA 255
A VEF D VI AL L G L G+ + +Q +A+ N AA
Sbjct: 133 VAYVEFYDVESVIKALALTGQMLLGRPII-------VQSSQAEKNRAA 173
Score = 33.7 bits (77), Expect = 0.16
Identities = 50/252 (19%), Positives = 94/252 (37%), Gaps = 65/252 (25%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSR-ICYVKFFDEKCVGIS 72
V V +A +A + F +GKV D++ I S +S+ + YV+F+D + V +
Sbjct: 92 VFVLQLALKARERDLYEFFSKVGKVRDVQC--IKDRNS--RRSKGVAYVEFYDVESVIKA 147
Query: 73 QHLTNTVFIDRALVVTPYNSGEIPDEQRALEIAAQQQGPNSGEPKLPAHVTNQIEGVPPN 132
LT + + R ++V + ++ RA + A Q G KL +V N
Sbjct: 148 LALTGQMLLGRPIIVQSSQA----EKNRAAKAATHQPGDIPNFLKL--YVGN-------- 193
Query: 133 QVISTHDPVLVQHGLPQYPPLPITYDTKKIEEIRRTLVAINIEESVSPQELVDFFQKVGT 192
+ NI E QEL F+ G
Sbjct: 194 -------------------------------------LHFNITE----QELRQIFEPFGD 212
Query: 193 VNYIRFCTRENDTNK---YALVEFSDQACVIPAL-KLNGTNLKGKTLQMFHSTQSIQKPE 248
+ ++ R+ +T + + ++F D AL +NG L G+ +++ ++ S +
Sbjct: 213 IEDVQL-HRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLD 271
Query: 249 AKSNEAAQREIE 260
A + + +
Sbjct: 272 AANTFEDIDKQQ 283
>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 = 42.9 bits (102), Expect = 6e-06
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 183 LVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALK-LNGTNLKGKTLQMFHS 240
L F G V I+ +A VEFS + A++ LNG G+ L++ +S
Sbjct: 1 LYKLFSPFGNVEKIKLL---KKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56
>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 = 43.0 bits (102), Expect = 1e-05
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPALK-LNGT 228
NI + ++L++ F +VG V R T + DT K Y EF D A++ LNG
Sbjct: 5 NIPYDATEEQLIEIFSEVGPVVSFRLVT-DRDTGKPKGYGFCEFEDIETAASAIRNLNGY 63
Query: 229 NLKGKTLQMFHS 240
G+ L++ +
Sbjct: 64 EFNGRALRVDFA 75
Score = 29.1 bits (66), Expect = 0.71
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRL 43
V V NI AT +Q+ +F +G V RL
Sbjct: 1 VFVGNIPYDATEEQLIEIFSEVGPVVSFRL 30
>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor SRSF1, SRSF4 and
similar proteins. This subfamily corresponds to the
RRM2 of several serine/arginine (SR) proteins that have
been classified into two subgroups. The first subgroup
consists of serine/arginine-rich splicing factor 4
(SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing
factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and
serine/arginine-rich splicing factor 6 (SRSF6 or SRp55).
The second subgroup is composed of serine/arginine-rich
splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich
splicing factor 9 (SRSF9 or SRp30C) and plant
pre-mRNA-splicing factor SF2 (SR1). These SR proteins
are mainly involved in regulating constitutive and
alternative pre-mRNA splicing. They also have been
implicated in transcription, genomic stability, mRNA
export and translation. All SR proteins in this family,
except SRSF5, undergo nucleocytoplasmic shuttling,
suggesting their widespread roles in gene expression.
These SR proteins share a common domain architecture
comprising two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by a C-terminal RS
domains rich in serine-arginine dipeptides. Both domains
can directly contact with RNA. The RRMs appear to
determine the binding specificity and the SR domain also
mediates protein-protein interactions. In addition, this
subfamily includes the yeast nucleolar protein 3
(Npl3p), also termed mitochondrial targeting suppressor
1 protein, or nuclear polyadenylated RNA-binding protein
1. It is a major yeast RNA-binding protein that competes
with 3'-end processing factors, such as Rna15, for
binding to the nascent RNA, protecting the transcript
from premature termination and coordinating
transcription termination and the packaging of the fully
processed transcript for export. It specifically
recognizes a class of G/U-rich RNAs. Npl3p is a
multi-domain protein with two RRMs, separated by a short
linker and a C-terminal domain rich in glycine, arginine
and serine residues. .
Length = 71
Score = 42.6 bits (101), Expect = 1e-05
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KLNGTNLK 231
+ E S Q+L DF ++ G V Y + D +VEF+ Q + AL KL+GT +
Sbjct: 7 GLPEGASWQDLKDFGRQAGDVTY---ADVDRDQEGEGVVEFTSQEDMERALRKLDGTEFR 63
Query: 232 GKTLQ 236
G+ ++
Sbjct: 64 GRRVR 68
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRF-CTRENDTNK----YALVEFSDQACVIPALKLNG 227
N++ + +L F K G V IR ++ + +A V F D + AL+LNG
Sbjct: 7 NLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQLNG 66
Query: 228 TNLKGKTL 235
T L G+ +
Sbjct: 67 TELGGRKI 74
>gnl|CDD|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in
nucleolin-like proteins mainly from plants. This
subfamily corresponds to the RRM1 of a group of plant
nucleolin-like proteins, including nucleolin 1 (also
termed protein nucleolin like 1) and nucleolin 2 (also
termed protein nucleolin like 2, or protein parallel
like 1). They play roles in the regulation of ribosome
synthesis and in the growth and development of plants.
Like yeast nucleolin, nucleolin-like proteins possess
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 77
Score = 40.8 bits (96), Expect = 5e-05
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSDQACVIPALKLN 226
TL N+ S +L +FF++ G V +R ++ +K + VEF+ + AL+ +
Sbjct: 1 TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60
Query: 227 GTNLKGKTL 235
G L G+ +
Sbjct: 61 GEELLGREI 69
>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 = 40.1 bits (94), Expect = 1e-04
Identities = 18/72 (25%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KL 225
RTL N+E++ + +L + F++ G + I ++ YA ++++D A V+ A+ K+
Sbjct: 3 RTLFIGNLEKTTTYSDLREAFERFGEIIDIDI-KKQGGNPAYAFIQYADIASVVKAMRKM 61
Query: 226 NGTNLKGKTLQM 237
+G L +++
Sbjct: 62 DGEYLGNNRVKL 73
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 40.0 bits (94), Expect = 1e-04
Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 10/72 (13%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-------YALVEFSDQACVIPALK- 224
N++ ++ L+ F K G + F + + Y V F + ALK
Sbjct: 6 NLDSRLTEFHLLKLFSKYGKIKKFDF--LFHKSGPLKGQPRGYCFVTFETKEEAEKALKS 63
Query: 225 LNGTNLKGKTLQ 236
LNG GK L
Sbjct: 64 LNGKTALGKKLV 75
>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 = 39.6 bits (93), Expect = 2e-04
Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 3/69 (4%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSDQACVIPALKLNGTNLK 231
N++ SV EL F K G + +R +K YA VEF ++ V ALKL+ +K
Sbjct: 6 NLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKLDRELIK 65
Query: 232 GKTLQMFHS 240
G+ MF S
Sbjct: 66 GRP--MFVS 72
>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 = 39.6 bits (93), Expect = 2e-04
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 166 RRTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALK- 224
+ ++ + V+ +EL + F + G + + R N TN +A ++F + A++
Sbjct: 3 KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVES 62
Query: 225 LNGTNLKGKTL 235
N + LK KT+
Sbjct: 63 ENHSMLKNKTM 73
>gnl|CDD|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate
RNA-binding protein 39 (RBM39). This subgroup
corresponds to the RRM1 of RBM39, also termed
hepatocellular carcinoma protein 1, or RNA-binding
region-containing protein 2, or splicing factor HCC1, a
nuclear autoantigen that contains an N-terminal
arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Based on the
specific domain composition, RBM39 has been classified
into a family of non-snRNP (small nuclear
ribonucleoprotein) splicing factors that are usually not
complexed to snRNAs. .
Length = 85
Score = 38.9 bits (90), Expect = 4e-04
Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 9/91 (9%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTREND--TNKYALVEFSDQACVIPALK 224
RT+ + + + P++L +FF VG V +R + N + A VEF D + V A+
Sbjct: 2 RTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIG 61
Query: 225 LNGTNLKGKTLQMFHSTQSIQKPEAKSNEAA 255
L G + G + +Q +A+ N AA
Sbjct: 62 LTGQRVLGVPI-------IVQASQAEKNRAA 85
>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM2 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 73
Score = 37.9 bits (89), Expect = 5e-04
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPALKLNGTN 229
N+ + +EL F+ G V +R R+ T + V F + V ALKLNG
Sbjct: 6 NLPFDIEEEELRKHFEDCGDVEAVRI-VRDRKTGIGKGFGYVLFKTKDSVALALKLNGIK 64
Query: 230 LKGKTL 235
LKG+ +
Sbjct: 65 LKGRKI 70
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 37.8 bits (88), Expect = 8e-04
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSDQACVIPA-LKLNGTNL 230
+ SV+ +EL F+K G V +R T + K A VE+ +++ A LK++GT +
Sbjct: 9 GLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEI 68
Query: 231 KGKTLQ 236
K KT+
Sbjct: 69 KEKTIS 74
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 37.2 bits (87), Expect = 0.001
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCT-RENDTNK-YALVEFSDQACVIPAL-KLNGTN 229
N+ +V+ ++L D F + G V R T RE ++ + VE A+ KLNGT+
Sbjct: 6 NLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTD 65
Query: 230 LKGKTL 235
G+TL
Sbjct: 66 FGGRTL 71
Score = 27.2 bits (61), Expect = 3.8
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 16 VANIAPQATRDQMQTLFGYLGKVEDLRL 43
V N+ T + ++ LFG G+V R+
Sbjct: 4 VGNLPYNVTEEDLKDLFGQFGEVTSARV 31
>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 = 36.7 bits (85), Expect = 0.001
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCT-RENDTNK-YALVEFSDQACVIPALK-LNGTN 229
NI + ++L D F +VG V R RE K Y E+ DQ + A++ LNG
Sbjct: 5 NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYE 64
Query: 230 LKGKTLQM 237
L G+ L++
Sbjct: 65 LNGRQLRV 72
Score = 27.1 bits (60), Expect = 4.1
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRL 43
V V NI +AT +Q++ +F +G V RL
Sbjct: 1 VFVGNIPYEATEEQLKDIFSEVGPVVSFRL 30
>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable
RNA-binding protein 23 (RBM23). This subgroup
corresponds to the RRM1 of RBM23, also termed
RNA-binding region-containing protein 4, or splicing
factor SF2, which may function as a pre-mRNA splicing
factor. It shows high sequence homology to RNA-binding
protein 39 (RBM39 or HCC1), a nuclear autoantigen that
contains an N-terminal arginine/serine rich (RS) motif
and three RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). In contrast to RBM39, RBM23 contains only two
RRMs. .
Length = 85
Score = 35.8 bits (82), Expect = 0.005
Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 9/91 (9%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTREND--TNKYALVEFSDQACVIPALK 224
RT+ + + + P++L DFF VG V +R + N + A VEF + V A+
Sbjct: 2 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 61
Query: 225 LNGTNLKGKTLQMFHSTQSIQKPEAKSNEAA 255
L G L G + +Q +A+ N A
Sbjct: 62 LTGQRLLGVPI-------IVQASQAEKNRLA 85
>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 = 35.4 bits (82), Expect = 0.005
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCT-RENDTNK-YALVEFSDQACVIPALKLNGTNL 230
N+ + ++L+ F+ G +R T ++ +K A VEF + ALKL+ T L
Sbjct: 7 NLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLHHTLL 66
Query: 231 KGK 233
KG+
Sbjct: 67 KGR 69
>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 = 35.0 bits (81), Expect = 0.005
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALK-LNGTNLK 231
N++ +V+ L + F ++G + + RE+ + YA VE+ D AL+ +NG +
Sbjct: 5 NLDRTVTEDLLAELFSQIGPIKSCKL-IREHGNDPYAFVEYYDHRSAAAALQTMNGRLIL 63
Query: 232 GK 233
G+
Sbjct: 64 GQ 65
Score = 27.7 bits (62), Expect = 2.2
Identities = 10/55 (18%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKC 68
+ V N+ T D + LF +G ++ +L + +V+++D +
Sbjct: 1 LYVGNLDRTVTEDLLAELFSQIGPIKSCKL------IREHGNDPYAFVEYYDHRS 49
>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 = 35.1 bits (81), Expect = 0.006
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKCVGISQ 73
V+V N++P+AT + F + G +E + I R QS+ YV F D + +
Sbjct: 1 VEVTNLSPKATERDIYDFFSFSGDIEYVE---IQRSGE---QSQTAYVTFKDPQAQETAL 54
Query: 74 HLTNTVFIDRALVVT 88
L+ +D+++ +T
Sbjct: 55 LLSGATIVDQSVTIT 69
Score = 30.5 bits (69), Expect = 0.24
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLNG 227
N+ + +++ DFF G + Y+ R + ++ A V F D AL L+G
Sbjct: 5 NLSPKATERDIYDFFSFSGDIEYVEI-QRSGEQSQTAYVTFKDPQAQETALLLSG 58
>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 = 35.2 bits (82), Expect = 0.006
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPAL-KLNGT 228
++ V+ L + F G V IR C R+ T + YA V F + A AL LN
Sbjct: 6 DLHPDVTEAMLYEIFSPAGPVLSIRVC-RDLITRRSLGYAYVNFQNPADAERALDTLNFD 64
Query: 229 NLKGK 233
+KGK
Sbjct: 65 VIKGK 69
>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 = 34.5 bits (80), Expect = 0.009
Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 173 NIEESVSPQELVDFFQKVGTVNY-IRFCTRENDTNK-YALVEFSDQACVIPALKLNGTNL 230
+ S + +++ DFF + I ++ A VEF+ AL+ + +
Sbjct: 6 GLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKHNNKM 65
Query: 231 KGKTLQMF 238
G+ +++F
Sbjct: 66 GGRYIEVF 73
>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like
proteins mainly from plants. This subfamily corresponds
to the RRM2 of a group of plant nucleolin-like proteins,
including nucleolin 1 (also termed protein nucleolin
like 1) and nucleolin 2 (also termed protein nucleolin
like 2, or protein parallel like 1). They play roles in
the regulation of ribosome synthesis and in the growth
and development of plants. Like yeast nucleolin,
nucleolin-like proteins possess two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 79
Score = 34.3 bits (79), Expect = 0.011
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 182 ELVDFFQKVGTVNYIRFCT-RENDTNK-YALVEFSDQACVIPALKLNGTNLKGKTL 235
L + F G + + T RE +K +A +EF V AL+L+G++L G L
Sbjct: 19 SLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNL 74
>gnl|CDD|215588 PLN03120, PLN03120, nucleic acid binding protein; Provisional.
Length = 260
Score = 36.9 bits (86), Expect = 0.012
Identities = 26/111 (23%), Positives = 53/111 (47%), Gaps = 10/111 (9%)
Query: 6 VAPVKTKVVQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFD 65
V V+T V+V+N++ +AT ++ F + G +E + + + +S+I YV F D
Sbjct: 1 VMQVRT--VKVSNVSLKATERDIKEFFSFSGDIEYVE---MQSENE---RSQIAYVTFKD 52
Query: 66 EKCVGISQHLTNTVFIDRALVVTPYNSGEIPDEQRALEIAAQQQGPNSGEP 116
+ + L+ +D+++ +TP ++P E AL + + E
Sbjct: 53 PQGAETALLLSGATIVDQSVTITPAEDYQLPPE--ALAPLSSNSPASGAES 101
Score = 28.5 bits (64), Expect = 5.8
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLN 226
RT+ N+ + +++ +FF G + Y+ EN+ ++ A V F D AL L+
Sbjct: 5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEM-QSENERSQIAYVTFKDPQGAETALLLS 63
Query: 227 G 227
G
Sbjct: 64 G 64
>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 = 33.7 bits (78), Expect = 0.015
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDT-NKYALVEFSDQACVIPALK-LNGTNL 230
N+ ++ + +EL F+K GTV E D Y V ++ A+K LNG
Sbjct: 6 NLPDATTSEELRALFEKYGTVT-------ECDVVKNYGFVHMEEEEDAEDAIKALNGYEF 58
Query: 231 KGKTLQ 236
GK +
Sbjct: 59 MGKRIN 64
>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 = 33.6 bits (77), Expect = 0.018
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKY-ALVEFSDQACVIPALK-L 225
TLV N++ SVS +L F G + I RE ++ +EF D ALK L
Sbjct: 3 TLVVFNLDPSVSNDDLHQIFGAYGEIKEI----RETPNKRHHKFIEFYDVRSAEAALKAL 58
Query: 226 NGTNLKGKTLQM 237
N + + GK +++
Sbjct: 59 NRSEIAGKRIKL 70
Score = 27.5 bits (61), Expect = 2.7
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 16 VANIAPQATRDQMQTLFGYLGKVEDLRLYPIAR 48
V N+ P + D + +FG G+++++R P R
Sbjct: 6 VFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKR 38
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 33.5 bits (77), Expect = 0.019
Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KLN 226
L+ N+ VS Q+L DF +K G V Y + N+ +VEF+ + + A+ KL+
Sbjct: 2 RLIVENLSSRVSWQDLKDFMRKAGEVTYAD--AHKQRPNE-GVVEFATYSDMKRAIEKLD 58
Query: 227 GTNLKGKTLQM 237
GT L G+ +++
Sbjct: 59 GTELNGRKIKL 69
>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate
RRM-containing coactivator activator/modulator (CoAA).
This subgroup corresponds to the RRM1 of CoAA, also
termed RNA-binding protein 14 (RBM14), or paraspeckle
protein 2 (PSP2), or synaptotagmin-interacting protein
(SYT-interacting protein), a heterogeneous nuclear
ribonucleoprotein (hnRNP)-like protein identified as a
nuclear receptor coactivator. It mediates
transcriptional coactivation and RNA splicing effects in
a promoter-preferential manner and is enhanced by
thyroid hormone receptor-binding protein (TRBP). CoAA
contains two N-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a TRBP-interacting
domain. It stimulates transcription through its
interactions with coactivators, such as TRBP and
CREB-binding protein CBP/p300, via the TRBP-interacting
domain and interaction with an RNA-containing complex,
such as DNA-dependent protein kinase-poly(ADP-ribose)
polymerase complexes, via the RRMs. .
Length = 69
Score = 32.9 bits (75), Expect = 0.036
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KLNGTNLK 231
N++E S +EL F+ G V ++A V +A A+ +LNG L
Sbjct: 7 NVDEDTSQEELRALFEAYGAVLSCAV------MRQFAFVHLRGEAAADRAIEELNGRELH 60
Query: 232 GKTLQMFHS 240
G+ L + HS
Sbjct: 61 GRKLVVEHS 69
>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing
protein YRA2 (Yra2p) and similar proteins. This
subfamily corresponds to the RRM of Yra2p, a
nonessential nuclear RNA-binding protein encoded by
Saccharomyces cerevisiae YRA2 gene. It may share some
overlapping functions with Yra1p, and is able to
complement an YRA1 deletion when overexpressed in yeast.
Yra2p belongs to the evolutionarily conserved REF (RNA
and export factor binding proteins) family of hnRNP-like
proteins. It is a major component of endogenous Yra1p
complexes. It interacts with Yra1p and functions as a
negative regulator of Yra1p. Yra2p consists of two
highly conserved N- and C-terminal boxes and a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 74
Score = 32.7 bits (75), Expect = 0.037
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KLNGTNLK 231
NI VS + D ++ G Y +F ++ ++ A+ EF D + + + K NG L
Sbjct: 7 NIPLDVSDYTIEDLIKEFGEPVYSKF--YDHKDSRTAVFEFEDPSILEKVVEKYNGKELN 64
Query: 232 GKTLQ 236
G ++
Sbjct: 65 GAKIE 69
>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8
(NOL8) and similar proteins. This model corresponds to
the RRM of NOL8 (also termed Nop132) encoded by a novel
NOL8 gene that is up-regulated in the majority of
diffuse-type, but not intestinal-type, gastric cancers.
Thus, NOL8 may be a good molecular target for treatment
of diffuse-type gastric cancer. Also, NOL8 is a
phosphorylated protein that contains an N-terminal RNA
recognition motif (RRM), also known as RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), suggesting
NOL8 is likely to function as a novel RNA-binding
protein. It may be involved in regulation of gene
expression at the post-transcriptional level or in
ribosome biogenesis in cancer cells.
Length = 78
Score = 32.5 bits (75), Expect = 0.045
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 14/73 (19%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTREND--TNKYALVEF--SDQACVIPALK---- 224
+ SV+ +L + F + GTV+ + +++ +A ++ S+ LK
Sbjct: 6 GLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEA-----QLKKCKS 60
Query: 225 -LNGTNLKGKTLQ 236
LNGT KG L+
Sbjct: 61 TLNGTKWKGSVLK 73
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 32.5 bits (75), Expect = 0.049
Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 11/78 (14%)
Query: 167 RTLVAINIEESVSPQELVDFF-QKVGTVNYIR-------FCTRENDTNKYALVEF-SDQA 217
R L N+ ++ +ELVDFF Q + + + N +A VEF + +
Sbjct: 2 RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKN-FAFVEFRTVEE 60
Query: 218 CVIPALKLNGTNLKGKTL 235
AL L+G KG+ L
Sbjct: 61 ATA-ALALDGIIFKGQPL 77
>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 = 35.2 bits (81), Expect = 0.067
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPAL-KLNGT 228
+++ V+ +L D F+ G V +R C R++ T + Y V F + A AL +N
Sbjct: 7 DLDPDVTEAKLYDLFKPFGPVLSVRVC-RDSVTRRSLGYGYVNFQNPADAERALETMNFK 65
Query: 229 NLKGK 233
L GK
Sbjct: 66 RLGGK 70
Score = 34.0 bits (78), Expect = 0.14
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSDQACVIPAL-KLNGTNL 230
N+++SV + L D F K G + + T EN ++ Y V F + A+ K+NG L
Sbjct: 95 NLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLL 154
Query: 231 KGK 233
K
Sbjct: 155 NDK 157
>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II
polyadenylate-binding protein 2 (PABP-2) and similar
proteins. This subgroup corresponds to the RRM of
PABP-2, also termed poly(A)-binding protein 2, or
nuclear poly(A)-binding protein 1 (PABPN1), or
poly(A)-binding protein II (PABII), which is a
ubiquitously expressed type II nuclear poly(A)-binding
protein that directs the elongation of mRNA poly(A)
tails during pre-mRNA processing. Although PABP-2 binds
poly(A) with high affinity and specificity as type I
poly(A)-binding proteins, it contains only one highly
conserved RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
which is responsible for the poly(A) binding. In
addition, PABP-2 possesses an acidic N-terminal domain
that is essential for the stimulation of PAP, and an
arginine-rich C-terminal domain. .
Length = 76
Score = 32.1 bits (73), Expect = 0.077
Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIR-FCTRENDTNK-YALVEFSDQACVIPALKLNGTNL 230
N++ + +EL F G+VN + C + + K +A +EFSD+ V AL L+ +
Sbjct: 6 NVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALDESLF 65
Query: 231 KGKTLQM 237
+G+ +++
Sbjct: 66 RGRQIKV 72
>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 = 32.0 bits (72), Expect = 0.081
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 2/81 (2%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KLN 226
TL N+ V+ ++ F ++G + T + Y VEF + AL +N
Sbjct: 1 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60
Query: 227 GTNLKGKTLQM-FHSTQSIQK 246
G + GK +++ + +T S QK
Sbjct: 61 GRKILGKEVKVNWATTPSSQK 81
>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 = 31.8 bits (73), Expect = 0.084
Identities = 22/74 (29%), Positives = 31/74 (41%), Gaps = 10/74 (13%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSD-----QACVIP 221
R L N+ +S +EL D F K G + IR +T A V + D AC
Sbjct: 3 RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGN-TKETRGTAFVVYEDIYDAKNACD-- 59
Query: 222 ALKLNGTNLKGKTL 235
L+G N+ + L
Sbjct: 60 --HLSGFNVANRYL 71
>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis
thaliana phragmoplastin interacting protein 1 (PHIP1)
and similar proteins. The CD corresponds to the RRM2 of
PHIP1. A. thaliana PHIP1 and its homologs represent a
novel class of plant-specific RNA-binding proteins that
may play a unique role in the polarized mRNA transport
to the vicinity of the cell plate. The family members
consist of multiple functional domains, including a
lysine-rich domain (KRD domain) that contains three
nuclear localization motifs (KKKR/NK), two RNA
recognition motifs (RRMs), and three CCHC-type zinc
fingers. PHIP1 is a peripheral membrane protein and is
localized at the cell plate during cytokinesis in
plants. In addition to phragmoplastin, PHIP1 interacts
with two Arabidopsis small GTP-binding proteins, Rop1
and Ran2. However, PHIP1 interacted only with the
GTP-bound form of Rop1 but not the GDP-bound form. It
also binds specifically to Ran2 mRNA. .
Length = 72
Score = 31.6 bits (72), Expect = 0.088
Identities = 18/68 (26%), Positives = 39/68 (57%), Gaps = 5/68 (7%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPALKLNGTN 229
N+ ++ ++ +FF K + +R T + +T + + V+F+D+ + ALKL+GT
Sbjct: 6 NLAWDITEDDVREFF-KGCEITSVRLAT-DKETGEFKGFGHVDFADEESLDAALKLDGTV 63
Query: 230 LKGKTLQM 237
L G+ +++
Sbjct: 64 LCGRPIRI 71
>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 = 31.8 bits (73), Expect = 0.093
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYP 45
V V N+ T +++Q F G +E++R++
Sbjct: 3 VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFK 34
Score = 30.7 bits (70), Expect = 0.19
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEF-SDQACVIPALKLNGTNLK 231
N+ ++ +EL F G + +R YA V F + +A + +NGT++
Sbjct: 7 NLPHGLTEEELQRTFSPFGAIEEVRV----FKDKGYAFVRFDTHEAAATAIVAVNGTSIN 62
Query: 232 GKTL 235
G+T+
Sbjct: 63 GQTV 66
>gnl|CDD|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like
proteins. This subgroup corresponds to the RRM1 of
Mei2-like proteins that represent an ancient eukaryotic
RNA-binding proteins family. Their corresponding
Mei2-like genes appear to have arisen early in eukaryote
evolution, been lost from some lineages such as
Saccharomyces cerevisiae and metazoans, and diversified
in the plant lineage. The plant Mei2-like genes may
function in cell fate specification during development,
rather than as stimulators of meiosis. Members in this
family contain three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The C-terminal RRM (RRM3)
is unique to Mei2-like proteins and it is highly
conserved between plants and fungi. Up to date, the
intracellular localization, RNA target(s), cellular
interactions and phosphorylation states of Mei2-like
proteins in plants remain unclear. .
Length = 77
Score = 31.9 bits (73), Expect = 0.099
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALK-L 225
RTL NI +V +EL F++ G + + + ++ + +V + D A + L
Sbjct: 2 RTLFVRNINSNVEDEELRALFEQFGDIRTL-YTACKH--RGFIMVSYYDIRAARRAKRAL 58
Query: 226 NGTNLKGKTLQMFHS 240
GT L G+ L + S
Sbjct: 59 QGTELGGRKLDIHFS 73
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
MRD1 is encoded by a novel yeast gene MRD1 (multiple
RNA-binding domain). It is well-conserved in yeast and
its homologs exist in all eukaryotes. MRD1 is present
in the nucleolus and the nucleoplasm. It interacts with
the 35 S precursor rRNA (pre-rRNA) and U3 small
nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the
35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which
may play an important structural role in organizing
specific rRNA processing events. .
Length = 76
Score = 31.4 bits (72), Expect = 0.10
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 10/82 (12%)
Query: 11 TKVVQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSR-ICYVKFF--DEK 67
TK++ V N+ +AT+ +++ LF G+V+ +RL P D S R +V+F E
Sbjct: 1 TKLI-VRNVPFEATKKELRELFSPFGQVKSVRL-PKKFDGS----HRGFAFVEFVTKQEA 54
Query: 68 CVGISQHLTNTVFIDRALVVTP 89
+ + L +T R LV+
Sbjct: 55 QNAM-EALKSTHLYGRHLVLEY 75
>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 = 31.5 bits (72), Expect = 0.13
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKY-ALVEFSDQACVIPALK-LNGTNL 230
++ESV+ Q L F + G V ++ D + ALV F A+ + G L
Sbjct: 14 GLDESVTEQYLTRHFSRYGPVVHVVI-----DRQRGQALVFFDKVEAAQAAVNEMKGRKL 68
Query: 231 KGKTLQ 236
G+ LQ
Sbjct: 69 GGRKLQ 74
>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis
thaliana CTC-interacting domain protein CID8, CID9,
CID10, CID11, CID12, CID 13 and similar proteins. This
subgroup corresponds to the RRM2 domains found in A.
thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and
mainly their plant homologs. These highly related
RNA-binding proteins contain an N-terminal PAM2 domain
(PABP-interacting motif 2), two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a basic region that
resembles a bipartite nuclear localization signal. The
biological role of this family remains unclear.
Length = 82
Score = 31.3 bits (71), Expect = 0.14
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 167 RTLVAINIEESVSPQELVDFFQKV-GTVNYIRFCTRENDTNKYALVEFSDQACVIPALKL 225
RT+ NI++ V+ ++ FF+ + G V+ +R + + + A VEF+ I AL
Sbjct: 5 RTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYHHSTRIAFVEFAMAESAIAALNC 64
Query: 226 NG 227
+G
Sbjct: 65 SG 66
>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 = 31.0 bits (71), Expect = 0.14
Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSD-QACVIPALKLN 226
TL+ N++ +S QEL F + G V IR T + K+ VEF D +A LN
Sbjct: 3 TLLVFNLDSPISDQELRSLFSQFGEVKDIRE-TPLRPSQKF--VEFYDIRAAEAALDALN 59
Query: 227 GTNLKGKTLQ 236
G G L+
Sbjct: 60 GRPFLGGRLK 69
Score = 27.9 bits (63), Expect = 2.0
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 15/76 (19%)
Query: 16 VANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFD----EKCVGI 71
V N+ + ++++LF G+V+D+R P+ +V+F+D E +
Sbjct: 6 VFNLDSPISDQELRSLFSQFGEVKDIRETPLRPSQ--------KFVEFYDIRAAEAAL-- 55
Query: 72 SQHLTNTVFIDRALVV 87
L F+ L V
Sbjct: 56 -DALNGRPFLGGRLKV 70
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional
and post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus.
.
Length = 75
Score = 31.1 bits (70), Expect = 0.15
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKCV 69
V V ++P T +Q++ FG G++E++ L P+ D + C+V + DE+ V
Sbjct: 2 VFVGGLSPDTTEEQIKEYFGAFGEIENIEL-PM--DTKTNERRGFCFVTYTDEEPV 54
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 31.0 bits (71), Expect = 0.18
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 8/68 (11%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSD----QACVIPALKLNG 227
N+ E + ++L + F K G + + + +K + V F + Q V +LNG
Sbjct: 8 NLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVE---ELNG 64
Query: 228 TNLKGKTL 235
+ GK L
Sbjct: 65 KEVNGKKL 72
>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 = 31.5 bits (71), Expect = 0.22
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 175 EESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALK-LNGTNLKGK 233
EE V+PQ L F G V ++ + D+ AL++ +D A+ LNG + GK
Sbjct: 23 EEMVTPQSLFTLFGVYGDVQRVKILYNKKDS---ALIQMADGNQSQLAMSHLNGQKMYGK 79
Query: 234 TLQMFHST-QSIQKP 247
+++ S Q++Q P
Sbjct: 80 IIRVTLSKHQTVQLP 94
>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family
proteins. Thid subfamily corresponds to the RRM1 of
IGF2BPs (or IMPs) found in the VICKZ family that have
been implicated in the post-transcriptional regulation
of several different RNAs and in subcytoplasmic
localization of mRNAs during embryogenesis. IGF2BPs are
composed of two RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and four hnRNP K homology
(KH) domains.
Length = 73
Score = 30.4 bits (69), Expect = 0.27
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KLNGTNLK 231
N+ V+ +L F++ + YA V+ DQ+ A+ KLNG L+
Sbjct: 5 NLSSDVNESDLRQLFEEHKIPVSSVLVKK----GGYAFVDCPDQSWADKAIEKLNGKILQ 60
Query: 232 GKTLQMFHST 241
GK +++ HS
Sbjct: 61 GKVIEVEHSV 70
>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 = 30.3 bits (69), Expect = 0.28
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 174 IEESVSPQELVDFFQKVGTVNYIRF-CTRENDTNKYALVEFSDQACVIPALKLNGTNLKG 232
I + +EL DFF + G+V ++ R + Y V F Q L + N +G
Sbjct: 10 IPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGNLNFRG 69
Query: 233 KTL 235
K L
Sbjct: 70 KKL 72
>gnl|CDD|241210 cd12766, RRM2_SRSF6, RNA recognition motif 2 found in vertebrate
serine/arginine-rich splicing factor 6 (SRSF6). This
subgroup corresponds to the RRM2 of SRSF6, also termed
pre-mRNA-splicing factor SRp55, an essential splicing
regulatory serine/arginine (SR) protein that
preferentially interacts with a number of purine-rich
splicing enhancers (ESEs) to activate splicing of the
ESE-containing exon. It is the only protein from HeLa
nuclear extract or purified SR proteins that
specifically binds B element RNA after UV irradiation.
SRSF6 may also recognize different types of RNA sites.
For instance, it does not bind to the purine-rich
sequence in the calcitonin-specific ESE, but binds to a
region adjacent to the purine tract. Moreover, cellular
levels of SRSF6 may control tissue-specific alternative
splicing of the calcitonin/ calcitonin gene-related
peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 73
Score = 30.4 bits (68), Expect = 0.32
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 169 LVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KLNG 227
L+ N+ S Q+L DF ++ G V Y + N+ ++EF + + AL KL+G
Sbjct: 3 LIVENLSSRCSWQDLKDFMRQAGEVTYAD--AHKERANE-GVIEFRSYSDMKRALEKLDG 59
Query: 228 TNLKGKTLQM 237
T + G+ +++
Sbjct: 60 TEINGRKIRL 69
>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 = 30.1 bits (68), Expect = 0.37
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPALKL 225
N+ + EL F +VG + +R T E D+ K +A V+F + ALK
Sbjct: 5 NLSFETTEDELRAHFGRVGRIRRVRMMTFE-DSGKCKGFAFVDFEEIEFATNALKG 59
>gnl|CDD|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins
related to the La autoantigen. This subfamily
corresponds to the RRM of plant La-like proteins related
to the La autoantigen. A variety of La-related proteins
(LARPs or La ribonucleoproteins), with differing domain
architecture, appear to function as RNA-binding proteins
in eukaryotic cellular processes. Members in this family
contain an LAM domain followed by an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 30.6 bits (69), Expect = 0.38
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTREND 204
RT+VA N+ E S + L + F VG+V +R C
Sbjct: 1 RTVVAENLPEDHSIENLEEIFGTVGSVKNVRICDPGRV 38
>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 = 29.8 bits (67), Expect = 0.38
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALK-LN 226
TLV N++ +VS + L FQ G V +R T ++ VEF D AL+ +N
Sbjct: 3 TLVIFNLDPTVSSETLRSIFQVYGDVKELRE-TPCKREQRF--VEFFDVRDAAKALRAMN 59
Query: 227 GTNLKGKTLQM 237
G + GK + +
Sbjct: 60 GKEISGKPVVI 70
>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 = 29.8 bits (67), Expect = 0.39
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLNGTNLKG 232
NI + +++ DFF G ++ + ++ A + F + AL L+ L G
Sbjct: 5 NISPKTTEKQISDFFSFCGKIS--NLDLTNDGESQTATITFEKPSAAKTALLLDNALLGG 62
Query: 233 KTLQM 237
K +Q+
Sbjct: 63 KVIQV 67
Score = 27.9 bits (62), Expect = 1.9
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDL 41
V V+NI+P+ T Q+ F + GK+ +L
Sbjct: 1 VYVSNISPKTTEKQISDFFSFCGKISNL 28
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46),
belonging to the Aly/REF family of RNA binding proteins
that have been implicated in coupling transcription
with pre-mRNA splicing and nucleo-cytoplasmic mRNA
transport. SKAR is widely expressed and localizes to
the nucleus. It may be a critical player in the
function of S6K1 in cell and organism growth control by
binding the activated, hyperphosphorylated form of S6K1
but not S6K2. Furthermore, SKAR functions as a protein
partner of the p50 subunit of DNA polymerase delta. In
addition, SKAR may have particular importance in
pancreatic beta cell size determination and insulin
secretion. SKAR contains a well conserved RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain).
Length = 69
Score = 29.5 bits (67), Expect = 0.45
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRL 43
+ V+N+ P T D + LF +G ++ RL
Sbjct: 3 LVVSNLHPSVTEDDIVELFSAIGALKRARL 32
>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 = 30.0 bits (68), Expect = 0.46
Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 7/69 (10%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFS--DQACVIPALKLNG 227
N+ L F G V ++ R+ TNK Y V + ++A LNG
Sbjct: 8 NLPPDADESLLWQLFSPFGAVTNVKV-IRDLTTNKCKGYGFVTMTNYEEAYS-AIASLNG 65
Query: 228 TNLKGKTLQ 236
L G+ LQ
Sbjct: 66 YRLGGRVLQ 74
>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein
34 (RBM34) and similar proteins. This subfamily
corresponds to the RRM1 of RBM34, a putative RNA-binding
protein containing two RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). Although the function of
RBM34 remains unclear currently, its RRM domains may
participate in mRNA processing. RBM34 may act as an mRNA
processing-related protein. .
Length = 91
Score = 29.9 bits (68), Expect = 0.50
Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 19/88 (21%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCT--RENDT-----------------NK 207
RT+ N+ + ++L F++ G + +RF + + N
Sbjct: 1 RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60
Query: 208 YALVEFSDQACVIPALKLNGTNLKGKTL 235
A V F ++ ALKLNGT +G +
Sbjct: 61 NAYVVFKEEESAEKALKLNGTEFEGHHI 88
>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 = 29.7 bits (66), Expect = 0.63
Identities = 12/53 (22%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDE 66
V V +++P+ T + +++ F GK+ D R + +D++ +V F+++
Sbjct: 4 VFVGDLSPEITTEDIKSAFAPFGKISDAR---VVKDMATGKSKGYGFVSFYNK 53
>gnl|CDD|213381 cd12196, MARK1-3_C, C-terminal, kinase associated domain 1 (KA1), a
phospholipid binding domain, of microtubule
affinity-regulating kinases 1-3. Microtubule-associated
protein/microtubule affinity regulating kinases (MARKs),
also called partition-defective (Par-1) kinases, are
serine/threonine protein kinases (STKs) that catalyze
the transfer of the gamma-phosphoryl group from ATP to
S/T residues on protein substrates. They phosphorylate
the tau protein and related microtubule-associated
proteins (MAPs) on tubulin binding sites to induce
detachment from microtubules, and are involved in the
regulation of cell shape and polarity, cell cycle
control, transport, and the cytoskeleton. Mammals
contain four proteins, MARK1-4, encoded by distinct
genes belonging to this subfamily, with additional
isoforms arising from alternative splicing. MARK1/2,
through their activation by death-associated protein
kinase (DAPK), modulates polarized neurite outgrowth.
MARK1, also called Par-1c, is also involved in
axon-dendrite specification, and SNPs on the MARK1 gene
is associated with autism spectrum disorders. MARK2,
also called Par-1b, is implicated in many physiological
processes including fertility, immune system
homeostasis, learning and memory, growth, and
metabolism. MARK3, also called Par-1a, is implicated in
gluconeogenesis and adiposity; mice deficient with MARK3
display reduced adiposity, resistance to hepatic
steatosis, and defective gluconeogensis. MARKs contain
an N-terminal catalytic kinase domain, a
ubiquitin-associated domain (UBA), and a C-terminal
kinase associated domain (KA1). The KA1 domain binds
anionic phospholipids and may be involved in membrane
localization as well as in auto-inhibition of the kinase
domain.
Length = 98
Score = 29.7 bits (67), Expect = 0.67
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 14/70 (20%)
Query: 162 IEEIRRTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIP 221
+ EIR+ L A N D+ Q+ ++ FC D +LV++ + C +P
Sbjct: 23 MREIRKVLDANNC----------DYEQRE---RFLLFCV-HGDGRTDSLVQWEMEVCKLP 68
Query: 222 ALKLNGTNLK 231
L LNG K
Sbjct: 69 RLSLNGVRFK 78
>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding
protein 19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM6 of RBM19, also termed
RNA-binding domain-1 (RBD-1), which is a nucleolar
protein conserved in eukaryotes. It is involved in
ribosome biogenesis by processing rRNA. In addition, it
is essential for preimplantation development. RBM19 has
a unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 29.3 bits (66), Expect = 0.68
Identities = 11/33 (33%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 11 TKVVQVANIAPQATRDQMQTLFGYLGKVEDLRL 43
+K++ V NI +AT +++ LF G+++ +RL
Sbjct: 1 SKIL-VRNIPFEATVKELRELFSTFGELKTVRL 32
>gnl|CDD|240946 cd12502, RRM2_RMB19, RNA recognition motif 2 in RNA-binding protein
19 (RBM19) and similar proteins. This subfamily
corresponds to the RRM2 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA and is also essential for
preimplantation development. RBM19 has a unique domain
organization containing 6 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 72
Score = 29.3 bits (66), Expect = 0.73
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 178 VSPQELVDFFQKVGTVNYIRFC--TRENDTNKYALVEFSDQACVIPALKLNGTNLKGKTL 235
V + + +FF + V IR T +A V+ + + ALK N + G+ +
Sbjct: 12 VKEKHIREFFSPLKPVA-IRIVKNDHGRKTG-FAFVDLKSEEDLKKALKRNKDYMGGRYI 69
Query: 236 QMF 238
++F
Sbjct: 70 ELF 72
>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type
II embryonic polyadenylate-binding protein 2 (ePABP-2).
This subgroup corresponds to the RRM of ePABP-2, also
termed embryonic poly(A)-binding protein 2, or
poly(A)-binding protein nuclear-like 1 (PABPN1L).
ePABP-2 is a novel embryonic-specific cytoplasmic type
II poly(A)-binding protein that is expressed during the
early stages of vertebrate development and in adult
ovarian tissue. It may play an important role in the
poly(A) metabolism of stored mRNAs during early
vertebrate development. ePABP-2 shows significant
sequence similarity to the ubiquitously expressed
nuclear polyadenylate-binding protein 2 (PABP-2 or
PABPN1). Like PABP-2, ePABP-2 contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), which is
responsible for the poly(A) binding. In addition, it
possesses an acidic N-terminal domain predicted to form
a coiled-coil and an arginine-rich C-terminal domain. .
Length = 77
Score = 29.1 bits (65), Expect = 0.78
Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIR-FCTRENDTNK-YALVEFSDQACVIPALKLNGTNL 230
N++ + +EL F G +N + C + + K YA +EF+ + V A+ L+ ++
Sbjct: 6 NVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALDESSF 65
Query: 231 KGKTLQMF 238
+G+ +++
Sbjct: 66 RGRVIKVL 73
>gnl|CDD|241208 cd12764, RRM2_SRSF4, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 4 (SRSF4). This
subgroup corresponds to the RRM2 of SRSF4, also termed
pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing
factor, arginine/serine-rich 4 (SFRS4), a splicing
regulatory serine/arginine (SR) protein that plays an
important role in both constitutive splicing and
alternative splicing of many pre-mRNAs. For instance, it
interacts with heterogeneous nuclear ribonucleoproteins,
hnRNP G and hnRNP E2, and further regulates the 5'
splice site of tau exon 10, whose misregulation causes
frontotemporal dementia. SFRS4 also induces production
of HIV-1 vpr mRNA through the inhibition of the
5'-splice site of exon 3. In addition, SRSF4 activates
splicing of the cardiac troponin T (cTNT) alternative
exon by direct interactions with the cTNT exon 5
enhancer RNA. SRSF4 can shuttle between the nucleus and
cytoplasm. It contains an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a glycine-rich region, an
internal region homologous to the RRM, and a very long,
highly phosphorylated C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 28.9 bits (64), Expect = 0.88
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 169 LVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLNGT 228
L+ N+ S Q+L D+ ++ G V Y + +SD + KL+GT
Sbjct: 3 LIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRKNEGVIEFRSYSDMKRALE--KLDGT 60
Query: 229 NLKGKTLQM 237
+ G+ +++
Sbjct: 61 EVNGRKIRL 69
>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 = 29.1 bits (66), Expect = 0.88
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCT-RENDTNKYALVEFSD----QACVIPA 222
TL N S ++ D F++ G + IRF + R N T ++ V+F+ A V
Sbjct: 2 TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAV--- 58
Query: 223 LKLNGTNLKGKTLQ 236
LNG +G L
Sbjct: 59 ALLNGKLGEGYKLV 72
>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 = 28.8 bits (64), Expect = 0.95
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCT-RENDTNKYALVEFSDQACVIPALK- 224
RTL N+E V + L + F + G + + C +E + V F V A+
Sbjct: 2 RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIAL 61
Query: 225 LNGTNLKGKTLQM 237
LNG L G+ +++
Sbjct: 62 LNGIRLYGRPIKV 74
>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or
LARP3) and similar proteins. This subfamily corresponds
to the RRM1 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). It
also possesses a short basic motif (SBM) and a nuclear
localization signal (NLS) at the C-terminus. .
Length = 72
Score = 28.3 bits (64), Expect = 1.2
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 10/58 (17%)
Query: 182 ELVDFFQKVGTVNYIRFCTRENDTNKY---ALVEFS--DQACVI---PALKLNGTNLK 231
++ +FF+K G VN IR R + K+ VEF + A LK L
Sbjct: 15 DIQEFFEKFGKVNNIRM--RRDLDKKFKGSVFVEFKTEEDAKKFLEKEKLKYKEKELT 70
>gnl|CDD|240740 cd12294, RRM_Rrp7A, RNA recognition motif in ribosomal
RNA-processing protein 7 homolog A (Rrp7A) and similar
proteins. This subfamily corresponds to the RRM of
Rrp7A, also termed gastric cancer antigen Zg14, a
homolog of yeast ribosomal RNA-processing protein 7
(Rrp7p), and mainly found in Metazoa. Rrp7p is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. In contrast, the cellular function of Rrp7A
remains unclear currently. Rrp7A harbors an N-terminal
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
a C-terminal Rrp7 domain. .
Length = 102
Score = 29.2 bits (66), Expect = 1.2
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 16 VANIAPQATRDQMQTLFGYLGKVEDLRL 43
V N+ P T + ++ LF GKVE + L
Sbjct: 5 VLNVPPYCTEESLKRLFSRCGKVESVEL 32
>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted
PIP5K1A-regulated poly(A) polymerase (Star-PAP) and
similar proteins. This subfamily corresponds to the RRM
of Star-PAP, also termed RNA-binding motif protein 21
(RBM21), which is a ubiquitously expressed U6
snRNA-specific terminal uridylyltransferase (U6-TUTase)
essential for cell proliferation. Although it belongs to
the well-characterized poly(A) polymerase protein
superfamily, Star-PAP is highly divergent from both, the
poly(A) polymerase (PAP) and the terminal uridylyl
transferase (TUTase), identified within the editing
complexes of trypanosomes. Star-PAP predominantly
localizes at nuclear speckles and catalyzes
RNA-modifying nucleotidyl transferase reactions. It
functions in mRNA biosynthesis and may be regulated by
phosphoinositides. It binds to glutathione S-transferase
(GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a
nucleotide substrate and possesses PAP activity that is
stimulated by PtdIns4,5P2. It contains an N-terminal
C2H2-type zinc finger motif followed by an RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a split PAP
domain linked by a proline-rich region, a PAP catalytic
and core domain, a PAP-associated domain, an RS repeat,
and a nuclear localization signal (NLS). .
Length = 74
Score = 28.5 bits (64), Expect = 1.2
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL--- 223
R++ + S ++L+D+F G V + + D YA+VEF + V L
Sbjct: 3 RSVFVSGFKRGTSEEQLMDYFSAFGPVMNV---IMDKDKGVYAIVEFDSKEGVDKVLSEP 59
Query: 224 --KLNGTNL 230
LNG L
Sbjct: 60 QHTLNGHRL 68
>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 = 28.3 bits (64), Expect = 1.5
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSDQACVIPAL-KLNG 227
N+ E +L + F+ G ++ + + ++ +T + +A V F + A+ KLNG
Sbjct: 6 NLSEDADEDDLRELFRPFGPISRV-YLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63
Score = 27.5 bits (62), Expect = 2.9
Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 14 VQVANIAPQATRDQMQTLFGYLGKVEDLRLYPIARD 49
++V N++ A D ++ LF G + R+Y +A+D
Sbjct: 2 IRVTNLSEDADEDDLRELFRPFGPIS--RVY-LAKD 34
>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast
nucleolar protein 12 (Nop12p) and similar proteins.
This subgroup corresponds to the RRM2 of Nop12p, which
is encoded by YOL041C from Saccharomyces cerevisiae. It
is a novel nucleolar protein required for pre-25S rRNA
processing and normal rates of cell growth at low
temperatures. Nop12p shares high sequence similarity
with nucleolar protein 13 (Nop13p). Both, Nop12p and
Nop13p, are not essential for growth. However, unlike
Nop13p that localizes primarily to the nucleolus but is
also present in the nucleoplasm to a lesser extent,
Nop12p is localized to the nucleolus. Nop12p contains
two RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). .
Length = 79
Score = 28.3 bits (63), Expect = 1.5
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 174 IEESVSPQELVDFFQKVGTVNYIRFCTRENDTN---KYALVEFSDQACVIPALKLNGTN- 229
+EE L F K G + Y+R R+ TN +A V+F D+ V AL LN
Sbjct: 12 VEEG-----LWRVFGKCGGIEYVRI-VRDPKTNVGKGFAYVQFKDENAVEKALLLNEKKF 65
Query: 230 --LKGKTLQM 237
+ + L++
Sbjct: 66 PPMLPRELRV 75
>gnl|CDD|241163 cd12719, RRM_SYNJ1, RNA recognition motif in synaptojanin-1 and
similar proteins. This subgroup corresponds to the RRM
of synaptojanin-1, also termed synaptojanin, or synaptic
inositol-1,4,5-trisphosphate 5-phosphatase 1, originally
identified as one of the major Grb2-binding proteins
that may participate in synaptic vesicle endocytosis. It
also acts as a Src homology 3 (SH3) domain-binding
brain-specific inositol 5-phosphatase with a putative
role in clathrin-mediated endocytosis. Synaptojanin-1
contains an N-terminal domain homologous to the
cytoplasmic portion of the yeast protein Sac1p, a
central inositol 5-phosphatase domain followed by a
putative RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal proline-rich region mediating the
binding of synaptojanin-1 to various SH3
domain-containing proteins including amphiphysin, SH3p4,
SH3p8, SH3p13, and Grb2. Synaptojanin-1 has two
tissue-specific alternative splicing isoforms,
synaptojanin-145 expressed in brain and synaptojanin-170
expressed in peripheral tissues. Synaptojanin-145 is
very abundant in nerve terminals and may play an
essential role in the clathrin-mediated endocytosis of
synaptic vesicles. In contrast to synaptojanin-145,
synaptojanin-170 contains three unique
asparagine-proline-phenylalanine (NPF) motifs in the
C-terminal region and may functions as a potential
binding partner for Eps15, a clathrin coat-associated
protein acting as a major substrate for the tyrosine
kinase activity of the epidermal growth factor receptor.
.
Length = 77
Score = 28.5 bits (64), Expect = 1.5
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 182 ELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLNGTNLKGKTL 235
L+ F G V IRF D V F + + AL LNGT + GKT+
Sbjct: 25 ALLQQFASFGEVILIRFVA---DK---MWVTFLEGQSALNALSLNGTEVLGKTI 72
>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation
initiation factor 4H (eIF-4H) and similar proteins.
This subfamily corresponds to the RRM of eIF-4H, also
termed Williams-Beuren syndrome chromosomal region 1
protein, which, together with elf-4B/eIF-4G, serves as
the accessory protein of RNA helicase eIF-4A. eIF-4H
contains a well conserved RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). It stimulates protein
synthesis by enhancing the helicase activity of eIF-4A
in the initiation step of mRNA translation. .
Length = 76
Score = 28.4 bits (64), Expect = 1.5
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 192 TVNYIRFCTRENDTNK---YALVEFSDQACVIPALKLNGTNLKGKTLQ 236
+V +R R+ +T+K + VEF D + AL+ +G ++L+
Sbjct: 26 SVKSVRL-VRDKETDKFKGFCYVEFEDVESLKEALEYDGALFDDRSLR 72
>gnl|CDD|237266 PRK13011, PRK13011, formyltetrahydrofolate deformylase; Reviewed.
Length = 286
Score = 30.3 bits (69), Expect = 1.6
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 134 VISTH---DPVLVQHGLPQYPPLPITYDTKKIEEIR 166
V+S H +P+ HG+P + PIT DTK +E +
Sbjct: 122 VVSNHPDLEPLAAWHGIP-FHHFPITPDTKPQQEAQ 156
>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 = 28.0 bits (63), Expect = 1.7
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 12 KVVQVANIAPQATRDQMQTLFGYLGKVE 39
KV+ V N+ T +Q++ LF G+VE
Sbjct: 2 KVLYVRNLPLSTTEEQLRELFSEYGEVE 29
>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 = 28.1 bits (63), Expect = 1.9
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFC-TRENDTNKYALVEFSD 215
RTL N+E +++ +EL F++ G V + N YA V+F +
Sbjct: 3 RTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLN 52
>gnl|CDD|219174 pfam06780, Erp_C, Erp protein C-terminus. This family represents
the C-terminus of bacterial Erp proteins that seem to be
specific to Borrelia burgdorferi (a causative agent of
Lyme disease). Borrelia Erp proteins are particularly
heterogeneous, which might enable them to interact with
a wide variety of host components.
Length = 141
Score = 29.3 bits (66), Expect = 1.9
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 159 TKKIEEIRRTLVAINIEESVSPQELVD 185
T KI+EI R + +I + SVS +E+ D
Sbjct: 5 TDKIDEINRDIDSIKGQTSVSGKEVED 31
>gnl|CDD|241209 cd12765, RRM2_SRSF5, RNA recognition motif 2 in vertebrate
serine/arginine-rich splicing factor 5 (SRSF5). This
subgroup corresponds to the RRM2 of SRSF5, also termed
delayed-early protein HRS, or pre-mRNA-splicing factor
SRp40, or splicing factor, arginine/serine-rich 5
(SFRS5), is an essential splicing regulatory
serine/arginine (SR) protein that regulates both
alternative splicing and basal splicing. It is the only
SR protein efficiently selected from nuclear extracts
(NE) by the splicing enhancer (ESE) and it is necessary
for enhancer activation. SRSF5 also functions as a
factor required for insulin-regulated splice site
selection for protein kinase C (PKC) betaII mRNA. It is
involved in the regulation of PKCbetaII exon inclusion
by insulin via its increased phosphorylation by a
phosphatidylinositol 3-kinase (PI 3-kinase) signaling
pathway. Moreover, SRSF5 can regulate alternative
splicing in exon 9 of glucocorticoid receptor pre-mRNA
in a dose-dependent manner. SRSF5 contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), followed by a C-terminal RS domains rich in
serine-arginine dipeptides. The specific RNA binding by
SRSF5 requires the phosphorylation of its SR domain. .
Length = 75
Score = 28.1 bits (62), Expect = 2.1
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 169 LVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPAL-KLNG 227
L+ N+ VS Q+L DF ++ G V F +VEF+ + + A+ KL+G
Sbjct: 6 LIVENLSSRVSWQDLKDFMRQAGEVT---FADAHRPKLNEGVVEFASYSDLKNAIEKLSG 62
Query: 228 TNLKGKTLQM 237
+ G+ +++
Sbjct: 63 KEINGRKIKL 72
>gnl|CDD|237920 PRK15194, PRK15194, type-1 fimbrial protein subunit A; Provisional.
Length = 185
Score = 29.5 bits (66), Expect = 2.2
Identities = 28/91 (30%), Positives = 36/91 (39%), Gaps = 11/91 (12%)
Query: 181 QELVDFFQKVG-TVNYIRFCTRENDTN----KYALVEFSDQACVIPALKL------NGTN 229
Q F VG T I F + ND + A V FS QA L N T
Sbjct: 61 QYRTAIFTAVGNTTALIPFTIQLNDCDPVVAATAAVAFSGQADATNDNLLAVASSTNTTT 120
Query: 230 LKGKTLQMFHSTQSIQKPEAKSNEAAQREIE 260
G +++ +T SI KP+ + A Q IE
Sbjct: 121 ATGVGIEILDNTSSILKPDGATFSANQNLIE 151
>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 = 27.8 bits (62), Expect = 2.7
Identities = 10/29 (34%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 16 VANIAPQA-TRDQMQTLFGYLGKVEDLRL 43
+ N PQ T+D++++LF +G++E +L
Sbjct: 5 IVNYLPQNMTQDEIRSLFSSIGEIESCKL 33
>gnl|CDD|241164 cd12720, RRM_SYNJ2, RNA recognition motif in synaptojanin-2 and
similar proteins. This subgroup corresponds to the RRM
of synaptojanin-2, also termed synaptic
inositol-1,4,5-trisphosphate 5-phosphatase 2, an
ubiquitously expressed central regulatory enzyme in the
phosphoinositide-signaling cascade. As a novel Rac1
effector regulating the early step of clathrin-mediated
endocytosis, synaptojanin-2 acts as a
polyphosphoinositide phosphatase directly and
specifically interacting with Rac1 in a GTP-dependent
manner. It mediates the inhibitory effect of Rac1 on
endocytosis and plays an important role in the
Rac1-mediated control of cell growth. Synaptojanin-2
shows high sequence homology to the N-terminal Sac1p
homology domain, the central inositol 5-phosphatase
domain, the putative RNA recognition motif (RRM) of
synaptojanin-1, but differs in the proline-rich region.
.
Length = 78
Score = 27.5 bits (61), Expect = 2.9
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 182 ELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLNGTNLKGKTLQM 237
EL+ + G V +R + +V F+D + L L+G + GKT+++
Sbjct: 26 ELLQTLEGYGDVVLVRIAGGQ------MIVTFADSRSALEVLDLDGIKVLGKTVKI 75
>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in
azoospermia-like (DAZL) proteins. This subgroup
corresponds to the RRM of DAZL, also termed
SPGY-like-autosomal, encoded by the autosomal homolog of
DAZ gene, DAZL. It is ancestral to the deleted in
azoospermia (DAZ) protein. DAZL is germ-cell-specific
RNA-binding protein that contains a RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain), and a DAZ motif, a
protein-protein interaction domain. Although their
specific biochemical functions remain to be
investigated, DAZL proteins may interact with
poly(A)-binding proteins (PABPs), and act as
translational activators of specific mRNAs during
gametogenesis. .
Length = 82
Score = 27.5 bits (61), Expect = 3.1
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 168 TLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK-YALVEFSDQACVIPALKLN 226
T+ I+ + E+ FF K G+V ++ T +K Y V F D V ++ +
Sbjct: 7 TVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVE-S 65
Query: 227 GTNLKGKTLQM 237
N GK L++
Sbjct: 66 QINFHGKKLKL 76
>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 = 29.5 bits (66), Expect = 3.4
Identities = 32/170 (18%), Positives = 55/170 (32%), Gaps = 16/170 (9%)
Query: 80 FIDRALVVTPYNSGEIPDEQRALEIAAQQQGPNSGEPKLPAHVTNQIEGVPPNQVISTHD 139
+ P ++ + AA + P++G+ Q V
Sbjct: 186 VQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRAS 245
Query: 140 PV---LVQHGLPQYPPLPITYDTKKIEEIRRTLVAINIEESVSPQELVDFFQKVGTVNYI 196
P GL + I ++ + +E+V L F G V +
Sbjct: 246 PPATDGQTAGLAAGAQIA--ASDGAGYCIFVYNLSPDTDETV----LWQLFGPFGAVQNV 299
Query: 197 RFCTRENDTNK---YALVEFS--DQACVIPALKLNGTNLKGKTLQMFHST 241
+ R+ TN+ Y V + D+A + L LNG L + LQ+ T
Sbjct: 300 KI-IRDLTTNQCKGYGFVSMTNYDEA-AMAILSLNGYTLGNRVLQVSFKT 347
>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6
(LARP6) and similar proteins. This subfamily
corresponds to the RRM of LARP6, also termed Acheron
(Achn), a novel member of the lupus antigen (La) family.
It is expressed predominantly in neurons and muscle in
vertebrates. LARP6 functions as a key regulatory protein
that may play a role in mediating a variety of
developmental and homeostatic processes in animals,
including myogenesis, neurogenesis and possibly
metastasis. LARP6 binds to Ca2+/calmodulin-dependent
serine protein kinase (CASK), and forms a complex with
inhibitor of differentiation transcription factors. It
is structurally related to the La autoantigen and
contains a La motif (LAM), nuclear localization and
export (NLS and NES) signals, and an RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 93
Score = 27.6 bits (62), Expect = 3.4
Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 17/85 (20%)
Query: 167 RTLVAINI-EESVSPQELVDFFQKVGTVNYIR----FCTRENDTNKY------------A 209
RT+VA+N+ EE + + +++ F G + IR T D +Y A
Sbjct: 1 RTVVAVNLPEEESTIESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKECA 60
Query: 210 LVEFSDQACVIPALKLNGTNLKGKT 234
+VEF A++ +
Sbjct: 61 VVEFEKLEAARKAVEELSARDDWRD 85
>gnl|CDD|240886 cd12440, RRM_SYNJ, RNA recognition motif in synaptojanin-1,
synaptojanin-2 and similar proteins. This subfamily
corresponds to the RRM of two active
phosphatidylinositol phosphate phosphatases,
synaptojanin-1 and synaptojanin-2. They have different
interaction partners and are likely to have different
biological functions. Synaptojanin-1 was originally
identified as one of the major Grb2-binding proteins
that may participate in synaptic vesicle endocytosis. It
also acts as a Src homology 3 (SH3) domain-binding
brain-specific inositol 5-phosphatase with a putative
role in clathrin-mediated endocytosis. Synaptojanin-2 is
a ubiquitously expressed homolog of synaptojanin-1. It
is a novel Rac1 effector regulating the early step of
clathrin-mediated endocytosis. Synaptojanin-2 directly
and specifically interacts with Rac1 in a GTP-dependent
manner. It mediates the inhibitory effect of Rac1 on
endocytosis and plays an important role in the
Rac1-mediated control of cell growth. Both,
synaptojanin-1 and synaptojanin-2, have two
tissue-specific alternative splicing isoforms, a shorter
isoform expressed in brain and a longer isoform in
peripheral tissues. Synaptojanin-1 contains an
N-terminal domain homologous to the cytoplasmic portion
of the yeast protein Sac1p, a central inositol
5-phosphatase domain followed by a putative RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal proline-rich region mediating the binding of
synaptojanin-1 to various SH3 domain-containing proteins
including amphiphysin, SH3p4, SH3p8, SH3p13, and Grb2.
Synaptojanin-2 shows high sequence homology to the
N-terminal Sac1p homology domain, the central inositol
5-phosphatase domain, the putative RNA recognition motif
(RRM) of synaptojanin-1, but differs in the proline-rich
region. .
Length = 78
Score = 27.5 bits (61), Expect = 3.4
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 182 ELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLNGTNLKGKTLQM 237
EL Q G V IRF ++ LV F D + L L+G + + L +
Sbjct: 26 ELTQVNQSAGDVLLIRF------AHEGMLVTFRDGVSALAVLALSGLQINHRRLGI 75
>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM1 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 27.2 bits (61), Expect = 3.6
Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLNGTNLKG 232
N+ + + ++ FF+ G + ++ E++ A++EF + + AL + L G
Sbjct: 7 NLPKDTTENKIRQFFKDCGEIREVKI--VESEGGLVAVIEFETEDEALAALTKDHKRLGG 64
Query: 233 KTLQ 236
+
Sbjct: 65 NEIS 68
>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 = 27.1 bits (60), Expect = 4.3
Identities = 11/33 (33%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 11 TKVVQVANIAPQATRDQMQTLFGYLGKVEDLRL 43
TK++ V N+ +AT+ ++TLF G+++ +R+
Sbjct: 1 TKIL-VKNLPFEATKKDVRTLFSSYGQLKSVRV 32
>gnl|CDD|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53
and similar proteins. This subfamily corresponds to the
RRM domain of nucleoporin Nup53, also termed mitotic
phosphoprotein 44 (MP-44), or nuclear pore complex
protein Nup53, required for normal cell growth and
nuclear morphology in vertebrate. It tightly associates
with the nuclear envelope membrane and the nuclear
lamina where it interacts with lamin B. It may also
interact with a group of nucleoporins including Nup93,
Nup155, and Nup205 and play a role in the association of
the mitotic checkpoint protein Mad1 with the nuclear
pore complex (NPC). The family also includes
Saccharomyces cerevisiae Nup53p, an ortholog of
vertebrate nucleoporin Nup53. A unique property of yeast
Nup53p is that it contains an additional Kap121p-binding
domain and interacts specifically with the karyopherin
Kap121p, which is involved in the assembly of Nup53p
into NPCs. Both, vertebrate Nup35 and yeast Nup53p,
contain an atypical RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a C-terminal amphipathic
alpha-helix and several FG repeats. This family
corresponds to the RRM domain which lacks the conserved
residues that typically bind RNA in canonical RRM
domains.
Length = 73
Score = 26.8 bits (60), Expect = 4.5
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 4/54 (7%)
Query: 181 QELVDFFQKVGTVNYIRFCTRENDTNKYALVEFSDQACVIPALKLNGTNLKGKT 234
++ F GT+ +R+ N + +++S + AL NGT + G
Sbjct: 15 NLVLREFSSCGTILEVRYPPGAN----WIHLKYSSRLEAERALSKNGTIINGGV 64
>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of
rDNA transcription protein 5 (RRT5) and similar
proteins. This subfamily corresponds to the RRM1 of the
lineage specific family containing a group of
uncharacterized yeast regulators of rDNA transcription
protein 5 (RRT5), which may play roles in the modulation
of rDNA transcription. RRT5 contains two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains). .
Length = 84
Score = 27.0 bits (60), Expect = 4.7
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 8/71 (11%)
Query: 173 NIEESVSPQELVDFFQKVGTVNYI-------RFCTRENDTNKYALVEFSDQACVIPALK- 224
N+ S S ++L +F + V+ + F +R A EFS +K
Sbjct: 6 NLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKVVKD 65
Query: 225 LNGTNLKGKTL 235
LNG K + L
Sbjct: 66 LNGKVFKNRKL 76
>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12
small nuclear ribonucleoprotein 35 kDa protein
(U11/U12-35K) and similar proteins. This subfamily
corresponds to the RRM of U11/U12-35K, also termed
protein HM-1, or U1 snRNP-binding protein homolog, and
is one of the components of the U11/U12 snRNP, which is
a subunit of the minor (U12-dependent) spliceosome
required for splicing U12-type nuclear pre-mRNA
introns. U11/U12-35K is highly conserved among
bilateria and plants, but lacks in some organisms, such
as Saccharomyces cerevisiae and Caenorhabditis elegans.
Moreover, U11/U12-35K shows significant sequence
homology to U1 snRNP-specific 70 kDa protein (U1-70K or
snRNP70). It contains a conserved RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by an adjacent
glycine-rich region, and Arg-Asp and Arg-Glu dipeptide
repeats rich domain, making U11/U12-35K a possible
functional analog of U1-70K. It may facilitate 5'
splice site recognition in the minor spliceosome and
play a role in exon bridging, interacting with
components of the major spliceosome bound to the
pyrimidine tract of an upstream U2-type intron. The
family corresponds to the RRM of U11/U12-35K that may
directly contact the U11 or U12 snRNA through the RRM
domain.
Length = 93
Score = 27.2 bits (61), Expect = 5.7
Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 16 VANIAPQATRDQMQTLFGYLGKVEDLRLYPIARDVSIPVQSRICYVKFFDEKCVGISQHL 75
V ++ Q T + ++ +F G + LRL RD+ +V++ E+ +
Sbjct: 8 VGRLSLQTTEETLREVFSRYGDIRRLRL---VRDIVTGFSKGYAFVEYEHERDALRAYRD 64
Query: 76 TNTVFIDRALVVTPYN 91
+ + ID + + +
Sbjct: 65 AHKLVIDGSEIFVDFE 80
>gnl|CDD|217709 pfam03744, BioW, 6-carboxyhexanoate--CoA ligase. This family
contains the enzyme 6-carboxyhexanoate--CoA ligase
EC:6.2.1.14. This enzyme is involved in the first step
of biotin synthesis, where it converts pimelate into
pimeloyl-CoA. The enzyme requires magnesium as a
cofactor and forms a homodimer.
Length = 232
Score = 28.4 bits (64), Expect = 6.6
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 151 PPLPI-TYDTKKIEEIRRTLVAINIEESVSPQ 181
LPI T ++K EE R + E VS Q
Sbjct: 63 KALPIKTLESKSPEEARAFARNLLSNEGVSEQ 94
>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 = 26.4 bits (59), Expect = 7.9
Identities = 20/79 (25%), Positives = 30/79 (37%), Gaps = 15/79 (18%)
Query: 167 RTLVAINIEESVSPQELVDFFQKVGTVNYIRFCTRENDTNK---YALVEFSD----QAC- 218
RT+ N+ + +EL + F + G V Y R ++ T A V+F Q C
Sbjct: 1 RTVFIRNLPFDATEEELKELFSQFGEVKYARIV-KDKLTGHSKGTAFVKFKTKESAQKCL 59
Query: 219 ------VIPALKLNGTNLK 231
L L+G L
Sbjct: 60 EAADNAEDSGLSLDGRRLI 78
>gnl|CDD|217632 pfam03599, CdhD, CO dehydrogenase/acetyl-CoA synthase delta
subunit.
Length = 384
Score = 28.3 bits (63), Expect = 8.2
Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 5/62 (8%)
Query: 128 GVPPNQVISTHDPVLVQHGLPQYPPLPITYDTKKIEEIRRTLVAINIEESVSPQELVDFF 187
G V+ + VL + LP P IT D + + + E + ++++
Sbjct: 5 GAGEKAVVIGGEEVLYRFELPFPNPTAITID---VFDNLSPELLKARRERI--EDVMFDP 59
Query: 188 QK 189
+K
Sbjct: 60 KK 61
>gnl|CDD|214526 smart00129, KISc, Kinesin motor, catalytic domain. ATPase.
Microtubule-dependent molecular motors that play
important roles in intracellular transport of organelles
and in cell division.
Length = 335
Score = 27.9 bits (63), Expect = 9.6
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 262 AMSRVKEAQ--NMISAAIDPVIGILSKDKKKSHSPVR 296
R+KEA N +A+ VI L++ K H P R
Sbjct: 245 EGDRLKEAGNINKSLSALGNVINALAQHSKSRHIPYR 281
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.135 0.381
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,880,856
Number of extensions: 2089142
Number of successful extensions: 2347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2317
Number of HSP's successfully gapped: 141
Length of query: 405
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 306
Effective length of database: 6,546,556
Effective search space: 2003246136
Effective search space used: 2003246136
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.8 bits)